Query psy11392
Match_columns 169
No_of_seqs 147 out of 468
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 17:14:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11392.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11392hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1095 RPB7 DNA-directed RNA 100.0 1.6E-30 3.5E-35 213.3 12.1 102 5-107 19-120 (183)
2 PTZ00162 DNA-directed RNA poly 100.0 1.1E-29 2.4E-34 206.1 11.1 108 5-112 19-132 (176)
3 TIGR00448 rpoE DNA-directed RN 100.0 5.9E-29 1.3E-33 200.3 11.3 97 5-101 19-115 (179)
4 PRK08563 DNA-directed RNA poly 99.9 8.1E-28 1.8E-32 193.8 11.1 114 5-118 19-145 (187)
5 KOG3297|consensus 99.9 3.1E-25 6.8E-30 182.8 9.6 113 6-118 20-152 (202)
6 KOG3298|consensus 99.9 4.3E-23 9.3E-28 167.1 10.5 112 3-114 17-134 (170)
7 cd04330 RNAP_III_Rpc25_N RNAP_ 99.8 1.4E-19 3E-24 130.5 8.8 63 5-67 18-80 (80)
8 cd00655 RNAP_Rpb7_N_like RNAP_ 99.8 3.9E-19 8.4E-24 128.0 8.9 63 5-67 18-80 (80)
9 cd04329 RNAP_II_Rpb7_N RNAP_II 99.8 4.5E-19 9.8E-24 127.8 8.5 63 5-67 18-80 (80)
10 cd04331 RNAP_E_N RNAP_E_N: Rpo 99.8 2.4E-18 5.3E-23 124.2 8.2 62 5-66 18-79 (80)
11 PF03876 SHS2_Rpb7-N: SHS2 dom 99.5 2.7E-13 5.9E-18 93.5 8.3 58 6-63 13-70 (70)
12 COG0539 RpsA Ribosomal protein 99.3 3.1E-12 6.7E-17 119.5 7.3 109 9-117 92-244 (541)
13 cd04328 RNAP_I_Rpa43_N RNAP_I_ 99.0 1.3E-09 2.9E-14 79.1 7.0 60 7-67 27-89 (89)
14 PRK07899 rpsA 30S ribosomal pr 98.7 1.4E-08 3.1E-13 94.0 6.3 92 10-102 110-243 (486)
15 PRK07400 30S ribosomal protein 98.7 4.6E-08 1E-12 85.9 7.0 107 10-118 106-249 (318)
16 cd05686 S1_pNO40 S1_pNO40: pNO 98.6 2.9E-08 6.3E-13 68.9 3.3 38 65-102 1-40 (73)
17 cd04462 S1_RNAPII_Rpb7 S1_RNAP 98.6 3.5E-08 7.5E-13 72.1 3.8 31 67-97 1-31 (88)
18 PRK06299 rpsA 30S ribosomal pr 98.6 8E-08 1.7E-12 88.8 6.7 95 8-102 100-236 (565)
19 PF00575 S1: S1 RNA binding do 98.6 3.7E-08 8.1E-13 67.3 3.1 39 64-102 1-40 (74)
20 PRK13806 rpsA 30S ribosomal pr 98.5 2.4E-07 5.1E-12 85.3 6.0 93 10-102 103-238 (491)
21 PRK12269 bifunctional cytidyla 98.4 3.6E-07 7.8E-12 89.8 6.8 98 21-118 498-633 (863)
22 cd04452 S1_IF2_alpha S1_IF2_al 98.4 1.9E-07 4.2E-12 63.9 2.8 54 65-118 1-59 (76)
23 PF08292 RNA_pol_Rbc25: RNA po 98.4 1.7E-07 3.6E-12 72.8 2.6 53 65-118 1-70 (122)
24 TIGR00717 rpsA ribosomal prote 98.4 5.5E-07 1.2E-11 82.0 6.3 93 10-102 88-222 (516)
25 COG0539 RpsA Ribosomal protein 98.4 7.8E-07 1.7E-11 83.7 7.5 76 27-102 205-313 (541)
26 PRK12269 bifunctional cytidyla 98.4 6E-07 1.3E-11 88.2 6.7 93 10-102 386-528 (863)
27 cd05705 S1_Rrp5_repeat_hs14 S1 98.4 1.9E-07 4.1E-12 65.7 2.4 37 66-102 2-39 (74)
28 PRK06676 rpsA 30S ribosomal pr 98.4 6.2E-07 1.3E-11 79.3 6.0 92 11-102 94-227 (390)
29 cd05694 S1_Rrp5_repeat_hs2_sc2 98.3 3.3E-07 7.3E-12 64.6 2.6 37 66-102 3-41 (74)
30 PTZ00248 eukaryotic translatio 98.3 4E-07 8.7E-12 80.8 2.8 39 64-102 14-55 (319)
31 cd04453 S1_RNase_E S1_RNase_E: 98.3 6.5E-07 1.4E-11 65.2 2.9 38 64-101 4-44 (88)
32 cd05706 S1_Rrp5_repeat_sc10 S1 98.3 8.9E-07 1.9E-11 60.5 3.3 37 66-102 2-39 (73)
33 cd04461 S1_Rrp5_repeat_hs8_sc7 98.2 5.9E-07 1.3E-11 63.4 2.1 54 65-118 12-68 (83)
34 cd05690 S1_RPS1_repeat_ec5 S1_ 98.2 7.2E-07 1.6E-11 60.0 2.2 51 68-118 1-55 (69)
35 cd05708 S1_Rrp5_repeat_sc12 S1 98.2 7.2E-07 1.6E-11 60.7 2.1 52 67-118 2-57 (77)
36 cd05692 S1_RPS1_repeat_hs4 S1_ 98.2 7.8E-07 1.7E-11 58.6 2.2 35 68-102 1-36 (69)
37 cd05707 S1_Rrp5_repeat_sc11 S1 98.2 8E-07 1.7E-11 60.2 2.1 50 68-117 1-53 (68)
38 cd05684 S1_DHX8_helicase S1_DH 98.2 1.1E-06 2.3E-11 61.4 2.7 36 68-103 1-40 (79)
39 cd05688 S1_RPS1_repeat_ec3 S1_ 98.2 9.7E-07 2.1E-11 58.5 2.3 36 67-102 1-36 (68)
40 PRK13806 rpsA 30S ribosomal pr 98.1 4.9E-06 1.1E-10 76.7 6.9 82 21-102 207-328 (491)
41 cd04471 S1_RNase_R S1_RNase_R: 98.1 1.6E-06 3.4E-11 60.0 2.7 37 67-103 1-39 (83)
42 PRK08582 hypothetical protein; 98.1 2E-06 4.4E-11 67.7 3.6 38 65-102 3-41 (139)
43 cd05704 S1_Rrp5_repeat_hs13 S1 98.1 1.1E-06 2.4E-11 61.1 1.8 36 67-102 3-40 (72)
44 cd05698 S1_Rrp5_repeat_hs6_sc5 98.1 1.5E-06 3.3E-11 58.8 2.1 35 68-102 1-36 (70)
45 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.1 1.6E-06 3.4E-11 58.9 2.1 36 68-103 1-37 (69)
46 PRK07899 rpsA 30S ribosomal pr 98.1 6.7E-06 1.5E-10 76.4 6.7 92 27-118 221-347 (486)
47 PRK07252 hypothetical protein; 98.1 2.3E-06 5.1E-11 65.9 2.8 52 67-118 3-57 (120)
48 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.1 2.1E-06 4.5E-11 59.5 2.3 35 68-102 1-38 (71)
49 cd05689 S1_RPS1_repeat_ec4 S1_ 98.1 3E-06 6.5E-11 57.7 2.9 36 67-102 3-39 (72)
50 PRK00087 4-hydroxy-3-methylbut 98.1 4.7E-06 1E-10 79.1 5.2 93 10-102 377-512 (647)
51 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.1 2.6E-06 5.7E-11 60.1 2.5 39 63-101 2-41 (86)
52 COG1098 VacB Predicted RNA bin 98.0 4.2E-06 9.1E-11 65.9 3.3 38 65-102 3-41 (129)
53 PRK07400 30S ribosomal protein 98.0 1E-05 2.2E-10 71.2 6.0 82 21-102 36-153 (318)
54 PRK05807 hypothetical protein; 98.0 4.2E-06 9.1E-11 65.6 3.0 37 66-102 4-40 (136)
55 cd05703 S1_Rrp5_repeat_hs12_sc 98.0 4.8E-06 1E-10 58.2 2.5 35 68-102 1-36 (73)
56 TIGR03591 polynuc_phos polyrib 98.0 1.5E-06 3.3E-11 83.3 -0.3 71 29-102 581-654 (684)
57 cd05691 S1_RPS1_repeat_ec6 S1_ 98.0 4.6E-06 9.9E-11 56.3 2.1 35 68-102 1-36 (73)
58 cd04472 S1_PNPase S1_PNPase: P 97.9 7.6E-06 1.6E-10 54.3 2.4 51 68-118 1-54 (68)
59 cd05687 S1_RPS1_repeat_ec1_hs1 97.9 7E-06 1.5E-10 55.6 2.2 35 68-102 1-36 (70)
60 TIGR02696 pppGpp_PNP guanosine 97.9 6.5E-06 1.4E-10 79.8 2.8 54 64-117 644-704 (719)
61 cd04465 S1_RPS1_repeat_ec2_hs2 97.8 1E-05 2.2E-10 54.8 2.2 35 68-102 1-35 (67)
62 cd05685 S1_Tex S1_Tex: The C-t 97.8 1.1E-05 2.4E-10 53.0 1.7 35 68-102 1-36 (68)
63 PRK03987 translation initiatio 97.8 1.5E-05 3.2E-10 68.9 2.4 54 64-117 5-63 (262)
64 smart00316 S1 Ribosomal protei 97.8 1.7E-05 3.7E-10 51.6 2.2 36 67-102 2-38 (72)
65 PLN00207 polyribonucleotide nu 97.7 1.5E-05 3.2E-10 78.9 1.5 56 63-118 749-808 (891)
66 PRK04163 exosome complex RNA-b 97.7 2.6E-05 5.6E-10 65.9 2.8 40 63-102 59-99 (235)
67 cd04460 S1_RpoE S1_RpoE: RpoE, 97.7 2.7E-05 5.8E-10 56.9 2.4 35 69-103 1-35 (99)
68 cd04455 S1_NusA S1_NusA: N-uti 97.6 4.3E-05 9.4E-10 52.2 2.7 37 66-102 2-38 (67)
69 PRK06676 rpsA 30S ribosomal pr 97.6 8.4E-05 1.8E-09 65.8 5.0 37 66-102 276-313 (390)
70 TIGR00717 rpsA ribosomal prote 97.6 6.3E-05 1.4E-09 68.7 4.3 51 52-102 320-395 (516)
71 PRK08059 general stress protei 97.6 4.3E-05 9.3E-10 58.5 2.6 54 65-118 5-61 (123)
72 cd05702 S1_Rrp5_repeat_hs11_sc 97.6 5.3E-05 1.2E-09 51.8 2.8 35 68-102 1-36 (70)
73 PRK09521 exosome complex RNA-b 97.6 0.0002 4.4E-09 58.3 6.6 66 30-102 33-110 (189)
74 cd05695 S1_Rrp5_repeat_hs3 S1_ 97.5 6.4E-05 1.4E-09 51.4 2.4 33 68-100 1-34 (66)
75 PRK11824 polynucleotide phosph 97.5 7.1E-05 1.5E-09 72.0 3.4 40 63-102 617-657 (693)
76 cd04473 S1_RecJ_like S1_RecJ_l 97.4 0.00012 2.6E-09 51.3 3.1 36 64-99 13-49 (77)
77 PRK06299 rpsA 30S ribosomal pr 97.4 0.00012 2.6E-09 67.8 4.0 37 66-102 372-409 (565)
78 cd04454 S1_Rrp4_like S1_Rrp4_l 97.4 0.00013 2.7E-09 51.3 2.9 39 63-101 2-41 (82)
79 cd05693 S1_Rrp5_repeat_hs1_sc1 97.4 9E-05 2E-09 55.1 1.9 37 66-102 2-39 (100)
80 COG1093 SUI2 Translation initi 97.4 9.8E-05 2.1E-09 64.4 2.4 38 65-102 9-49 (269)
81 PHA02945 interferon resistance 97.4 0.00015 3.3E-09 54.0 3.0 35 64-99 8-45 (88)
82 PRK00087 4-hydroxy-3-methylbut 97.1 0.0005 1.1E-08 65.5 4.7 37 66-102 561-598 (647)
83 cd00164 S1_like S1_like: Ribos 97.1 0.00022 4.8E-09 45.6 1.2 32 71-102 1-33 (65)
84 KOG4134|consensus 97.0 0.0049 1.1E-07 53.2 8.9 95 7-102 46-145 (253)
85 TIGR02063 RNase_R ribonuclease 96.9 0.0007 1.5E-08 65.0 2.9 39 63-101 623-663 (709)
86 PRK11642 exoribonuclease R; Pr 96.7 0.0013 2.7E-08 64.8 3.4 39 64-102 640-680 (813)
87 TIGR00358 3_prime_RNase VacB a 96.5 0.0014 3E-08 62.7 2.5 39 64-102 569-609 (654)
88 COG1185 Pnp Polyribonucleotide 96.3 0.0033 7.1E-08 61.1 3.3 41 62-102 614-655 (692)
89 COG2183 Tex Transcriptional ac 96.3 0.0026 5.6E-08 62.5 2.6 36 66-101 657-693 (780)
90 PRK09202 nusA transcription el 96.2 0.0025 5.5E-08 59.3 2.0 36 67-102 134-169 (470)
91 PRK12327 nusA transcription el 95.7 0.0054 1.2E-07 55.5 2.0 45 66-110 133-183 (362)
92 TIGR01953 NusA transcription t 95.2 0.011 2.4E-07 53.0 2.1 46 66-111 130-182 (341)
93 cd05791 S1_CSL4 S1_CSL4: CSL4, 94.7 0.047 1E-06 40.0 3.9 38 63-100 2-48 (92)
94 TIGR00757 RNaseEG ribonuclease 94.0 0.042 9.1E-07 50.4 2.9 38 65-102 23-63 (414)
95 PRK05054 exoribonuclease II; P 92.2 0.11 2.4E-06 50.0 2.8 35 66-100 558-596 (644)
96 cd05790 S1_Rrp40 S1_Rrp40: Rrp 91.2 0.27 5.9E-06 36.2 3.4 35 63-97 2-37 (86)
97 PRK12328 nusA transcription el 89.5 0.22 4.9E-06 45.5 2.1 46 66-111 137-189 (374)
98 PF13509 S1_2: S1 domain; PDB: 88.6 0.26 5.7E-06 33.4 1.5 50 67-116 1-55 (61)
99 COG0557 VacB Exoribonuclease R 87.9 0.63 1.4E-05 45.1 4.1 36 66-101 621-658 (706)
100 COG1097 RRP4 RNA-binding prote 86.2 3.4 7.3E-05 35.9 7.2 67 24-101 30-99 (239)
101 PHA02858 EIF2a-like PKR inhibi 84.2 1 2.3E-05 33.5 2.8 38 64-102 13-53 (86)
102 KOG2916|consensus 83.5 1 2.2E-05 40.1 2.9 39 64-102 13-54 (304)
103 TIGR02062 RNase_B exoribonucle 80.8 1.3 2.8E-05 42.8 2.7 36 66-101 554-593 (639)
104 KOG1067|consensus 80.4 3.9 8.4E-05 40.1 5.7 36 66-101 667-703 (760)
105 PF02944 BESS: BESS motif; In 78.8 2.9 6.2E-05 25.8 3.0 33 118-151 5-37 (37)
106 COG1107 Archaea-specific RecJ- 75.7 2.1 4.5E-05 42.0 2.4 42 60-101 108-157 (715)
107 PRK12329 nusA transcription el 72.4 2.3 5E-05 40.0 1.8 48 64-111 149-208 (449)
108 COG1530 CafA Ribonucleases G a 67.5 7.4 0.00016 36.6 4.1 61 41-101 11-74 (487)
109 PRK11712 ribonuclease G; Provi 65.4 5.5 0.00012 37.6 2.9 35 65-99 36-73 (489)
110 PF10447 EXOSC1: Exosome compo 63.1 12 0.00027 27.2 3.7 36 65-100 2-56 (82)
111 PRK10811 rne ribonuclease E; R 60.5 8.1 0.00018 39.8 3.1 36 65-100 36-74 (1068)
112 KOG1070|consensus 54.6 14 0.0003 39.7 3.7 37 66-102 598-635 (1710)
113 COG2996 Predicted RNA-bindinin 51.9 11 0.00025 33.6 2.3 34 66-99 154-188 (287)
114 cd05699 S1_Rrp5_repeat_hs7 S1_ 50.9 28 0.0006 25.0 3.8 31 68-98 1-36 (72)
115 KOG3013|consensus 47.0 18 0.00039 32.4 2.8 60 62-121 80-140 (301)
116 KOG3440|consensus 44.7 20 0.00043 28.4 2.4 25 125-149 47-71 (122)
117 PF10246 MRP-S35: Mitochondria 42.9 42 0.00091 25.9 3.9 27 63-89 19-45 (104)
118 PF01135 PCMT: Protein-L-isoas 41.3 5.9 0.00013 33.0 -1.0 28 114-141 9-36 (209)
119 KOG1070|consensus 41.0 23 0.00049 38.2 2.8 37 66-102 1250-1289(1710)
120 COG2996 Predicted RNA-bindinin 39.7 46 0.001 29.8 4.2 53 66-118 4-63 (287)
121 COG1096 Predicted RNA-binding 37.5 30 0.00065 29.2 2.6 43 64-107 61-114 (188)
122 KOG1004|consensus 37.2 85 0.0018 27.3 5.3 94 53-151 51-175 (230)
123 KOG3409|consensus 34.6 51 0.0011 27.9 3.5 49 64-112 65-127 (193)
124 PRK13942 protein-L-isoaspartat 32.6 13 0.00028 30.4 -0.4 30 113-142 12-41 (212)
125 PF04280 Tim44: Tim44-like dom 30.2 1E+02 0.0022 23.1 4.3 39 49-87 88-132 (147)
126 PTZ00248 eukaryotic translatio 28.4 76 0.0017 28.6 3.8 79 20-98 21-144 (319)
127 PF07238 PilZ: PilZ domain; I 27.9 1.9E+02 0.004 19.2 5.6 35 54-88 8-42 (102)
128 PF01330 RuvA_N: RuvA N termin 27.1 36 0.00078 22.7 1.2 32 70-101 4-35 (61)
129 PF08592 DUF1772: Domain of un 25.9 66 0.0014 23.7 2.5 27 124-150 9-35 (139)
130 PF02237 BPL_C: Biotin protein 25.2 1.2E+02 0.0025 19.3 3.3 19 67-85 11-29 (48)
131 TIGR00080 pimt protein-L-isoas 24.7 22 0.00047 28.8 -0.3 22 120-141 20-41 (215)
132 PF04491 Pox_T4_N: Poxvirus T4 24.0 1E+02 0.0022 20.6 2.8 25 27-51 5-38 (46)
133 COG1206 Gid NAD(FAD)-utilizing 23.4 29 0.00064 32.4 0.2 82 69-157 117-236 (439)
134 KOG4078|consensus 21.7 1.1E+02 0.0023 25.3 3.1 31 59-89 74-104 (173)
135 PF09953 DUF2187: Uncharacteri 21.2 2.1E+02 0.0046 19.8 4.1 22 71-92 16-37 (57)
136 COG2106 Uncharacterized conser 20.8 79 0.0017 28.1 2.4 27 64-90 102-128 (272)
No 1
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=99.97 E-value=1.6e-30 Score=213.30 Aligned_cols=102 Identities=25% Similarity=0.459 Sum_probs=97.4
Q ss_pred ccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEecceeE
Q psy11392 5 ITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVH 84 (169)
Q Consensus 5 ~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~~GiF 84 (169)
+.++++++.+.|+++|+||+++++|+||+|+++.++++|+|.||||++|++|+|+|++|+|+.||||+|+|++++++|+|
T Consensus 19 g~~~~~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~~gEVV~GeVv~~~~~G~f 98 (183)
T COG1095 19 GEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFGAF 98 (183)
T ss_pred CccHHHHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEeccccEEEEEEEEEeecceE
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeCCCCCCccCCccccccccce
Q psy11392 85 DSQSSNQPEQPISDSTVKDILKY 107 (169)
Q Consensus 85 V~lGp~dGlIhISd~s~~e~i~~ 107 (169)
|++||+||++|+| +-+|+|+.+
T Consensus 99 V~igp~dglvh~s-qi~dd~~~~ 120 (183)
T COG1095 99 VRIGPLDGLVHVS-QIMDDYIDY 120 (183)
T ss_pred EEeccccccccHh-hccCccccc
Confidence 9999999999999 666666655
No 2
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=99.96 E-value=1.1e-29 Score=206.11 Aligned_cols=108 Identities=15% Similarity=0.197 Sum_probs=97.3
Q ss_pred ccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEecceeE
Q psy11392 5 ITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVH 84 (169)
Q Consensus 5 ~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~~GiF 84 (169)
+.++++++.++|+++|+||+++++|+||||+||.++++|+|.||||+++++|+|||++||||+|||++|+|++++++|+|
T Consensus 19 ~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf~gEVv~g~V~~v~~~G~~ 98 (176)
T PTZ00162 19 GPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFF 98 (176)
T ss_pred CccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecCCCCEEEEEEEEEecceEE
Confidence 46799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeCCCCCCccCC----cccccc--ccceecccC
Q psy11392 85 DSQSSNQPEQPIS----DSTVKD--ILKYFAEKD 112 (169)
Q Consensus 85 V~lGp~dGlIhIS----d~s~~e--~i~~~~~~d 112 (169)
+++||+++++|.+ ++.|++ -..||.++|
T Consensus 99 v~~Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~ 132 (176)
T PTZ00162 99 AQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSD 132 (176)
T ss_pred EEeeCeEEEEcHHHCCCccEECCCCCcceEecCC
Confidence 9999999999865 344442 334665544
No 3
>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=99.96 E-value=5.9e-29 Score=200.28 Aligned_cols=97 Identities=29% Similarity=0.449 Sum_probs=93.8
Q ss_pred ccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEecceeE
Q psy11392 5 ITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVH 84 (169)
Q Consensus 5 ~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~~GiF 84 (169)
+.++++++.++|+++|+||+++++|+||+|+||.++++|+|.||||+++++|+||+++|+|++||+++|+|++++++|+|
T Consensus 19 ~~~~~~~i~~~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~~gEvv~G~V~~v~~~Gif 98 (179)
T TIGR00448 19 GEDLEEVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPELGEIVEGEVIEIVEFGAF 98 (179)
T ss_pred CccHHHHHHHHHHHHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEeccCCCEEEEEEEEEEeeEEE
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeCCCCCCccCCcccc
Q psy11392 85 DSQSSNQPEQPISDSTV 101 (169)
Q Consensus 85 V~lGp~dGlIhISd~s~ 101 (169)
|++||++|++|.+++..
T Consensus 99 V~lg~~~gi~~~~~l~~ 115 (179)
T TIGR00448 99 VSLGPFDGLFHVSQVTD 115 (179)
T ss_pred EEeCCceEEEEcHHhCC
Confidence 99999999999997764
No 4
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=99.95 E-value=8.1e-28 Score=193.84 Aligned_cols=114 Identities=20% Similarity=0.269 Sum_probs=102.7
Q ss_pred ccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEecceeE
Q psy11392 5 ITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVH 84 (169)
Q Consensus 5 ~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~~GiF 84 (169)
+.++++++.++|+++|+||+++++|+||+|+||.++++|+|.||||+++++|+|++++|+|++|||++|+|++++++|+|
T Consensus 19 ~~~~~~~i~~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~~GEVv~g~V~~v~~~Gi~ 98 (187)
T PRK08563 19 GEDLEEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEVVEVVEFGAF 98 (187)
T ss_pred CccHHHHHHHHHHHHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEeccCCCEEEEEEEEEEccEEE
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeCCCCCCccCCcccccc--c-----------cceecccCCCcchh
Q psy11392 85 DSQSSNQPEQPISDSTVKD--I-----------LKYFAEKDKPDPVR 118 (169)
Q Consensus 85 V~lGp~dGlIhISd~s~~e--~-----------i~~~~~~d~~~~~~ 118 (169)
|++||++|++|.+++.++- | .+.++..++.+|+|
T Consensus 99 V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~Vrvr 145 (187)
T PRK08563 99 VRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRAR 145 (187)
T ss_pred EEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEE
Confidence 9999999999998776531 1 23445667777765
No 5
>KOG3297|consensus
Probab=99.92 E-value=3.1e-25 Score=182.77 Aligned_cols=113 Identities=36% Similarity=0.595 Sum_probs=101.8
Q ss_pred cchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEecceeEE
Q psy11392 6 TKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHD 85 (169)
Q Consensus 6 t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~~GiFV 85 (169)
.++++++.++|++||.||+++|+||||||+||..+++|+|.||||+.+.+|.||+++||||.|||+.|+|+++++.|+.+
T Consensus 20 ~~~~~ai~~eL~~k~anKvl~nvGLCI~vyDi~~v~e~~v~pGDGas~~~V~FR~vVFrPF~gEVi~gki~~cs~eG~rv 99 (202)
T KOG3297|consen 20 KPLEDAIKEELNRKLANKVLPNVGLCICVYDILEVEEGIVLPGDGASYARVWFRVVVFRPFVGEVITGKIKECSEEGLRV 99 (202)
T ss_pred chHHHHHHHHHHHHHHhhhcccccEEEEEeEeeeecceEEecCCCceEEEEEEEEEEEecccceEEEEEeecCCccceEE
Confidence 57889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeCCCCCCcc------------CCccccc--------cccceecccCCCcchh
Q psy11392 86 SQSSNQPEQP------------ISDSTVK--------DILKYFAEKDKPDPVR 118 (169)
Q Consensus 86 ~lGp~dGlIh------------ISd~s~~--------e~i~~~~~~d~~~~~~ 118 (169)
++||||.+.- .-++.|= +.-+.|...+|.||-|
T Consensus 100 tl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFR 152 (202)
T KOG3297|consen 100 TLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFR 152 (202)
T ss_pred EEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEE
Confidence 9999985321 1245552 2568899999999987
No 6
>KOG3298|consensus
Probab=99.89 E-value=4.3e-23 Score=167.06 Aligned_cols=112 Identities=19% Similarity=0.255 Sum_probs=102.9
Q ss_pred ccccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEecce
Q psy11392 3 YDITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82 (169)
Q Consensus 3 ~~~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~~G 82 (169)
|=+..+++.+...|.+..+||+.++.|++|+|+++.+|++|+|.|++|.+.|+|+|++++||||+|||++|+|+++++.|
T Consensus 17 ~~gp~~~~~l~~~L~~~veg~ctg~~Gyvi~vt~ld~Ig~g~I~~~~G~v~FpVky~av~FkpfKGEVvdgvV~~Vnk~G 96 (170)
T KOG3298|consen 17 YFGPNLQAILKRKLLAEVEGKCTGKYGYVIAVTTLDNIGEGRIRPGTGFVTFPVKYKAVTFKPFKGEVVDGVVTKVNKMG 96 (170)
T ss_pred ccCchHHHHHHHHHHHHhhccccccccEEEEEEEhhhccCCccccCCceEEEEEEEEEEEEeecCCcEEEEEEEEEeeee
Confidence 45677899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEeCCCCCCc----cCCccccc--cccceecccCCC
Q psy11392 83 VHDSQSSNQPEQ----PISDSTVK--DILKYFAEKDKP 114 (169)
Q Consensus 83 iFV~lGp~dGlI----hISd~s~~--e~i~~~~~~d~~ 114 (169)
+|+++||+.-++ .-+|+.++ |..+||.+.|+-
T Consensus 97 ~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s 134 (170)
T KOG3298|consen 97 VFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDES 134 (170)
T ss_pred EEEeccceEeeeecccCCCCcccCCCCCCCcccccccc
Confidence 999999998655 24678776 667899999983
No 7
>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.
Probab=99.81 E-value=1.4e-19 Score=130.46 Aligned_cols=63 Identities=52% Similarity=0.857 Sum_probs=61.2
Q ss_pred ccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecCC
Q psy11392 5 ITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFV 67 (169)
Q Consensus 5 ~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf~ 67 (169)
+.++++++.++|+++|+||+++++|+||+|+|+.++++|+|.||||+++++|+||+++||||+
T Consensus 18 g~~~~~~i~~~L~~ky~gkv~~~~Gl~v~v~di~~i~eG~I~~gdG~~~~~V~Fr~lvFrPf~ 80 (80)
T cd04330 18 SRPLNDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80 (80)
T ss_pred CcCHHHHHHHHHHHHhCCcEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEECCC
Confidence 568999999999999999999999999999999999999999999999999999999999985
No 8
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.
Probab=99.79 E-value=3.9e-19 Score=127.99 Aligned_cols=63 Identities=29% Similarity=0.433 Sum_probs=61.2
Q ss_pred ccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecCC
Q psy11392 5 ITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFV 67 (169)
Q Consensus 5 ~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf~ 67 (169)
+.++++++.++|+++|+||+++++|+||+++|+.++++|+|.||||+++++|+|++++||||+
T Consensus 18 ~~~~~~~i~~~L~~k~~gkv~~~~G~~v~v~di~~i~~G~I~~gdG~~~~~V~F~~ivFrPf~ 80 (80)
T cd00655 18 GDDCKGVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPFS 80 (80)
T ss_pred CccHHHHHHHHHHHHhCCeEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEEcCC
Confidence 568999999999999999999999999999999999999999999999999999999999985
No 9
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter.
Probab=99.79 E-value=4.5e-19 Score=127.78 Aligned_cols=63 Identities=21% Similarity=0.371 Sum_probs=61.2
Q ss_pred ccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecCC
Q psy11392 5 ITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFV 67 (169)
Q Consensus 5 ~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf~ 67 (169)
+.++++++.++|+++|+||+.+++|+||||+||.++++|+|.||||+++++|+|+|++||||+
T Consensus 18 g~~l~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~~G~I~~gdG~~~~~V~F~aivfrPf~ 80 (80)
T cd04329 18 GPNLKEYLEQKLLEEVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPFK 80 (80)
T ss_pred CccHHHHHHHHHHHHhCCcCcCceeEEEEEEEeeEecCcEEEcCCCCEEEEEEEEEEEEEccC
Confidence 568999999999999999999999999999999999999999999999999999999999985
No 10
>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.
Probab=99.76 E-value=2.4e-18 Score=124.19 Aligned_cols=62 Identities=23% Similarity=0.383 Sum_probs=60.4
Q ss_pred ccchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEEecC
Q psy11392 5 ITKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPF 66 (169)
Q Consensus 5 ~t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvFrPf 66 (169)
+.++++++.++|+++|+||+.+++|+||+|+||.++++|+|.||||+++++|+|||++|||.
T Consensus 18 g~~~~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~eG~I~~gdG~~~~~V~F~~ivFrP~ 79 (80)
T cd04331 18 GEDLEEAVLEILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFKPE 79 (80)
T ss_pred CcCHHHHHHHHHHHHhcCcCcCCCCEEEEEEEEEEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence 56899999999999999999999999999999999999999999999999999999999996
No 11
>PF03876 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; InterPro: IPR005576 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable []. This entry represents the N-terminal, heterodimerisation domain of RPB7.; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2C35_F 3HKZ_E 2PMZ_T 2CKZ_D 2Y0S_E 2RF4_A 2JA7_G 1Y1V_G 2JA5_G 4A3D_G ....
Probab=99.47 E-value=2.7e-13 Score=93.54 Aligned_cols=58 Identities=33% Similarity=0.516 Sum_probs=55.5
Q ss_pred cchHHHHHHHhhhhcCceeeCCeeEEEEEeeeeeeccceEeeCCCceeEEEEEEEEEE
Q psy11392 6 TKIEDSVIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVF 63 (169)
Q Consensus 6 t~l~~~I~~eL~ekyegKVi~~vGLiV~V~dI~~I~eG~I~pgDG~~~~~V~FraIvF 63 (169)
.++++.+.++|+++|+||+.+++|+||++++|..+++|+|.++||+++++|+|++++|
T Consensus 13 ~~~~~~i~~~L~~~~~~k~~~~~G~~i~v~~i~~~~~g~I~~~~g~~~~~V~f~~lvF 70 (70)
T PF03876_consen 13 PDLKDGIKEQLLDKYEGKYIPELGVVIAVTDIKEISEGKIIPGDGFVYFKVTFRALVF 70 (70)
T ss_dssp STHHHHHHHHHHHHHTTEEETTTEEEEEEEEEEEESCEEE-TTTSSEEEEEEEEEEEE
T ss_pred cCHHHHHHHHHHHHHhCcCcCCceEEEEEeeeeEecCcEEECCCCCEEEEEEEEEEEC
Confidence 3899999999999999999999999999999999999999999999999999999998
No 12
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.32 E-value=3.1e-12 Score=119.54 Aligned_cols=109 Identities=16% Similarity=0.126 Sum_probs=90.5
Q ss_pred HHHHHHHhhhhc------CceeeCCe--eEEEEEeeee------eeccceEeeCCCceeEEEEEEEEEEec---------
Q psy11392 9 EDSVIIPGDGAS------HTKVFPNV--GLCMMLYDIT------KIEDSVIIPGDGASHTKVEFRYVVFRP--------- 65 (169)
Q Consensus 9 ~~~I~~eL~eky------egKVi~~v--GLiV~V~dI~------~I~eG~I~pgDG~~~~~V~FraIvFrP--------- 65 (169)
....|+.|.+++ .+++...+ |++|.+.++. +++...|.+.+...+.+++|+++.+++
T Consensus 92 ~~~~w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~gvr~FlP~S~v~~r~v~d~~~~~Gk~~~~kiie~d~~~n~vv~Sr 171 (541)
T COG0539 92 RERAWEKLEEAFENGEIVEGKITGKVKGGLTVDIEGVRAFLPGSLVDVRPVRDLDPLIGKELEFKILELDKKRNNVVLSR 171 (541)
T ss_pred HHHhHHHHHHHHhcCCeEEEEEEEEecCcEEEEECCEEEeccHHHhcccccccccccCCceEEEEEEEEccccCcEEEEh
Confidence 456788888888 44555555 9999998776 688888988999999999999999988
Q ss_pred -------------------CCCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc--cccceecccCCCcch
Q psy11392 66 -------------------FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK--DILKYFAEKDKPDPV 117 (169)
Q Consensus 66 -------------------f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~--e~i~~~~~~d~~~~~ 117 (169)
..|++++|+|+++|+||+||++|++||++|+|+|||+ +.++=++.-.+-+.+
T Consensus 172 R~~~e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~Vkv 244 (541)
T COG0539 172 RAVLEEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKV 244 (541)
T ss_pred HHHhhHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEecCeeeEEehhhccccccCCHHHhcccCCEEEE
Confidence 8899999999999999999999999999999999997 555444444444443
No 13
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo
Probab=99.00 E-value=1.3e-09 Score=79.12 Aligned_cols=60 Identities=17% Similarity=0.225 Sum_probs=55.7
Q ss_pred chHHHHHHHhhhhcCceeeCCe-eEEEEEeeeeeecc--ceEeeCCCceeEEEEEEEEEEecCC
Q psy11392 7 KIEDSVIIPGDGASHTKVFPNV-GLCMMLYDITKIED--SVIIPGDGASHTKVEFRYVVFRPFV 67 (169)
Q Consensus 7 ~l~~~I~~eL~ekyegKVi~~v-GLiV~V~dI~~I~e--G~I~pgDG~~~~~V~FraIvFrPf~ 67 (169)
+..+.+.++|++++. |+.+++ |+|++++|+..+++ ++|.+++|..+.+|+|++++|||+.
T Consensus 27 ~~~~~i~~~l~~~l~-ky~~~l~Gv~l~~~di~~~~~~~~~i~~~~~~~~~~V~~~~lVFrP~~ 89 (89)
T cd04328 27 NPLTGIKAQLLNPLL-KYSPKLKGVVLAYSNIKLLEGELAKIVDDSPFIFVWISADFLVFRPKI 89 (89)
T ss_pred CHhHHHHHHHhhhHh-hhcccCCeEEEEecceEeccccceeeeCCCcEEEEEEEEEEEEEecCC
Confidence 345599999999999 999999 99999999998866 9999999999999999999999984
No 14
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.75 E-value=1.4e-08 Score=93.97 Aligned_cols=92 Identities=11% Similarity=0.031 Sum_probs=73.3
Q ss_pred HHHHHHhhhhc------CceeeCC--eeEEEEEeeee------eeccceEeeCCCceeEEEEEEEEEEec----------
Q psy11392 10 DSVIIPGDGAS------HTKVFPN--VGLCMMLYDIT------KIEDSVIIPGDGASHTKVEFRYVVFRP---------- 65 (169)
Q Consensus 10 ~~I~~eL~eky------egKVi~~--vGLiV~V~dI~------~I~eG~I~pgDG~~~~~V~FraIvFrP---------- 65 (169)
...|+.|++.+ .|+|... .|++|.+ ++. +++...+.+.+..++.+|+++++.+++
T Consensus 110 ~~~w~~ie~~~e~g~~V~G~V~~v~k~G~~Vdl-Gi~gflP~Sel~~~~~~~~~~~vGq~V~vkVleid~~~~~ivLSrr 188 (486)
T PRK07899 110 ERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVEMRRVRDLQPYIGQEIEAKIIELDKNRNNVVLSRR 188 (486)
T ss_pred cchHHHHHHHhcCCCEEEEEEEEEECCeEEEEE-CCEEEEEhhHhcccccCChhhcCCCEEEEEEEEEECCCCEEEEEhH
Confidence 45677887777 3455442 2898888 654 344455555566789999999999877
Q ss_pred ------------------CCCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 66 ------------------FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 66 ------------------f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
..|+++.|+|++++++|+||++|+++|+||+|+++|+
T Consensus 189 ~~l~~~~~~~~~~~~~~lk~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~ 243 (486)
T PRK07899 189 AWLEQTQSEVRSEFLNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWK 243 (486)
T ss_pred HHHHhhhHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCc
Confidence 3799999999999999999999999999999999996
No 15
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.68 E-value=4.6e-08 Score=85.86 Aligned_cols=107 Identities=11% Similarity=0.093 Sum_probs=79.2
Q ss_pred HHHHHHhhhhcC------ceeeC--CeeEEEEEeeee------eeccceEeeCCCceeEEEEEEEEEEec----------
Q psy11392 10 DSVIIPGDGASH------TKVFP--NVGLCMMLYDIT------KIEDSVIIPGDGASHTKVEFRYVVFRP---------- 65 (169)
Q Consensus 10 ~~I~~eL~ekye------gKVi~--~vGLiV~V~dI~------~I~eG~I~pgDG~~~~~V~FraIvFrP---------- 65 (169)
...|+.+.+.++ |+|.. +.|++|.+.++. +++..... +-.+...++++++.++|
T Consensus 106 ~~~w~~l~~~~~~~~~V~g~V~~~~~~G~~V~l~Gv~gfip~s~ls~~~~~--~~~vG~~i~~kVl~id~~~~~i~lS~K 183 (318)
T PRK07400 106 MRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPK--EELVGEELPLKFLEVDEERNRLVLSHR 183 (318)
T ss_pred hhHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCccCCc--cccCCCEEEEEEEEEEcccCEEEEEhh
Confidence 356888888874 33332 239999887664 44443322 34588899999999988
Q ss_pred -----------CCCcEEEEEEEEEecceeEEEeCCCCCCccCCcccccc--ccceecccCCCcchh
Q psy11392 66 -----------FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVKD--ILKYFAEKDKPDPVR 118 (169)
Q Consensus 66 -----------f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~e--~i~~~~~~d~~~~~~ 118 (169)
..|++++|+|++++++|+||++++++|++|+|+++|+- -+.-.+...+.++++
T Consensus 184 ~~~~~~~~~~~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~~~~~~~~~~~vGd~Vkvk 249 (318)
T PRK07400 184 RALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVNDEMKVM 249 (318)
T ss_pred HhhhhhhhccCCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccccccChhhccCCCCEEEEE
Confidence 66999999999999999999999999999999999972 233334555666553
No 16
>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=98.62 E-value=2.9e-08 Score=68.86 Aligned_cols=38 Identities=18% Similarity=0.163 Sum_probs=35.2
Q ss_pred cCCCcEEEEEEEEEecceeEEEeCC--CCCCccCCccccc
Q psy11392 65 PFVSEIIIGKIRSCSKEGVHDSQSS--NQPEQPISDSTVK 102 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~~GiFV~lGp--~dGlIhISd~s~~ 102 (169)
|..|++++|+|++++++|+||++.. .+|++|+|+++|+
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~ 40 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSC 40 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCC
Confidence 5689999999999999999999955 5999999999997
No 17
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=98.61 E-value=3.5e-08 Score=72.13 Aligned_cols=31 Identities=13% Similarity=0.052 Sum_probs=29.0
Q ss_pred CCcEEEEEEEEEecceeEEEeCCCCCCccCC
Q psy11392 67 VSEIIIGKIRSCSKEGVHDSQSSNQPEQPIS 97 (169)
Q Consensus 67 ~GEVVeG~V~~vt~~GiFV~lGp~dGlIhIS 97 (169)
+|||++|+|++++++|+|+++||+++++|.+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~ 31 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRH 31 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEee
Confidence 6999999999999999999999999999854
No 18
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.60 E-value=8e-08 Score=88.75 Aligned_cols=95 Identities=13% Similarity=0.117 Sum_probs=74.0
Q ss_pred hHHHHHHHhhhhc------CceeeCCe--eEEEEEeeee------eeccceEeeCCCceeEEEEEEEEEEec--------
Q psy11392 8 IEDSVIIPGDGAS------HTKVFPNV--GLCMMLYDIT------KIEDSVIIPGDGASHTKVEFRYVVFRP-------- 65 (169)
Q Consensus 8 l~~~I~~eL~eky------egKVi~~v--GLiV~V~dI~------~I~eG~I~pgDG~~~~~V~FraIvFrP-------- 65 (169)
.....|+.|.+.+ +|+|.... |+.|.+.++. +++...+.+.+-.++.+++|+++.+++
T Consensus 100 ~~~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~~~g~~gfip~s~~~~~~~~~~~~~vG~~i~~~V~~~d~~~~~i~lS 179 (565)
T PRK06299 100 KRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVDVRPVRDTDPLEGKELEFKVIKLDKKRNNIVVS 179 (565)
T ss_pred HHHHHHHHHHHHhhCCCEEEEEEEEEECCEEEEEECCEEEEEEHHHccCcCCCChHHhCCCEEEEEEEEEECCCCEEEEE
Confidence 4556777787776 34444322 8888887654 455555544445678899999988865
Q ss_pred --------------------CCCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 66 --------------------FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 66 --------------------f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
..|++++|+|++++++|+||++|+++|++|+|+++|+
T Consensus 180 ~k~~~~~~~~~~~~~~~~~l~~G~iv~g~V~~v~~~G~~V~i~g~~glv~~se~s~~ 236 (565)
T PRK06299 180 RRAVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWK 236 (565)
T ss_pred hHHhhhhhhhhHHHHHHhcCCCCCEEEEEEEEEeCCeEEEEECCEEEEEEHHHhccc
Confidence 5899999999999999999999999999999999996
No 19
>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=98.59 E-value=3.7e-08 Score=67.27 Aligned_cols=39 Identities=23% Similarity=0.225 Sum_probs=36.8
Q ss_pred ecCCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
+|..|++++|+|++++++|+||++| +.+|++|+++++|+
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~ 40 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDD 40 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc
Confidence 4789999999999999999999999 99999999999986
No 20
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.47 E-value=2.4e-07 Score=85.33 Aligned_cols=93 Identities=11% Similarity=0.036 Sum_probs=69.9
Q ss_pred HHHHHHhhhhc------CceeeCC--eeEEEEEeeee------eeccceEeeCCCceeEEEEEEEEEEec----------
Q psy11392 10 DSVIIPGDGAS------HTKVFPN--VGLCMMLYDIT------KIEDSVIIPGDGASHTKVEFRYVVFRP---------- 65 (169)
Q Consensus 10 ~~I~~eL~eky------egKVi~~--vGLiV~V~dI~------~I~eG~I~pgDG~~~~~V~FraIvFrP---------- 65 (169)
...|+.|.++| +|+|... -|+.|.+.++. +++...+.+.+-.+..+++|+++.+++
T Consensus 103 ~~~~~~l~~~~~~g~~v~g~V~~~~~~G~~V~i~g~~~flP~s~~~~~~~~~~~~~vG~~i~~~V~~id~~~~~v~lSrk 182 (491)
T PRK13806 103 QGGAAMLEEAYENGVPVEGKVTGTCKGGFNVEVLGRRAFCPVSQIDLRYVEDPESYVGQTFQFLITRVEENGRNIVVSRR 182 (491)
T ss_pred hhhHHHHHHHHhCCCEEEEEEEEEEcCCEEEEECCEEEEEEHHHhccccCCChHHcCCCeEEEEEEEEECCCCeEEEEee
Confidence 35677777777 4455432 28888876653 344444444444577888888887755
Q ss_pred ------------------CCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 66 ------------------FVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 66 ------------------f~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
..|++++|+|++++++|+||+++ +++|++|+|+++|+
T Consensus 183 ~~~~~~~~~~~~~~~~~l~~G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~ 238 (491)
T PRK13806 183 ALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWS 238 (491)
T ss_pred hhhhhhhHHHHHHHHhhCCCCCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCc
Confidence 58999999999999999999995 79999999999996
No 21
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.44 E-value=3.6e-07 Score=89.78 Aligned_cols=98 Identities=9% Similarity=0.042 Sum_probs=69.5
Q ss_pred CceeeC--CeeEEEEEeeee------eeccceEeeCCCc--eeEEEEEEEEEEec------------------------C
Q psy11392 21 HTKVFP--NVGLCMMLYDIT------KIEDSVIIPGDGA--SHTKVEFRYVVFRP------------------------F 66 (169)
Q Consensus 21 egKVi~--~vGLiV~V~dI~------~I~eG~I~pgDG~--~~~~V~FraIvFrP------------------------f 66 (169)
.|+|.. +.|+.|.+.++. +++.+++.+.... ...+++++++.++| .
T Consensus 498 ~G~Vk~i~~~G~fVdl~Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSlK~l~~~p~~~~~~~~~ 577 (863)
T PRK12269 498 SGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENKFG 577 (863)
T ss_pred EEEEEEEeCCcEEEEECCEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEEeccccchhhhhhccCC
Confidence 444432 348888886543 4555555422222 57899999999887 4
Q ss_pred CCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc---cccceecccCCCcchh
Q psy11392 67 VSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK---DILKYFAEKDKPDPVR 118 (169)
Q Consensus 67 ~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~---e~i~~~~~~d~~~~~~ 118 (169)
.|++++|+|++++++|+||+++ +++|++|+||++|. ..++-.+...+-+.++
T Consensus 578 vG~iV~G~V~~I~~fG~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vk 633 (863)
T PRK12269 578 VNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECM 633 (863)
T ss_pred CCCEEEEEEEEEeCCeEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEE
Confidence 7899999999999999999997 69999999999993 2333344555555444
No 22
>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=98.40 E-value=1.9e-07 Score=63.88 Aligned_cols=54 Identities=13% Similarity=0.188 Sum_probs=43.0
Q ss_pred cCCCcEEEEEEEEEecceeEEEeC---CCCCCccCCcccccc--ccceecccCCCcchh
Q psy11392 65 PFVSEIIIGKIRSCSKEGVHDSQS---SNQPEQPISDSTVKD--ILKYFAEKDKPDPVR 118 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~~GiFV~lG---p~dGlIhISd~s~~e--~i~~~~~~d~~~~~~ 118 (169)
|.+|+++.|+|+++.++|+||++. +++|++|+|+++|+- .++-.+...+.++++
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vk 59 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVK 59 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEE
Confidence 668999999999999999999995 389999999999862 223334666666654
No 23
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=98.39 E-value=1.7e-07 Score=72.83 Aligned_cols=53 Identities=28% Similarity=0.378 Sum_probs=37.3
Q ss_pred cCCCcEEEEEEEEEecceeEEEeCCCCCCccCCc------cccc-----------cccceecccCCCcchh
Q psy11392 65 PFVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISD------STVK-----------DILKYFAEKDKPDPVR 118 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd------~s~~-----------e~i~~~~~~d~~~~~~ 118 (169)
||+|||+.|+|+++++.|+.|++|||+. |+|+. ..|+ +.-++|+..++.||.|
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFdd-I~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFR 70 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDD-IFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFR 70 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEE-EEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEeccccc-EEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEE
Confidence 8999999999999999999999999986 55431 2222 4456677788888877
No 24
>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=98.39 E-value=5.5e-07 Score=82.04 Aligned_cols=93 Identities=15% Similarity=0.194 Sum_probs=69.8
Q ss_pred HHHHHHhhhhc------CceeeCCe--eEEEEEeeee------eeccceEeeCCCceeEEEEEEEEEEec----------
Q psy11392 10 DSVIIPGDGAS------HTKVFPNV--GLCMMLYDIT------KIEDSVIIPGDGASHTKVEFRYVVFRP---------- 65 (169)
Q Consensus 10 ~~I~~eL~eky------egKVi~~v--GLiV~V~dI~------~I~eG~I~pgDG~~~~~V~FraIvFrP---------- 65 (169)
...|+.|++++ +|+|.... |+.|.+.++. +++...+.+.+-.++.+++|.++.+++
T Consensus 88 ~~~~~~l~~a~~~g~~v~g~V~~~~~~g~~V~i~g~~~flP~s~~~~~~~~~~~~~vG~~i~~~v~~~~~~~~~iv~Srk 167 (516)
T TIGR00717 88 HELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQVDVKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRR 167 (516)
T ss_pred hHHHHHHHHHhhCCCeEEEEEEEEECCEEEEEECCEEEEEeHHHhcCcccCchhhhCCCEEEEEEEEEECCCCcEEEEHH
Confidence 34677777766 45555433 8888886654 233332233344577889999888755
Q ss_pred ------------------CCCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 66 ------------------FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 66 ------------------f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
..|++++|+|++++++|+||++|.++|++|.|+++|+
T Consensus 168 ~~l~~~~~~~~~~~~~~l~~G~~v~g~V~~i~~~G~~V~l~g~~g~lp~~e~s~~ 222 (516)
T TIGR00717 168 AYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWK 222 (516)
T ss_pred HHHHHHHHHHHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCCC
Confidence 5799999999999999999999999999999999995
No 25
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.39 E-value=7.8e-07 Score=83.71 Aligned_cols=76 Identities=11% Similarity=0.099 Sum_probs=64.6
Q ss_pred CeeEEEEEeeee------eeccceEeeCCCc--eeEEEEEEEEEEec------------------------CCCcEEEEE
Q psy11392 27 NVGLCMMLYDIT------KIEDSVIIPGDGA--SHTKVEFRYVVFRP------------------------FVSEIIIGK 74 (169)
Q Consensus 27 ~vGLiV~V~dI~------~I~eG~I~pgDG~--~~~~V~FraIvFrP------------------------f~GEVVeG~ 74 (169)
+.|..|.+.++. +++.+++...+-. ++.+|+.+++.+++ .+|.++.|+
T Consensus 205 ~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~l~~dPw~~i~~~~~~g~~v~G~ 284 (541)
T COG0539 205 DYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQLEEDPWEGIEKKYPVGDKVEGK 284 (541)
T ss_pred cCcEEEEecCeeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehhcccCcHHHHhhhcCCCCEEEEE
Confidence 459999888865 6777777654433 66899999999997 889999999
Q ss_pred EEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 75 IRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 75 V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
|++++++|+||.++ +++|++|+|+|||.
T Consensus 285 Vt~i~~~GafVei~~GvEGlvhvSEisw~ 313 (541)
T COG0539 285 VTNLTDYGAFVEIEEGVEGLVHVSEISWT 313 (541)
T ss_pred EEEeecCcEEEEecCCccceeechhhccc
Confidence 99999999999997 59999999999996
No 26
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.38 E-value=6e-07 Score=88.25 Aligned_cols=93 Identities=9% Similarity=0.054 Sum_probs=69.9
Q ss_pred HHHHHHhhhhc------CceeeC--Ce--eEEEEEe-eee------eeccceEeeCCCceeEEEEEEEEEEec-------
Q psy11392 10 DSVIIPGDGAS------HTKVFP--NV--GLCMMLY-DIT------KIEDSVIIPGDGASHTKVEFRYVVFRP------- 65 (169)
Q Consensus 10 ~~I~~eL~eky------egKVi~--~v--GLiV~V~-dI~------~I~eG~I~pgDG~~~~~V~FraIvFrP------- 65 (169)
...|+.|.++| +|+|+. +. |++|.+. ++. +++.....+.+..+..+++|.++.+++
T Consensus 386 ~~~~~~l~~a~~~g~~V~G~Vv~v~~~kgG~~Vdig~~~~gfiP~se~~~~~~~~~~~~vG~~ie~~V~~~~~~~~~~~~ 465 (863)
T PRK12269 386 LGLKVKLRDAERDGTPVEGRIVRLTEKKSGFEVDLGAGMMAFLPISQSDCQKVDAPESLIGLTSKFYIERISQSKQHRGN 465 (863)
T ss_pred hHHHHHHHHHHhCCCeEEEEEEEEEeecCEEEEEECCCcEEEEEHHHhccccccchHHhCCCeEEEEEEEEecccccCCC
Confidence 45788888887 566665 22 7888773 332 333333333444567788999888743
Q ss_pred --------------------------CCCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 66 --------------------------FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 66 --------------------------f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
..|++++|+|++++++|+||++|+++|++|+|+++|+
T Consensus 466 ~~iVlSrr~~l~e~~~~~~ee~~~~l~~G~~V~G~Vk~i~~~G~fVdl~Gv~Gfvp~SeiS~~ 528 (863)
T PRK12269 466 DNIVINRRRYLEERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWG 528 (863)
T ss_pred CeEEEEHHHHHHHHHHHHHHHHHhcCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEchhcccc
Confidence 3589999999999999999999999999999999996
No 27
>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=98.38 E-value=1.9e-07 Score=65.67 Aligned_cols=37 Identities=22% Similarity=0.145 Sum_probs=34.5
Q ss_pred CCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
.+|+++.|+|++++++|+||+++ .++|++|++++||+
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~ 39 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKY 39 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCc
Confidence 36999999999999999999997 59999999999996
No 28
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.37 E-value=6.2e-07 Score=79.27 Aligned_cols=92 Identities=12% Similarity=0.083 Sum_probs=66.6
Q ss_pred HHHHHhhhhc------CceeeC--CeeEEEEEeeee------eeccceEeeCCCceeEEEEEEEEEEec-----------
Q psy11392 11 SVIIPGDGAS------HTKVFP--NVGLCMMLYDIT------KIEDSVIIPGDGASHTKVEFRYVVFRP----------- 65 (169)
Q Consensus 11 ~I~~eL~eky------egKVi~--~vGLiV~V~dI~------~I~eG~I~pgDG~~~~~V~FraIvFrP----------- 65 (169)
..|+.+.+++ .|+|.. +.|+.|.+.++. +++..++.+.+..++..++|+++.+++
T Consensus 94 ~~~~~~~~~~~~G~~v~g~V~~v~~~G~~V~~~G~~gflp~~el~~~~~~~~~~~vG~~v~~~Vl~~d~~~~~i~lS~k~ 173 (390)
T PRK06676 94 KAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLISTRFVEDFSDFKGKTLEVKIIELDPEKNRVILSRRA 173 (390)
T ss_pred hhHHHHHHhccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCCccCCChHHcCCCEEEEEEEEEECCCCEEEEEeHH
Confidence 4577776665 455543 338888875542 233333332233467788888876654
Q ss_pred -----------------CCCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 66 -----------------FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 66 -----------------f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
..|++++|+|++++++|+||++|.++|++|+|+++|+
T Consensus 174 ~~~~~~~~~~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~ 227 (390)
T PRK06676 174 VVEEERAAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHE 227 (390)
T ss_pred HhhhhhhhHHHHHHhhCCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCcc
Confidence 4699999999999999999999999999999999985
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=98.32 E-value=3.3e-07 Score=64.62 Aligned_cols=37 Identities=14% Similarity=0.071 Sum_probs=34.6
Q ss_pred CCCcEEEEEEEEEecceeEEEeC--CCCCCccCCccccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQS--SNQPEQPISDSTVK 102 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lG--p~dGlIhISd~s~~ 102 (169)
.+|.++.|+|++++++|+|+++| .++|++|.++++|+
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~ 41 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF 41 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc
Confidence 36899999999999999999998 79999999999996
No 30
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.29 E-value=4e-07 Score=80.82 Aligned_cols=39 Identities=13% Similarity=0.111 Sum_probs=36.3
Q ss_pred ecCCCcEEEEEEEEEecceeEEEe---CCCCCCccCCccccc
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQ---SSNQPEQPISDSTVK 102 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~l---Gp~dGlIhISd~s~~ 102 (169)
-|..|++|.|+|++++++|+||++ |.++||||+|++||+
T Consensus 14 ~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ 55 (319)
T PTZ00248 14 FPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKR 55 (319)
T ss_pred CCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhccc
Confidence 367899999999999999999999 489999999999996
No 31
>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=98.26 E-value=6.5e-07 Score=65.16 Aligned_cols=38 Identities=16% Similarity=0.213 Sum_probs=35.1
Q ss_pred ecCCCcEEEEEEEEEecc--eeEEEeCC-CCCCccCCcccc
Q psy11392 64 RPFVSEIIIGKIRSCSKE--GVHDSQSS-NQPEQPISDSTV 101 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~--GiFV~lGp-~dGlIhISd~s~ 101 (169)
+|..|+++.|+|+++.++ |+||++++ .+|++|+|++||
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~ 44 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILP 44 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCc
Confidence 357899999999999997 99999984 899999999999
No 32
>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=98.25 E-value=8.9e-07 Score=60.53 Aligned_cols=37 Identities=16% Similarity=0.136 Sum_probs=34.4
Q ss_pred CCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
.+|+++.|+|++++++|+||+++ +++|++|+|+++|+
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~ 39 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDD 39 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCc
Confidence 47999999999999999999997 68999999999985
No 33
>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=98.23 E-value=5.9e-07 Score=63.35 Aligned_cols=54 Identities=13% Similarity=0.042 Sum_probs=42.1
Q ss_pred cCCCcEEEEEEEEEecceeEEEe-CCCCCCccCCccccccc--cceecccCCCcchh
Q psy11392 65 PFVSEIIIGKIRSCSKEGVHDSQ-SSNQPEQPISDSTVKDI--LKYFAEKDKPDPVR 118 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~~GiFV~l-Gp~dGlIhISd~s~~e~--i~~~~~~d~~~~~~ 118 (169)
+..|+++.|+|++++++|+||++ ++.+|++|+++++|+.+ +.-.++.+|.++++
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vk 68 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAK 68 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEE
Confidence 56899999999999999999999 47999999999998733 22334445544443
No 34
>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=98.21 E-value=7.2e-07 Score=59.95 Aligned_cols=51 Identities=18% Similarity=0.124 Sum_probs=39.7
Q ss_pred CcEEEEEEEEEecceeEEEeC-CCCCCccCCccccccc---cceecccCCCcchh
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVKDI---LKYFAEKDKPDPVR 118 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~e~---i~~~~~~d~~~~~~ 118 (169)
|+++.|+|++++++|+||+++ ..+|++|+|+++|... ..-.+...|.++++
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~ 55 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAV 55 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEE
Confidence 789999999999999999995 6899999999998532 22334555555554
No 35
>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=98.21 E-value=7.2e-07 Score=60.74 Aligned_cols=52 Identities=13% Similarity=0.063 Sum_probs=40.6
Q ss_pred CCcEEEEEEEEEecceeEEEeC--CCCCCccCCccccccc--cceecccCCCcchh
Q psy11392 67 VSEIIIGKIRSCSKEGVHDSQS--SNQPEQPISDSTVKDI--LKYFAEKDKPDPVR 118 (169)
Q Consensus 67 ~GEVVeG~V~~vt~~GiFV~lG--p~dGlIhISd~s~~e~--i~~~~~~d~~~~~~ 118 (169)
.|+++.|+|++++++|+||+++ +.+|++|+++++|+-. ++-.+...+.+++|
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~ 57 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAK 57 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEE
Confidence 5899999999999999999997 5899999999998521 12234555555554
No 36
>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=98.20 E-value=7.8e-07 Score=58.61 Aligned_cols=35 Identities=14% Similarity=0.080 Sum_probs=32.9
Q ss_pred CcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
|+++.|+|++++++|+||+++ +.+|++|+++++|+
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~ 36 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHK 36 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCc
Confidence 789999999999999999998 89999999999875
No 37
>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=98.20 E-value=8e-07 Score=60.23 Aligned_cols=50 Identities=10% Similarity=0.079 Sum_probs=38.1
Q ss_pred CcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc--cccceecccCCCcch
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK--DILKYFAEKDKPDPV 117 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~--e~i~~~~~~d~~~~~ 117 (169)
|+++.|+|+++.++|+||+++ .++|++|+|+++|+ +-+.-.+...+.+++
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~ 53 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKG 53 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEE
Confidence 789999999999999999996 59999999999876 222233344444444
No 38
>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=98.19 E-value=1.1e-06 Score=61.39 Aligned_cols=36 Identities=19% Similarity=0.163 Sum_probs=33.3
Q ss_pred CcEEEEEEEEEecceeEEEeC----CCCCCccCCcccccc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQS----SNQPEQPISDSTVKD 103 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lG----p~dGlIhISd~s~~e 103 (169)
|++++|+|++++++|+||+++ +.+|++|+|+++|+-
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~ 40 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEG 40 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCC
Confidence 689999999999999999998 689999999999863
No 39
>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=98.18 E-value=9.7e-07 Score=58.47 Aligned_cols=36 Identities=17% Similarity=0.175 Sum_probs=33.8
Q ss_pred CCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 67 VSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 67 ~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
+|+++.|+|++++++|+||+++..+|++|.++++|.
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e~~~~ 36 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWG 36 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCc
Confidence 489999999999999999999999999999999874
No 40
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.15 E-value=4.9e-06 Score=76.71 Aligned_cols=82 Identities=13% Similarity=0.086 Sum_probs=58.2
Q ss_pred CceeeC--CeeEEEEEe-eee------eeccceEeeCCCc--eeEEEEEEEEEEec------------------------
Q psy11392 21 HTKVFP--NVGLCMMLY-DIT------KIEDSVIIPGDGA--SHTKVEFRYVVFRP------------------------ 65 (169)
Q Consensus 21 egKVi~--~vGLiV~V~-dI~------~I~eG~I~pgDG~--~~~~V~FraIvFrP------------------------ 65 (169)
+|+|.. +.|+.|.+. ++. +++..++.+.+.. ++..++++++.+.+
T Consensus 207 ~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~K~~~~~p~~~~ 286 (491)
T PRK13806 207 EGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTV 286 (491)
T ss_pred EEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEehhhhcccchhh
Confidence 555543 448888774 222 4555555433332 55666666655432
Q ss_pred ----CCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 66 ----FVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 66 ----f~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
..|+++.|+|++++++|+||+++ +++|++|+|+++|.
T Consensus 287 ~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~ 328 (491)
T PRK13806 287 GDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWT 328 (491)
T ss_pred hccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcc
Confidence 35899999999999999999997 69999999999994
No 41
>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=98.14 E-value=1.6e-06 Score=59.98 Aligned_cols=37 Identities=16% Similarity=0.034 Sum_probs=33.8
Q ss_pred CCcEEEEEEEEEecceeEEEeCC--CCCCccCCcccccc
Q psy11392 67 VSEIIIGKIRSCSKEGVHDSQSS--NQPEQPISDSTVKD 103 (169)
Q Consensus 67 ~GEVVeG~V~~vt~~GiFV~lGp--~dGlIhISd~s~~e 103 (169)
.|++++|+|++++++|+||++++ .+|++|.|+++|+.
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~ 39 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDY 39 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCc
Confidence 38999999999999999999996 89999999998763
No 42
>PRK08582 hypothetical protein; Provisional
Probab=98.14 E-value=2e-06 Score=67.67 Aligned_cols=38 Identities=16% Similarity=0.090 Sum_probs=34.8
Q ss_pred cCCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 65 PFVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
...|++++|+|++++++|+||.++ ..+|+||+|+++|+
T Consensus 3 ~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~ 41 (139)
T PRK08582 3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADN 41 (139)
T ss_pred CcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcc
Confidence 357999999999999999999997 58999999999985
No 43
>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=98.13 E-value=1.1e-06 Score=61.06 Aligned_cols=36 Identities=8% Similarity=0.075 Sum_probs=33.2
Q ss_pred CCcEEEEEEEEEec-ceeEEEeC-CCCCCccCCccccc
Q psy11392 67 VSEIIIGKIRSCSK-EGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 67 ~GEVVeG~V~~vt~-~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
.|+++.|+|+++.+ +|+|++++ ..+|++|+|+++|+
T Consensus 3 ~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~ 40 (72)
T cd05704 3 EGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDS 40 (72)
T ss_pred CCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCc
Confidence 79999999999986 89999996 67999999999996
No 44
>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=98.11 E-value=1.5e-06 Score=58.81 Aligned_cols=35 Identities=17% Similarity=0.019 Sum_probs=32.5
Q ss_pred CcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
|+++.|+|++++++|+||+++ .++|++|+|+++++
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~ 36 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEA 36 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChh
Confidence 789999999999999999996 59999999999875
No 45
>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=98.10 E-value=1.6e-06 Score=58.91 Aligned_cols=36 Identities=17% Similarity=0.161 Sum_probs=33.2
Q ss_pred CcEEEEEEEEEecceeEEEeC-CCCCCccCCcccccc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVKD 103 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~e 103 (169)
|++++|+|++++++|+||+++ .++|++|+|+++|+.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~ 37 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVR 37 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCcc
Confidence 789999999999999999995 699999999999873
No 46
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.09 E-value=6.7e-06 Score=76.40 Aligned_cols=92 Identities=13% Similarity=0.070 Sum_probs=64.2
Q ss_pred CeeEEEEEeeee------eeccceEeeCCC--ceeEEEEEEEEEEec------------------------CCCcEEEEE
Q psy11392 27 NVGLCMMLYDIT------KIEDSVIIPGDG--ASHTKVEFRYVVFRP------------------------FVSEIIIGK 74 (169)
Q Consensus 27 ~vGLiV~V~dI~------~I~eG~I~pgDG--~~~~~V~FraIvFrP------------------------f~GEVVeG~ 74 (169)
+.|+.|.+.++. +++..++.+.+- .++..|+++++.++| .+|+++.|+
T Consensus 221 ~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK~~~~dPw~~~~~~~~vG~vv~G~ 300 (486)
T PRK07899 221 NFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQEDPWQQFARTHAIGQIVPGK 300 (486)
T ss_pred CCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEeeccccchhhhHHhcCCCCEEEEE
Confidence 338888775533 334333322211 256677888777765 369999999
Q ss_pred EEEEecceeEEEeC-CCCCCccCCcccccc--ccceecccCCCcchh
Q psy11392 75 IRSCSKEGVHDSQS-SNQPEQPISDSTVKD--ILKYFAEKDKPDPVR 118 (169)
Q Consensus 75 V~~vt~~GiFV~lG-p~dGlIhISd~s~~e--~i~~~~~~d~~~~~~ 118 (169)
|++++++|+||++. +++|++|+|+++|+. ..+-.+...+.+.++
T Consensus 301 V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~Vk 347 (486)
T PRK07899 301 VTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVK 347 (486)
T ss_pred EEEEeccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEE
Confidence 99999999999995 699999999999863 344445666666655
No 47
>PRK07252 hypothetical protein; Provisional
Probab=98.08 E-value=2.3e-06 Score=65.86 Aligned_cols=52 Identities=12% Similarity=0.064 Sum_probs=42.1
Q ss_pred CCcEEEEEEEEEecceeEEEeC-CCCCCccCCcccccc--ccceecccCCCcchh
Q psy11392 67 VSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVKD--ILKYFAEKDKPDPVR 118 (169)
Q Consensus 67 ~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~e--~i~~~~~~d~~~~~~ 118 (169)
.|+++.|+|++++++|+||+++ +.+|++|+|+++|+- .+...+...|.++++
T Consensus 3 vG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~Vk 57 (120)
T PRK07252 3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQ 57 (120)
T ss_pred CCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEE
Confidence 6999999999999999999994 689999999999862 233445666666655
No 48
>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=98.08 E-value=2.1e-06 Score=59.54 Aligned_cols=35 Identities=11% Similarity=-0.054 Sum_probs=32.0
Q ss_pred CcEEE-EEEEEE-ecceeEEEeC-CCCCCccCCccccc
Q psy11392 68 SEIII-GKIRSC-SKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 68 GEVVe-G~V~~v-t~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
||+++ |+|+++ .++|+||+++ .++|++|+|+++|+
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~ 38 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDD 38 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcc
Confidence 78999 999999 6999999996 49999999999875
No 49
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.07 E-value=3e-06 Score=57.74 Aligned_cols=36 Identities=11% Similarity=0.099 Sum_probs=33.5
Q ss_pred CCcEEEEEEEEEecceeEEEeCC-CCCCccCCccccc
Q psy11392 67 VSEIIIGKIRSCSKEGVHDSQSS-NQPEQPISDSTVK 102 (169)
Q Consensus 67 ~GEVVeG~V~~vt~~GiFV~lGp-~dGlIhISd~s~~ 102 (169)
+|++++|+|++++++|+||++.+ .+|++|+++++|.
T Consensus 3 ~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~ 39 (72)
T cd05689 3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWT 39 (72)
T ss_pred CCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCc
Confidence 68999999999999999999964 8999999999985
No 50
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.07 E-value=4.7e-06 Score=79.08 Aligned_cols=93 Identities=12% Similarity=0.081 Sum_probs=69.5
Q ss_pred HHHHHHhhhhc------CceeeC--CeeEEEEEeeee------eeccceEeeCCCceeEEEEEEEEEEec----------
Q psy11392 10 DSVIIPGDGAS------HTKVFP--NVGLCMMLYDIT------KIEDSVIIPGDGASHTKVEFRYVVFRP---------- 65 (169)
Q Consensus 10 ~~I~~eL~eky------egKVi~--~vGLiV~V~dI~------~I~eG~I~pgDG~~~~~V~FraIvFrP---------- 65 (169)
+..|+.|.+.+ .|+|.. +.|+.|.+.++. +++..++.+.+..+...++|+++.+++
T Consensus 377 ~~~~~~l~~~~~~G~iv~g~V~~v~~~G~~V~lggi~gfiP~sel~~~~~~d~~~~vG~~v~v~Vl~vd~e~~~~l~lS~ 456 (647)
T PRK00087 377 EKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVELGYVEDLSEYKGQELEVKIIEFNRKRRKKVVLSR 456 (647)
T ss_pred hhHHHHHHHHhhCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHhCccccCCHHHhCCCEEEEEEEEEEcCCCcEEEEEe
Confidence 45577776655 556654 338888876532 344455444444577888888877765
Q ss_pred -------------------CCCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 66 -------------------FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 66 -------------------f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
..|+++.|+|++++++|+||++++++|++|+|+++|+
T Consensus 457 k~~~~~~~~~~~~~~~~~l~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~ 512 (647)
T PRK00087 457 KAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWG 512 (647)
T ss_pred HHHhhhhhhhHHHHHHHhCCCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCcc
Confidence 2699999999999999999999999999999999985
No 51
>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=98.06 E-value=2.6e-06 Score=60.15 Aligned_cols=39 Identities=15% Similarity=0.349 Sum_probs=36.9
Q ss_pred EecCCCcEEEEEEEEEecceeEEEeC-CCCCCccCCcccc
Q psy11392 63 FRPFVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTV 101 (169)
Q Consensus 63 FrPf~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~ 101 (169)
|.|.+|++++|+|++++++|++|+++ +++|++|+|+++|
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~ 41 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNL 41 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccC
Confidence 67899999999999999999999998 7999999999987
No 52
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=98.02 E-value=4.2e-06 Score=65.95 Aligned_cols=38 Identities=18% Similarity=0.078 Sum_probs=34.7
Q ss_pred cCCCcEEEEEEEEEecceeEEEe-CCCCCCccCCccccc
Q psy11392 65 PFVSEIIIGKIRSCSKEGVHDSQ-SSNQPEQPISDSTVK 102 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~~GiFV~l-Gp~dGlIhISd~s~~ 102 (169)
+..|++++|+|+.+++|||||.+ |.-.||||||+++-+
T Consensus 3 ~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~ 41 (129)
T COG1098 3 MKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADG 41 (129)
T ss_pred ccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhh
Confidence 56899999999999999999999 568999999988875
No 53
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.02 E-value=1e-05 Score=71.17 Aligned_cols=82 Identities=10% Similarity=0.047 Sum_probs=58.0
Q ss_pred CceeeC--CeeEEEEEee----e---eeeccceEeeCCC--ceeEEEEEEEEEEec------------------------
Q psy11392 21 HTKVFP--NVGLCMMLYD----I---TKIEDSVIIPGDG--ASHTKVEFRYVVFRP------------------------ 65 (169)
Q Consensus 21 egKVi~--~vGLiV~V~d----I---~~I~eG~I~pgDG--~~~~~V~FraIvFrP------------------------ 65 (169)
+|+|.+ +-|+.|.+.. . .+++.+++.+.+. ....+++|.++-.++
T Consensus 36 ~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~~~~~~~w~~l~~~ 115 (318)
T PRK07400 36 NGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRAWERVRQL 115 (318)
T ss_pred EEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhhhhhhhHHHHHHHh
Confidence 455544 2388777742 1 1455554432221 134667777765554
Q ss_pred -CCCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 66 -FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 66 -f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
..|++++|+|+++++.|+||+++++.|++|+|++||.
T Consensus 116 ~~~~~~V~g~V~~~~~~G~~V~l~Gv~gfip~s~ls~~ 153 (318)
T PRK07400 116 QKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTR 153 (318)
T ss_pred ccCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcCcc
Confidence 3589999999999999999999999999999999995
No 54
>PRK05807 hypothetical protein; Provisional
Probab=98.00 E-value=4.2e-06 Score=65.57 Aligned_cols=37 Identities=14% Similarity=0.092 Sum_probs=34.4
Q ss_pred CCCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
.+|++++|+|+.++++|+||.+...+|+||+|+++++
T Consensus 4 ~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~ 40 (136)
T PRK05807 4 KAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADT 40 (136)
T ss_pred cCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccc
Confidence 4699999999999999999999889999999999873
No 55
>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=97.96 E-value=4.8e-06 Score=58.19 Aligned_cols=35 Identities=23% Similarity=0.196 Sum_probs=32.7
Q ss_pred CcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
|.++.|+|++++++|+||+++ .++|++|+|+++|+
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~ 36 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDD 36 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCc
Confidence 679999999999999999997 49999999999986
No 56
>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=97.95 E-value=1.5e-06 Score=83.33 Aligned_cols=71 Identities=17% Similarity=0.122 Sum_probs=54.9
Q ss_pred eEEEEEeeeeeeccceEeeCCCceeEEE--EEEEEEEecCCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 29 GLCMMLYDITKIEDSVIIPGDGASHTKV--EFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 29 GLiV~V~dI~~I~eG~I~pgDG~~~~~V--~FraIvFrPf~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
|.-|.| .+-+..+|...++.....+ ..+.+...|.+|++++|+|+++.++|+||++. +.+|++|+|+++|+
T Consensus 581 g~~I~i---~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~ 654 (684)
T TIGR03591 581 GAKIDI---EDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANE 654 (684)
T ss_pred CCEEEE---ecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCC
Confidence 555554 3345555666666665554 45556778999999999999999999999995 49999999999986
No 57
>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=97.95 E-value=4.6e-06 Score=56.32 Aligned_cols=35 Identities=11% Similarity=0.160 Sum_probs=32.6
Q ss_pred CcEEEEEEEEEecceeEEEe-CCCCCCccCCccccc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQ-SSNQPEQPISDSTVK 102 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~l-Gp~dGlIhISd~s~~ 102 (169)
|+++.|+|++++++|+||++ ++++|++|+|+++++
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~ 36 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRD 36 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCc
Confidence 78999999999999999999 579999999999886
No 58
>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=97.90 E-value=7.6e-06 Score=54.26 Aligned_cols=51 Identities=14% Similarity=0.097 Sum_probs=39.1
Q ss_pred CcEEEEEEEEEecceeEEEeC-CCCCCccCCccccccc--cceecccCCCcchh
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVKDI--LKYFAEKDKPDPVR 118 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~e~--i~~~~~~d~~~~~~ 118 (169)
|+++.|+|++++++|+|++++ ..+|++|+++++|+-+ +.-.++.++.++++
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~ 54 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVK 54 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEE
Confidence 689999999999999999997 4899999999998632 11234555555544
No 59
>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=97.89 E-value=7e-06 Score=55.62 Aligned_cols=35 Identities=20% Similarity=0.267 Sum_probs=32.9
Q ss_pred CcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
|+++.|+|++++++|+||++| ..+|++|.++++|+
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~ 36 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDD 36 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcc
Confidence 789999999999999999997 69999999999985
No 60
>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=97.89 E-value=6.5e-06 Score=79.77 Aligned_cols=54 Identities=17% Similarity=0.058 Sum_probs=41.7
Q ss_pred ecCCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccc---ccc---ccceecccCCCcch
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDST---VKD---ILKYFAEKDKPDPV 117 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s---~~e---~i~~~~~~d~~~~~ 117 (169)
.|..|++++|+|+++++||+||+++ ..+||+|+|+++ |+. -++-.+...+.+.+
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~V 704 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQV 704 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEE
Confidence 5899999999999999999999996 599999999886 642 23333444444443
No 61
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.84 E-value=1e-05 Score=54.76 Aligned_cols=35 Identities=23% Similarity=0.286 Sum_probs=33.3
Q ss_pred CcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
|++++|+|++++++|++|+++.++|++|.|+++|+
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~g~~gfip~s~~~~~ 35 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLR 35 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCc
Confidence 78999999999999999999999999999999885
No 62
>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=97.79 E-value=1.1e-05 Score=53.04 Aligned_cols=35 Identities=11% Similarity=0.108 Sum_probs=31.8
Q ss_pred CcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
|+++.|+|++++++|+||.++ ..+|++|.++++++
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~ 36 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADR 36 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCc
Confidence 689999999999999999997 47899999999875
No 63
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=97.75 E-value=1.5e-05 Score=68.87 Aligned_cols=54 Identities=11% Similarity=0.166 Sum_probs=41.7
Q ss_pred ecCCCcEEEEEEEEEecceeEEEeC---CCCCCccCCccccc--cccceecccCCCcch
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQS---SNQPEQPISDSTVK--DILKYFAEKDKPDPV 117 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~lG---p~dGlIhISd~s~~--e~i~~~~~~d~~~~~ 117 (169)
.|.+|+++.|+|+++.++|+||++. +++|++|+|+++|+ ..+.-.+...+.+++
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~v 63 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVC 63 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEE
Confidence 3889999999999999999999995 68999999999876 223333344444443
No 64
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=97.75 E-value=1.7e-05 Score=51.65 Aligned_cols=36 Identities=19% Similarity=0.266 Sum_probs=33.5
Q ss_pred CCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 67 VSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 67 ~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
+|+++.|+|++++++|+|++++ .++|++|.+++++.
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~ 38 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDK 38 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcc
Confidence 6999999999999999999999 89999999988764
No 65
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=97.68 E-value=1.5e-05 Score=78.91 Aligned_cols=56 Identities=16% Similarity=0.079 Sum_probs=42.8
Q ss_pred EecCCCcEEE-EEEEEEecceeEEEeC-CCCCCccCCccccc--cccceecccCCCcchh
Q psy11392 63 FRPFVSEIII-GKIRSCSKEGVHDSQS-SNQPEQPISDSTVK--DILKYFAEKDKPDPVR 118 (169)
Q Consensus 63 FrPf~GEVVe-G~V~~vt~~GiFV~lG-p~dGlIhISd~s~~--e~i~~~~~~d~~~~~~ 118 (169)
..|..|++++ |+|+++++||+||+++ ..+||+|+|+++|+ ...+-.+..-+.+.|+
T Consensus 749 ~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~Vk 808 (891)
T PLN00207 749 MVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVK 808 (891)
T ss_pred cCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEE
Confidence 4688999996 6999999999999996 58999999999997 2333334444444443
No 66
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=97.68 E-value=2.6e-05 Score=65.89 Aligned_cols=40 Identities=20% Similarity=0.378 Sum_probs=38.1
Q ss_pred EecCCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 63 FRPFVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 63 FrPf~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
+.|..|++|.|+|++++++|+|++++ +++|++|+|+++|.
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~ 99 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGR 99 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCC
Confidence 88999999999999999999999999 79999999999884
No 67
>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=97.67 E-value=2.7e-05 Score=56.86 Aligned_cols=35 Identities=14% Similarity=0.053 Sum_probs=32.4
Q ss_pred cEEEEEEEEEecceeEEEeCCCCCCccCCcccccc
Q psy11392 69 EIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVKD 103 (169)
Q Consensus 69 EVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~e 103 (169)
|++.|+|++++++|+||++++.+|++|+++++++.
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~ 35 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDY 35 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCc
Confidence 68999999999999999999999999999988763
No 68
>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=97.62 E-value=4.3e-05 Score=52.24 Aligned_cols=37 Identities=14% Similarity=0.151 Sum_probs=34.1
Q ss_pred CCCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
..|++++|+|.++++.|+||++|..+|++|.++++.+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~~ 38 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPG 38 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCCC
Confidence 5799999999999999999999999999999988753
No 69
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.60 E-value=8.4e-05 Score=65.80 Aligned_cols=37 Identities=16% Similarity=0.109 Sum_probs=34.4
Q ss_pred CCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
..|+++.|+|++++++|+||++. +++|++|+|+++|+
T Consensus 276 ~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~ 313 (390)
T PRK06676 276 PEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHK 313 (390)
T ss_pred cCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCcc
Confidence 47999999999999999999995 79999999999986
No 70
>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=97.60 E-value=6.3e-05 Score=68.66 Aligned_cols=51 Identities=20% Similarity=0.192 Sum_probs=44.2
Q ss_pred eeEEEEEEEEEEec------------------------CCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 52 SHTKVEFRYVVFRP------------------------FVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 52 ~~~~V~FraIvFrP------------------------f~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
++..++++++.++| ..|+++.|+|++++++|+||++| +++|++|+|+++|+
T Consensus 320 vG~~v~v~V~~id~~~~~i~lS~k~~~~~p~~~~~~~~~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~ 395 (516)
T TIGR00717 320 KGDEVEVMILDIDPERRRLSLGLKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWD 395 (516)
T ss_pred CCCEEEEEEEEEcCCCCEEEEEehhcccCcHHHHHHhCCCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCc
Confidence 55677777766655 36999999999999999999998 89999999999995
No 71
>PRK08059 general stress protein 13; Validated
Probab=97.59 E-value=4.3e-05 Score=58.46 Aligned_cols=54 Identities=19% Similarity=0.152 Sum_probs=41.4
Q ss_pred cCCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccccc--cceecccCCCcchh
Q psy11392 65 PFVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVKDI--LKYFAEKDKPDPVR 118 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~e~--i~~~~~~d~~~~~~ 118 (169)
..+|+++.|+|++++++|+||+++ +.+|++|+|+++++-. +.-.+...+.++++
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vk 61 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVK 61 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEE
Confidence 457999999999999999999998 5899999999987521 12234455555554
No 72
>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=97.59 E-value=5.3e-05 Score=51.81 Aligned_cols=35 Identities=9% Similarity=0.151 Sum_probs=32.6
Q ss_pred CcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
|+++.|+|++++++|++|+++ .++|++|+++++|+
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~ 36 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDE 36 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccc
Confidence 789999999999999999996 79999999999875
No 73
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=97.58 E-value=0.0002 Score=58.29 Aligned_cols=66 Identities=14% Similarity=0.034 Sum_probs=47.4
Q ss_pred EEEEEeeeeeecc-ceEeeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEecceeEEEeC-----------CCCCCccCC
Q psy11392 30 LCMMLYDITKIED-SVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQS-----------SNQPEQPIS 97 (169)
Q Consensus 30 LiV~V~dI~~I~e-G~I~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~~GiFV~lG-----------p~dGlIhIS 97 (169)
+..++.++.+++. .+...-+ -++.....|..|++|.|+|++++++|+||+++ +++|++|+|
T Consensus 33 i~as~~G~~~id~~~~~Isv~-------P~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s 105 (189)
T PRK09521 33 VYASVVGKVFIDDINRKISVI-------PFKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHIS 105 (189)
T ss_pred EEEEeeEEEEEcCCCCEEEEe-------cCcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhh
Confidence 5666667766542 2111111 12222367789999999999999999999997 577999999
Q ss_pred ccccc
Q psy11392 98 DSTVK 102 (169)
Q Consensus 98 d~s~~ 102 (169)
+++|+
T Consensus 106 ~i~~~ 110 (189)
T PRK09521 106 QVSDG 110 (189)
T ss_pred HcChh
Confidence 99985
No 74
>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=97.51 E-value=6.4e-05 Score=51.44 Aligned_cols=33 Identities=9% Similarity=0.045 Sum_probs=30.1
Q ss_pred CcEEEEEEEEEecceeEEEe-CCCCCCccCCccc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQ-SSNQPEQPISDST 100 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~l-Gp~dGlIhISd~s 100 (169)
|.+++|+|++++++|+||++ +.++|++|.|+++
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~ 34 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLD 34 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcC
Confidence 78999999999999999998 6799999998765
No 75
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.50 E-value=7.1e-05 Score=72.05 Aligned_cols=40 Identities=23% Similarity=0.135 Sum_probs=36.9
Q ss_pred EecCCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 63 FRPFVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 63 FrPf~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
..|.+|+++.|+|++++++|+||+++ ..+|++|+|+++|+
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~ 657 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADE 657 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCc
Confidence 45789999999999999999999996 58999999999986
No 76
>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=97.45 E-value=0.00012 Score=51.35 Aligned_cols=36 Identities=19% Similarity=0.121 Sum_probs=32.5
Q ss_pred ecCCCcEEEEEEEEEecceeEEEeCC-CCCCccCCcc
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQSS-NQPEQPISDS 99 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~lGp-~dGlIhISd~ 99 (169)
....|++++|+|++++++|+|+.+.+ .+|++|.|++
T Consensus 13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~ 49 (77)
T cd04473 13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL 49 (77)
T ss_pred hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhc
Confidence 35689999999999999999999975 8999999975
No 77
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.44 E-value=0.00012 Score=67.82 Aligned_cols=37 Identities=16% Similarity=0.193 Sum_probs=34.8
Q ss_pred CCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
..|+++.|+|++++++|+||++| +++|++|+|+++|+
T Consensus 372 ~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~ 409 (565)
T PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWD 409 (565)
T ss_pred CCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCcc
Confidence 36999999999999999999998 89999999999985
No 78
>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=97.41 E-value=0.00013 Score=51.29 Aligned_cols=39 Identities=18% Similarity=0.159 Sum_probs=35.7
Q ss_pred EecCCCcEEEEEEEEEecceeEEEeC-CCCCCccCCcccc
Q psy11392 63 FRPFVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTV 101 (169)
Q Consensus 63 FrPf~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~ 101 (169)
|-|.+|.++.|+|+++++.|++|++| .++|++|+|+++-
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~ 41 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATE 41 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccC
Confidence 56999999999999999999999996 7899999998763
No 79
>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=97.37 E-value=9e-05 Score=55.14 Aligned_cols=37 Identities=14% Similarity=0.162 Sum_probs=34.2
Q ss_pred CCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
.+|.++.|+|++++++|+||++. .++|++|+++++|+
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~ 39 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDA 39 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHH
Confidence 36999999999999999999995 79999999999985
No 80
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.37 E-value=9.8e-05 Score=64.42 Aligned_cols=38 Identities=18% Similarity=0.256 Sum_probs=34.7
Q ss_pred cCCCcEEEEEEEEEecceeEEEe---CCCCCCccCCccccc
Q psy11392 65 PFVSEIIIGKIRSCSKEGVHDSQ---SSNQPEQPISDSTVK 102 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~~GiFV~l---Gp~dGlIhISd~s~~ 102 (169)
|..||+|-|+|+++.++|+||.| |+.+|++|+||.+-.
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~ 49 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASG 49 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHH
Confidence 89999999999999999999999 578899999987653
No 81
>PHA02945 interferon resistance protein; Provisional
Probab=97.37 E-value=0.00015 Score=53.98 Aligned_cols=35 Identities=14% Similarity=0.117 Sum_probs=32.0
Q ss_pred ecCCCcEEEEEEEEEecceeEEEe---CCCCCCccCCcc
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQ---SSNQPEQPISDS 99 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~l---Gp~dGlIhISd~ 99 (169)
-|..||++.|+|++ .++|+||++ |..+|++|+|+.
T Consensus 8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~sev 45 (88)
T PHA02945 8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQ 45 (88)
T ss_pred CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehh
Confidence 48999999999999 999999999 578999999955
No 82
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.15 E-value=0.0005 Score=65.48 Aligned_cols=37 Identities=22% Similarity=0.167 Sum_probs=34.2
Q ss_pred CCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
..|+++.|+|++++++|+||.++ +++|++|+|+++|+
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~ 598 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWK 598 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCcc
Confidence 47999999999999999999995 69999999999985
No 83
>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=97.09 E-value=0.00022 Score=45.56 Aligned_cols=32 Identities=28% Similarity=0.237 Sum_probs=29.2
Q ss_pred EEEEEEEEecceeEEEeC-CCCCCccCCccccc
Q psy11392 71 IIGKIRSCSKEGVHDSQS-SNQPEQPISDSTVK 102 (169)
Q Consensus 71 VeG~V~~vt~~GiFV~lG-p~dGlIhISd~s~~ 102 (169)
+.|+|++++++|+||+++ +.+|++|.|+++++
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~ 33 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDK 33 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCc
Confidence 479999999999999998 88999999988875
No 84
>KOG4134|consensus
Probab=97.00 E-value=0.0049 Score=53.22 Aligned_cols=95 Identities=15% Similarity=0.166 Sum_probs=68.3
Q ss_pred chHHHHHHHhhhhcCceeeCCe-eEEEEEeeeeeec-cceEeeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEecceeE
Q psy11392 7 KIEDSVIIPGDGASHTKVFPNV-GLCMMLYDITKIE-DSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVH 84 (169)
Q Consensus 7 ~l~~~I~~eL~ekyegKVi~~v-GLiV~V~dI~~I~-eG~I~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~~GiF 84 (169)
++.-.+.+.|+.+. .+..+.+ |+++++.+|+-.+ .++|.+.++..+..++-...+|+|..|.+++|+|-.++..-+=
T Consensus 46 pl~~~i~ehld~~v-l~y~~~l~GivLgydnIKvLg~~aki~~D~pf~hlwi~adfyVf~Pk~Gd~LeG~Vn~vS~sHIg 124 (253)
T KOG4134|consen 46 PLHALIEEHLDTKV-LFYDSGLDGIVLGYDNIKVLGQTAKIRADDPFMHLWINADFYVFRPKAGDILEGVVNHVSRSHIG 124 (253)
T ss_pred hhHHHHHHHhhHHH-hhhccCCCceEEeecceEeeccccceecCCCceEEEEeeeEEEECCCCCCeeeeeeeecchhhhc
Confidence 34445555555554 3333444 9999999998654 6899999999999999999999999999999999999886443
Q ss_pred EE-eCCCCCCccCCc--cccc
Q psy11392 85 DS-QSSNQPEQPISD--STVK 102 (169)
Q Consensus 85 V~-lGp~dGlIhISd--~s~~ 102 (169)
+= .|-|+.-|+..+ -+|.
T Consensus 125 lLIhg~FNASIpk~nip~dw~ 145 (253)
T KOG4134|consen 125 LLIHGVFNASIPKTNIPADWE 145 (253)
T ss_pred eeehhhhhccCCCCCCcccee
Confidence 22 255555555433 4454
No 85
>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=96.86 E-value=0.0007 Score=65.01 Aligned_cols=39 Identities=15% Similarity=0.049 Sum_probs=35.3
Q ss_pred EecCCCcEEEEEEEEEecceeEEEeCC--CCCCccCCcccc
Q psy11392 63 FRPFVSEIIIGKIRSCSKEGVHDSQSS--NQPEQPISDSTV 101 (169)
Q Consensus 63 FrPf~GEVVeG~V~~vt~~GiFV~lGp--~dGlIhISd~s~ 101 (169)
.++..|++++|+|++++++|+||.+.+ .+|++|+|++++
T Consensus 623 l~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~ 663 (709)
T TIGR02063 623 MSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKD 663 (709)
T ss_pred hhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCC
Confidence 445889999999999999999999985 899999999884
No 86
>PRK11642 exoribonuclease R; Provisional
Probab=96.70 E-value=0.0013 Score=64.79 Aligned_cols=39 Identities=15% Similarity=0.014 Sum_probs=35.4
Q ss_pred ecCCCcEEEEEEEEEecceeEEEeC--CCCCCccCCccccc
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQS--SNQPEQPISDSTVK 102 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~lG--p~dGlIhISd~s~~ 102 (169)
....|++++|+|++++++|+||.+. +++|++|+|++.|+
T Consensus 640 ~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d 680 (813)
T PRK11642 640 LDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDND 680 (813)
T ss_pred hccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCc
Confidence 4478999999999999999999997 49999999999875
No 87
>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=96.54 E-value=0.0014 Score=62.70 Aligned_cols=39 Identities=18% Similarity=0.047 Sum_probs=35.6
Q ss_pred ecCCCcEEEEEEEEEecceeEEEeC--CCCCCccCCccccc
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQS--SNQPEQPISDSTVK 102 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~lG--p~dGlIhISd~s~~ 102 (169)
+...|++++|+|++++++|+||.+. +++|++|+|++.|+
T Consensus 569 ~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d 609 (654)
T TIGR00358 569 LDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHND 609 (654)
T ss_pred hhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCc
Confidence 3478999999999999999999997 58999999999985
No 88
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.28 E-value=0.0033 Score=61.06 Aligned_cols=41 Identities=15% Similarity=0.012 Sum_probs=36.9
Q ss_pred EEecCCCcEEEEEEEEEecceeEEEeCC-CCCCccCCccccc
Q psy11392 62 VFRPFVSEIIIGKIRSCSKEGVHDSQSS-NQPEQPISDSTVK 102 (169)
Q Consensus 62 vFrPf~GEVVeG~V~~vt~~GiFV~lGp-~dGlIhISd~s~~ 102 (169)
+=.|.+||+.+|+|+++.+||+||++-| -+|++|+|.++|.
T Consensus 614 ~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~ 655 (692)
T COG1185 614 TREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKE 655 (692)
T ss_pred HhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhh
Confidence 3456999999999999999999999955 6899999999996
No 89
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=96.28 E-value=0.0026 Score=62.48 Aligned_cols=36 Identities=17% Similarity=0.079 Sum_probs=33.5
Q ss_pred CCCcEEEEEEEEEecceeEEEeCC-CCCCccCCcccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQSS-NQPEQPISDSTV 101 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lGp-~dGlIhISd~s~ 101 (169)
..|.+++|+|+++++||+||++|- -||+||+|.+|-
T Consensus 657 k~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~ 693 (780)
T COG2183 657 KPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSD 693 (780)
T ss_pred cCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhh
Confidence 889999999999999999999996 689999998776
No 90
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.19 E-value=0.0025 Score=59.29 Aligned_cols=36 Identities=17% Similarity=0.287 Sum_probs=33.8
Q ss_pred CCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc
Q psy11392 67 VSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK 102 (169)
Q Consensus 67 ~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~ 102 (169)
.|++|.|+|+++++.|++|++|..+|++|.|+++-+
T Consensus 134 ~GeIV~G~V~ri~~~giiVDLggvea~LP~sE~ip~ 169 (470)
T PRK09202 134 VGEIITGVVKRVERGNIIVDLGRAEAILPRKEQIPR 169 (470)
T ss_pred cCCEEEEEEEEEecCCEEEEECCeEEEecHHHcCCC
Confidence 799999999999999999999999999999988754
No 91
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=95.75 E-value=0.0054 Score=55.47 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=38.5
Q ss_pred CCCcEEEEEEEEEecceeEEEeCCCCCCccCCccccc------cccceecc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTVK------DILKYFAE 110 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~~------e~i~~~~~ 110 (169)
..|+++.|+|.+.++.|+||++|..+|++|.++++-+ +.+++++.
T Consensus 133 k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~E~ip~e~~~~Gd~Ika~V~ 183 (362)
T PRK12327 133 REGDIVTGVVQRRDNRFVYVNLGKIEAVLPPAEQIPGETYKHGDRIKVYVV 183 (362)
T ss_pred hcCCEEEEEEEEEeCCcEEEEeCCeEEEecHHHcCCCCCCCCCCEEEEEEE
Confidence 7999999999999999999999999999997665443 66777764
No 92
>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=95.19 E-value=0.011 Score=52.96 Aligned_cols=46 Identities=17% Similarity=0.254 Sum_probs=39.2
Q ss_pred CCCcEEEEEEEEEecce-eEEEeCCCCCCccCCccccc------cccceeccc
Q psy11392 66 FVSEIIIGKIRSCSKEG-VHDSQSSNQPEQPISDSTVK------DILKYFAEK 111 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~G-iFV~lGp~dGlIhISd~s~~------e~i~~~~~~ 111 (169)
..|+++.|+|.++++.| ++|++|..+|++|.++++-+ +.+++++.+
T Consensus 130 k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP~~E~ip~E~~~~Gd~ik~~V~~ 182 (341)
T TIGR01953 130 KEGEIISGTVKRVNRRGNLYVELGKTEGILPKKEQIPGEKFRIGDRIKAYVYE 182 (341)
T ss_pred hcCCEEEEEEEEEecCCcEEEEECCeEEEecHHHcCCCcCCCCCCEEEEEEEE
Confidence 59999999999999998 69999999999999888743 666777654
No 93
>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=94.71 E-value=0.047 Score=39.98 Aligned_cols=38 Identities=16% Similarity=0.084 Sum_probs=34.2
Q ss_pred EecCCCcEEEEEEEEEecceeEEEe---------CCCCCCccCCccc
Q psy11392 63 FRPFVSEIIIGKIRSCSKEGVHDSQ---------SSNQPEQPISDST 100 (169)
Q Consensus 63 FrPf~GEVVeG~V~~vt~~GiFV~l---------Gp~dGlIhISd~s 100 (169)
+-|.+|.+|.|+|++++..-+.+++ .++.|.+|+|++.
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~ 48 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIR 48 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHcc
Confidence 4689999999999999999999998 5789999999764
No 94
>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=94.00 E-value=0.042 Score=50.44 Aligned_cols=38 Identities=11% Similarity=0.011 Sum_probs=34.5
Q ss_pred cCCCcEEEEEEEEEecc--eeEEEeCC-CCCCccCCccccc
Q psy11392 65 PFVSEIIIGKIRSCSKE--GVHDSQSS-NQPEQPISDSTVK 102 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~~--GiFV~lGp-~dGlIhISd~s~~ 102 (169)
+.+|.|..|+|+++.+. ||||++|. -+|++|++|+.|+
T Consensus 23 ~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~ 63 (414)
T TIGR00757 23 QLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPN 63 (414)
T ss_pred CCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCch
Confidence 46999999999999998 99999997 5899999998764
No 95
>PRK05054 exoribonuclease II; Provisional
Probab=92.18 E-value=0.11 Score=49.99 Aligned_cols=35 Identities=14% Similarity=-0.008 Sum_probs=30.7
Q ss_pred CCC--cEEEEEEEEEecceeEEEeC--CCCCCccCCccc
Q psy11392 66 FVS--EIIIGKIRSCSKEGVHDSQS--SNQPEQPISDST 100 (169)
Q Consensus 66 f~G--EVVeG~V~~vt~~GiFV~lG--p~dGlIhISd~s 100 (169)
..| +..+|.|+.++++|+||.+- +++|+||+|.+.
T Consensus 558 ~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~ 596 (644)
T PRK05054 558 KAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLH 596 (644)
T ss_pred ccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccC
Confidence 665 49999999999999999996 589999999764
No 96
>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=91.20 E-value=0.27 Score=36.15 Aligned_cols=35 Identities=11% Similarity=0.119 Sum_probs=31.7
Q ss_pred EecCCCcEEEEEEEEEecceeEEEeC-CCCCCccCC
Q psy11392 63 FRPFVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPIS 97 (169)
Q Consensus 63 FrPf~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhIS 97 (169)
|.|..|++|-|+|++++..+.+|++| +.++.+|.+
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~ 37 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYL 37 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechH
Confidence 67999999999999999999999995 668888875
No 97
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=89.46 E-value=0.22 Score=45.53 Aligned_cols=46 Identities=15% Similarity=0.259 Sum_probs=39.0
Q ss_pred CCCcEEEEEEEEEecc-eeEEEeCCCCCCccCCccccc------cccceeccc
Q psy11392 66 FVSEIIIGKIRSCSKE-GVHDSQSSNQPEQPISDSTVK------DILKYFAEK 111 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~-GiFV~lGp~dGlIhISd~s~~------e~i~~~~~~ 111 (169)
..||++.|+|.+++.. +++|++|..++.++.+++.-+ +.+++++.+
T Consensus 137 ~~Geiv~g~V~r~~~~~~i~vdlg~~ea~LP~~eqip~E~~~~Gdrik~~i~~ 189 (374)
T PRK12328 137 KVGKIVFGTVVRVDNEENTFIEIDEIRAVLPMKNRIKGEKFKVGDVVKAVLKR 189 (374)
T ss_pred hcCcEEEEEEEEEecCCCEEEEcCCeEEEeCHHHcCCCCcCCCCCEEEEEEEE
Confidence 8999999999999975 599999999999987766643 788888754
No 98
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=88.60 E-value=0.26 Score=33.40 Aligned_cols=50 Identities=20% Similarity=0.175 Sum_probs=26.8
Q ss_pred CCcEEEEEEEEEecceeEEEeCC-CCCCccCCccc----cccccceecccCCCcc
Q psy11392 67 VSEIIIGKIRSCSKEGVHDSQSS-NQPEQPISDST----VKDILKYFAEKDKPDP 116 (169)
Q Consensus 67 ~GEVVeG~V~~vt~~GiFV~lGp-~dGlIhISd~s----~~e~i~~~~~~d~~~~ 116 (169)
.|++...+|++.+++|+|++.|. -+=++|.+++. -+|.+.-|+=.|..-|
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~~~~~Gd~v~VFvY~D~~~r 55 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPEPLKVGDEVEVFVYLDKEGR 55 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG------TTSEEEEEEEE-TTS-
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCCCCCCCCEEEEEEEECCCCC
Confidence 48889999999999999999887 55566666543 3466666665555444
No 99
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=87.89 E-value=0.63 Score=45.13 Aligned_cols=36 Identities=17% Similarity=0.012 Sum_probs=31.6
Q ss_pred CCCcEEEEEEEEEecceeEEEeCC--CCCCccCCcccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQSS--NQPEQPISDSTV 101 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lGp--~dGlIhISd~s~ 101 (169)
..||+.+|+|++++.+|+||.+-. ++|++|+|.+.-
T Consensus 621 ~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~ 658 (706)
T COG0557 621 RVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPD 658 (706)
T ss_pred hcCCEEEEEEEEEEeccEEEEecccccccceEcccCCC
Confidence 688999999999999999999954 699999995543
No 100
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=86.23 E-value=3.4 Score=35.95 Aligned_cols=67 Identities=19% Similarity=0.309 Sum_probs=48.4
Q ss_pred eeCCeeEEEEEeeeeeeccceE--eeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEecceeEEEeC-CCCCCccCCccc
Q psy11392 24 VFPNVGLCMMLYDITKIEDSVI--IPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQS-SNQPEQPISDST 100 (169)
Q Consensus 24 Vi~~vGLiV~V~dI~~I~eG~I--~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~~GiFV~lG-p~dGlIhISd~s 100 (169)
...+-.+..++.+..++.+..+ .|..| -|.|..|.+|-|.|.++...|-.|++| |+.+.+|+|+.-
T Consensus 30 y~~~~~iyssv~G~~~~~~~~v~VIpl~g-----------~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~ 98 (239)
T COG1097 30 YFEGGKIYSSVVGLLDVKGKLVRVIPLEG-----------RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFL 98 (239)
T ss_pred EecCCEEEEEEEeEEEEeCCEEEEEeCCC-----------cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhh
Confidence 3333345666666665544432 12222 478999999999999999999999997 599999999883
Q ss_pred c
Q psy11392 101 V 101 (169)
Q Consensus 101 ~ 101 (169)
|
T Consensus 99 ~ 99 (239)
T COG1097 99 R 99 (239)
T ss_pred c
Confidence 3
No 101
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=84.22 E-value=1 Score=33.54 Aligned_cols=38 Identities=8% Similarity=-0.087 Sum_probs=30.4
Q ss_pred ecCCCcEEEEEEEEEecceeEEEeCC--CCCCcc-CCccccc
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQSS--NQPEQP-ISDSTVK 102 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~lGp--~dGlIh-ISd~s~~ 102 (169)
-|..|+++. .|+.+.+.|++|++=- ++|+|- .|+++.+
T Consensus 13 ~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~ 53 (86)
T PHA02858 13 FPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNAD 53 (86)
T ss_pred cCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHH
Confidence 599999999 8999999999999832 677766 5655544
No 102
>KOG2916|consensus
Probab=83.49 E-value=1 Score=40.09 Aligned_cols=39 Identities=21% Similarity=0.226 Sum_probs=34.9
Q ss_pred ecCCCcEEEEEEEEEecceeEEEe---CCCCCCccCCccccc
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQ---SSNQPEQPISDSTVK 102 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~l---Gp~dGlIhISd~s~~ 102 (169)
-|..+|+|-+.|.++.++|++|++ +-+.|||-.|++|--
T Consensus 13 yPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrR 54 (304)
T KOG2916|consen 13 YPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRR 54 (304)
T ss_pred CCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHH
Confidence 489999999999999999999998 677899999988753
No 103
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=80.75 E-value=1.3 Score=42.81 Aligned_cols=36 Identities=11% Similarity=0.017 Sum_probs=30.4
Q ss_pred CCC--cEEEEEEEEEecceeEEEe--CCCCCCccCCcccc
Q psy11392 66 FVS--EIIIGKIRSCSKEGVHDSQ--SSNQPEQPISDSTV 101 (169)
Q Consensus 66 f~G--EVVeG~V~~vt~~GiFV~l--Gp~dGlIhISd~s~ 101 (169)
..| +..+|+|++++++|+||.+ .+++|+||++.+.-
T Consensus 554 ~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~ 593 (639)
T TIGR02062 554 KAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHA 593 (639)
T ss_pred ccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCC
Confidence 554 5899999999999999998 36899999987653
No 104
>KOG1067|consensus
Probab=80.37 E-value=3.9 Score=40.10 Aligned_cols=36 Identities=14% Similarity=-0.050 Sum_probs=30.7
Q ss_pred CCCcEEEEEEEEEecceeEEEeCCC-CCCccCCcccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQSSN-QPEQPISDSTV 101 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lGp~-dGlIhISd~s~ 101 (169)
..|-|..|+|+++.++|+||.+-|. .|++|.|+++-
T Consensus 667 ~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~ 703 (760)
T KOG1067|consen 667 EFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQ 703 (760)
T ss_pred EeeeEEEEEEeeecccceEEEecCCchhhccchhccc
Confidence 5677889999999999999999775 69999996553
No 105
>PF02944 BESS: BESS motif; InterPro: IPR004210 The BESS domain has been named after the three proteins that originally defined the domain: BEAF (Boundary element associated factor 32) [], Suvar(3)7 [] and Stonewall []). The BESS domain is 40 amino acid residues long and is predicted to be composed of three alpha helices, as such it might be related to the myb/SANT HTH domain. The BESS domain directs a variety of protein-protein interactions, including interactions with itself, with Dorsal, and with a TBP-associated factor. It is found in a single copy in Drosophila proteins and is often associated with the MADF domain [, , ]. Proteins known to contain a BESS domain include: Drosophila Boundary element associated factor 32 (BEAF-32). Drosophila Suppressor of variegation protein 3-7 (Su(var)3-7), which could play a role in chromosome condensation. Drosophila Ravus, which is homologous to the C-terminal part of Su(var)3-7 []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation. Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3). It functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. ; GO: 0003677 DNA binding
Probab=78.79 E-value=2.9 Score=25.79 Aligned_cols=33 Identities=27% Similarity=0.474 Sum_probs=28.0
Q ss_pred hhhhhhhhhhhhhhcchhhhhhhhHHHHHHhhhh
Q psy11392 118 RDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKY 151 (169)
Q Consensus 118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 (169)
+-||+ .++|.+++||...=+++|.+|.+.++++
T Consensus 5 ~~Fl~-Sl~p~~k~L~~~~k~~~k~~i~~ll~e~ 37 (37)
T PF02944_consen 5 ELFLL-SLLPHMKRLPPKQKLKFKMKILQLLFET 37 (37)
T ss_pred HHHHH-HhHHHHHhCCHHHHHHHHHHHHHHHHhC
Confidence 34665 4789999999999999999999988764
No 106
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=75.68 E-value=2.1 Score=41.96 Aligned_cols=42 Identities=17% Similarity=0.006 Sum_probs=36.2
Q ss_pred EEEEec-------CCCcEEEEEEEEEecceeEEEeCC-CCCCccCCcccc
Q psy11392 60 YVVFRP-------FVSEIIIGKIRSCSKEGVHDSQSS-NQPEQPISDSTV 101 (169)
Q Consensus 60 aIvFrP-------f~GEVVeG~V~~vt~~GiFV~lGp-~dGlIhISd~s~ 101 (169)
+.+|+| ..|++..|+|+++.++|+||++.. +.|++|-++++-
T Consensus 108 vy~l~~~c~~~Dve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~ 157 (715)
T COG1107 108 VYVLDNSCTMEDVEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGG 157 (715)
T ss_pred eEEeccccchhhcccceeeeccccchhhhcceeecChhhhccccccccCC
Confidence 455666 789999999999999999999976 789999987774
No 107
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=72.35 E-value=2.3 Score=39.98 Aligned_cols=48 Identities=10% Similarity=0.225 Sum_probs=37.0
Q ss_pred ecCCCcEEEEEEEEEecceeEEEe----CC--CCCCccCCccccc------cccceeccc
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQ----SS--NQPEQPISDSTVK------DILKYFAEK 111 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~l----Gp--~dGlIhISd~s~~------e~i~~~~~~ 111 (169)
++..|+++.|+|.++...+++|++ |- .+++++.+++.-+ +.+++++.+
T Consensus 149 ~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~E~y~~Gdrika~i~~ 208 (449)
T PRK12329 149 QDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPNDNYRANATFKVFLKE 208 (449)
T ss_pred HHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCCCcCCCCCEEEEEEEE
Confidence 338999999999999999999998 43 6777876666443 666776643
No 108
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=67.48 E-value=7.4 Score=36.56 Aligned_cols=61 Identities=13% Similarity=0.134 Sum_probs=44.9
Q ss_pred ccceEeeCCCceeEEEEEEEEEEecCCCcEEEEEEEEEec--ceeEEEeCC-CCCCccCCcccc
Q psy11392 41 EDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSK--EGVHDSQSS-NQPEQPISDSTV 101 (169)
Q Consensus 41 ~eG~I~pgDG~~~~~V~FraIvFrPf~GEVVeG~V~~vt~--~GiFV~lGp-~dGlIhISd~s~ 101 (169)
++-++.--++...+++.+.--.=+-.+|-+..|.|+++.+ ..+||++|- -.|++|.+++.|
T Consensus 11 ~e~rva~v~~~~l~el~ie~~~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~ 74 (487)
T COG1530 11 EETRVAVVDGGALQELDIERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP 74 (487)
T ss_pred ceeEEEEEeCCEEEEEEEecCCcEeeecCceEEEecccCccchhheeeccCCccceEEecccch
Confidence 4444444445555555555444444689999999999998 599999996 469999999888
No 109
>PRK11712 ribonuclease G; Provisional
Probab=65.45 E-value=5.5 Score=37.61 Aligned_cols=35 Identities=14% Similarity=0.092 Sum_probs=31.2
Q ss_pred cCCCcEEEEEEEEEec--ceeEEEeCC-CCCCccCCcc
Q psy11392 65 PFVSEIIIGKIRSCSK--EGVHDSQSS-NQPEQPISDS 99 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~--~GiFV~lGp-~dGlIhISd~ 99 (169)
..+|.|..|+|.++.+ .++||++|. -+|++|++|.
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~ 73 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDI 73 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhc
Confidence 3699999999999999 699999995 5799999976
No 110
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=63.14 E-value=12 Score=27.20 Aligned_cols=36 Identities=17% Similarity=0.150 Sum_probs=24.3
Q ss_pred cCCCcEEEEEEEEEecceeEEEeC-------------------CCCCCccCCccc
Q psy11392 65 PFVSEIIIGKIRSCSKEGVHDSQS-------------------SNQPEQPISDST 100 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~~GiFV~lG-------------------p~dGlIhISd~s 100 (169)
|..|.+|.|+|+++++.-+.+++= +|.|.+|.+|.-
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR 56 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVR 56 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGG
T ss_pred CCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeec
Confidence 889999999999999999987752 567778877544
No 111
>PRK10811 rne ribonuclease E; Reviewed
Probab=60.49 E-value=8.1 Score=39.85 Aligned_cols=36 Identities=17% Similarity=0.172 Sum_probs=31.7
Q ss_pred cCCCcEEEEEEEEEec--ceeEEEeCCC-CCCccCCccc
Q psy11392 65 PFVSEIIIGKIRSCSK--EGVHDSQSSN-QPEQPISDST 100 (169)
Q Consensus 65 Pf~GEVVeG~V~~vt~--~GiFV~lGp~-dGlIhISd~s 100 (169)
+..|.|..|+|.++.+ .|+||++|.= .|++|++|..
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~ 74 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIA 74 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhcc
Confidence 4679999999999999 6999999965 8999988774
No 112
>KOG1070|consensus
Probab=54.55 E-value=14 Score=39.73 Aligned_cols=37 Identities=14% Similarity=0.180 Sum_probs=33.7
Q ss_pred CCCcEEEEEEEEEecceeEEEe-CCCCCCccCCccccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQ-SSNQPEQPISDSTVK 102 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~l-Gp~dGlIhISd~s~~ 102 (169)
..|+++.|+|.++.++|+||+. |.+.|+.++|+|+-+
T Consensus 598 ~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~ 635 (1710)
T KOG1070|consen 598 IPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDD 635 (1710)
T ss_pred CCCceEEEEEeeeccCCeEEEecCccccccchhhhhhh
Confidence 5699999999999999999997 889999999988754
No 113
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=51.93 E-value=11 Score=33.57 Aligned_cols=34 Identities=6% Similarity=-0.064 Sum_probs=30.1
Q ss_pred CCCcEEEEEEEEEecceeEEEe-CCCCCCccCCcc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQ-SSNQPEQPISDS 99 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~l-Gp~dGlIhISd~ 99 (169)
.+|+.++|+|-+..+.|.||-+ +..-|+||.||.
T Consensus 154 l~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr 188 (287)
T COG2996 154 LKNQEVDATVYRLLESGTFVITENGYLGFIHKSER 188 (287)
T ss_pred hhcCeeeeEEEEEeccceEEEEcCCeEEEEcchhh
Confidence 4699999999999999999988 678899999864
No 114
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: 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 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=50.86 E-value=28 Score=25.03 Aligned_cols=31 Identities=10% Similarity=0.159 Sum_probs=25.6
Q ss_pred CcEEEEEEEEEecceeEEEeCCC--CCCc---cCCc
Q psy11392 68 SEIIIGKIRSCSKEGVHDSQSSN--QPEQ---PISD 98 (169)
Q Consensus 68 GEVVeG~V~~vt~~GiFV~lGp~--dGlI---hISd 98 (169)
|.+++|+|.+=++.++.|.+++. .|.+ |.||
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD 36 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD 36 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC
Confidence 67999999999999999999984 3333 6776
No 115
>KOG3013|consensus
Probab=47.03 E-value=18 Score=32.36 Aligned_cols=60 Identities=13% Similarity=0.255 Sum_probs=44.5
Q ss_pred EEecCCCcEEEEEEEEEecceeEEEeCC-CCCCccCCccccccccceecccCCCcchhhhh
Q psy11392 62 VFRPFVSEIIIGKIRSCSKEGVHDSQSS-NQPEQPISDSTVKDILKYFAEKDKPDPVRDFL 121 (169)
Q Consensus 62 vFrPf~GEVVeG~V~~vt~~GiFV~lGp-~dGlIhISd~s~~e~i~~~~~~d~~~~~~~~~ 121 (169)
-|.|..|.+|.|.|.++...--.|++++ .|+-+-.|.+....++-==.+-..-+..|+||
T Consensus 80 rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl 140 (301)
T KOG3013|consen 80 RYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFL 140 (301)
T ss_pred hcCCccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHh
Confidence 4667999999999999999999999987 45666677777765554444444445566665
No 116
>KOG3440|consensus
Probab=44.74 E-value=20 Score=28.38 Aligned_cols=25 Identities=36% Similarity=0.514 Sum_probs=21.4
Q ss_pred hhhhhhhcchhhhhhhhHHHHHHhh
Q psy11392 125 IAPALRSLPRHLFLKAKKEIFEAVH 149 (169)
Q Consensus 125 ~~~~~~~~~~~~~~~~~~~~~~~~~ 149 (169)
+.-|||.|||+++-.-+-.|-.|.|
T Consensus 47 vkeAlrRLPr~~~d~R~~Ri~RA~~ 71 (122)
T KOG3440|consen 47 VKEALRRLPRELYDARNYRIKRAMD 71 (122)
T ss_pred HHHHHHHCcHHHHHHHHHHHHHHHH
Confidence 5679999999999988888887765
No 117
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 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 [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=42.95 E-value=42 Score=25.89 Aligned_cols=27 Identities=19% Similarity=0.181 Sum_probs=24.6
Q ss_pred EecCCCcEEEEEEEEEecceeEEEeCC
Q psy11392 63 FRPFVSEIIIGKIRSCSKEGVHDSQSS 89 (169)
Q Consensus 63 FrPf~GEVVeG~V~~vt~~GiFV~lGp 89 (169)
.-|.+|.+|.|+|..+.+.-.||+.|.
T Consensus 19 lG~~~gk~V~G~I~hvv~ddLYIDfG~ 45 (104)
T PF10246_consen 19 LGDPEGKIVIGKIFHVVDDDLYIDFGG 45 (104)
T ss_pred cCCccCCEEEEEEEEEecCceEEEeCC
Confidence 346799999999999999999999996
No 118
>PF01135 PCMT: Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT); InterPro: IPR000682 Protein-L-isoaspartate(D-aspartate) O-methyltransferase (2.1.1.77 from EC) (PCMT) [] (which is also known as L-isoaspartyl protein carboxyl methyltransferase) is an enzyme that catalyses the transfer of a methyl group from S-adenosylmethionine to the free carboxyl groups of D-aspartyl or L-isoaspartyl residues in a variety of peptides and proteins. The enzyme does not act on normal L-aspartyl residues L-isoaspartyl and D-aspartyl are the products of the spontaneous deamidation and/or isomerisation of normal L-aspartyl and L-asparaginyl residues in proteins. PCMT plays a role in the repair and/or degradation of these damaged proteins; the enzymatic methyl esterification of the abnormal residues can lead to their conversion to normal L-aspartyl residues. The SAM domain is present in most of these proteins.; GO: 0004719 protein-L-isoaspartate (D-aspartate) O-methyltransferase activity, 0006464 protein modification process; PDB: 3LBF_A 1DL5_B 1JG3_B 1JG2_A 1JG1_A 1JG4_A 2YXE_A 2PBF_B 1VBF_C 1R18_A ....
Probab=41.29 E-value=5.9 Score=32.99 Aligned_cols=28 Identities=21% Similarity=0.222 Sum_probs=19.4
Q ss_pred Ccchhhhhhhhhhhhhhhcchhhhhhhh
Q psy11392 114 PDPVRDFLMGAIAPALRSLPRHLFLKAK 141 (169)
Q Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 141 (169)
+++-.+...-++.-|+|++|||.|+...
T Consensus 9 l~~~g~v~~~~v~~A~~~VpR~~Fvp~~ 36 (209)
T PF01135_consen 9 LIRPGDVTDPRVLDAFRAVPREDFVPPA 36 (209)
T ss_dssp HHHTTSS-SHHHHHHHHHS-GGGCSSCG
T ss_pred HHHcCCCCCHHHHHHHHhCCHHHhCchh
Confidence 3333345566788999999999999774
No 119
>KOG1070|consensus
Probab=40.95 E-value=23 Score=38.17 Aligned_cols=37 Identities=11% Similarity=-0.040 Sum_probs=31.8
Q ss_pred CCCcEEEEEEEEEecceeEEEeCCCC---CCccCCccccc
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQSSNQ---PEQPISDSTVK 102 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lGp~d---GlIhISd~s~~ 102 (169)
.+|+..+|+|.+++++|.|+++++-. |+.|+++.+=+
T Consensus 1250 ~~gd~~~g~v~~~~~~G~fi~l~~tv~~~g~~~~~e~~d~ 1289 (1710)
T KOG1070|consen 1250 KKGDREDGTVEVVDPFGLFIKLDVTVNMVGLCHISEEADD 1289 (1710)
T ss_pred hccccccceEEEecCCceEEEecCcceecccccceeecch
Confidence 78999999999999999999999854 88898855443
No 120
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=39.73 E-value=46 Score=29.79 Aligned_cols=53 Identities=19% Similarity=0.112 Sum_probs=39.2
Q ss_pred CCCcEEEEEEEEEecceeEEEeCCC--CCCccCCc-----cccccccceecccCCCcchh
Q psy11392 66 FVSEIIIGKIRSCSKEGVHDSQSSN--QPEQPISD-----STVKDILKYFAEKDKPDPVR 118 (169)
Q Consensus 66 f~GEVVeG~V~~vt~~GiFV~lGp~--dGlIhISd-----~s~~e~i~~~~~~d~~~~~~ 118 (169)
..|++....|.+.+++|.|+.-|-- +=++|.++ ++-.|.++.|.=.|...|.|
T Consensus 4 ~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~~e~evGdev~vFiY~D~~~rl~ 63 (287)
T COG2996 4 KIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEEDELEVGDEVTVFIYVDSEDRLI 63 (287)
T ss_pred cccceEEEEEEEeeceeEEEecCCCceEEeccccCCcCCccccCcEEEEEEEECCCCcee
Confidence 4689999999999999999999887 45566662 33447777776656555544
No 121
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=37.51 E-value=30 Score=29.19 Aligned_cols=43 Identities=9% Similarity=0.156 Sum_probs=33.2
Q ss_pred ecCCCcEEEEEEEEEecceeEEEeCC-----------CCCCccCCccccccccce
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQSS-----------NQPEQPISDSTVKDILKY 107 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~lGp-----------~dGlIhISd~s~~e~i~~ 107 (169)
-|..|.+|-|.|+++....+-|++-. ..+.+|+| ++-+.|++-
T Consensus 61 ~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs-~~~~~~~~~ 114 (188)
T COG1096 61 LPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVS-QVRDGYVEK 114 (188)
T ss_pred CCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEE-ecccccccc
Confidence 45777999999999999999988744 45678999 555655543
No 122
>KOG1004|consensus
Probab=37.21 E-value=85 Score=27.30 Aligned_cols=94 Identities=20% Similarity=0.182 Sum_probs=60.5
Q ss_pred eEEEEEEEEEEecCCCcEEEEEEEEEecceeEEEeCCCCCCccCCcccc-------------c---------------cc
Q psy11392 53 HTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQSSNQPEQPISDSTV-------------K---------------DI 104 (169)
Q Consensus 53 ~~~V~FraIvFrPf~GEVVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~-------------~---------------e~ 104 (169)
.+.|..+=..|-|-+|..|-|+|++....+..|++|.-+ ..-+|.+++ . -.
T Consensus 51 v~~vds~~kRYiP~~~D~VIGiV~~~~gd~ykVDigg~~-~a~L~~laFe~AtkrNrPnl~vGdliyakv~~a~~~~Epe 129 (230)
T KOG1004|consen 51 VYWVDSQQKRYIPVKGDHVIGIVTSKSGDIYKVDIGGSE-PASLSYLAFEGATKRNRPNLQVGDLIYAKVVDANKDMEPE 129 (230)
T ss_pred eEEEecccceecCCCCCEEEEEEEeccCceEEEecCCCC-eeeeeeccccCccccCCCccccccEEEEEEEecCCCcCcc
Confidence 557778888999999999999999999999999999822 112222222 1 23
Q ss_pred cceecccCCCcchhhh--hh-hhhhhhhhhcchhhhhhhhHHHHHHhhhh
Q psy11392 105 LKYFAEKDKPDPVRDF--LM-GAIAPALRSLPRHLFLKAKKEIFEAVHKY 151 (169)
Q Consensus 105 i~~~~~~d~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 (169)
+.|+=+- =|.+-| |- |+|.+.--++-|.|.+ -+-.+.++|-|+
T Consensus 130 l~Cids~---graaGfG~LkdG~if~vs~~~~R~Ll~-p~~~iLq~vGk~ 175 (230)
T KOG1004|consen 130 LTCIDST---GRAAGFGVLKDGMIFKVSLGLCRKLLL-PDCPILQTVGKK 175 (230)
T ss_pred eEEEccc---CcccCcccccCceEEEecHHHHHHHHc-CCCcHHHHhhcc
Confidence 3344321 222222 22 5566666667777777 666677776654
No 123
>KOG3409|consensus
Probab=34.61 E-value=51 Score=27.88 Aligned_cols=49 Identities=18% Similarity=0.163 Sum_probs=36.1
Q ss_pred ecCCCcEEEEEEEEEecceeEEEeCC---------CCCCccCCcccc-----ccccceecccC
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQSS---------NQPEQPISDSTV-----KDILKYFAEKD 112 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~lGp---------~dGlIhISd~s~-----~e~i~~~~~~d 112 (169)
-|+.|.||.++|++++..=+-|++=- |.|+||..|.-- -+-.|||.+-|
T Consensus 65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgD 127 (193)
T KOG3409|consen 65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGD 127 (193)
T ss_pred CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCc
Confidence 58999999999999999988887643 568887654432 26666776433
No 124
>PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional
Probab=32.60 E-value=13 Score=30.41 Aligned_cols=30 Identities=23% Similarity=0.207 Sum_probs=21.9
Q ss_pred CCcchhhhhhhhhhhhhhhcchhhhhhhhH
Q psy11392 113 KPDPVRDFLMGAIAPALRSLPRHLFLKAKK 142 (169)
Q Consensus 113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 142 (169)
+++|--+..--.+.-|++++|||.|+....
T Consensus 12 ~l~~~~~v~~~~v~~a~~~v~R~~fvp~~~ 41 (212)
T PRK13942 12 ELIREGYIKSKKVIDALLKVPRHLFVPEYL 41 (212)
T ss_pred HHHhcCCCCCHHHHHHHHcCCHhhcCCchh
Confidence 344444455567888999999999997653
No 125
>PF04280 Tim44: Tim44-like domain; InterPro: IPR007379 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane []. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region [].; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005744 mitochondrial inner membrane presequence translocase complex; PDB: 2CW9_A 2FXT_A 3QK9_A.
Probab=30.17 E-value=1e+02 Score=23.13 Aligned_cols=39 Identities=23% Similarity=0.258 Sum_probs=26.5
Q ss_pred CCceeEEEEEEE--EE-EecCCCcEEEE---EEEEEecceeEEEe
Q psy11392 49 DGASHTKVEFRY--VV-FRPFVSEIIIG---KIRSCSKEGVHDSQ 87 (169)
Q Consensus 49 DG~~~~~V~Fra--Iv-FrPf~GEVVeG---~V~~vt~~GiFV~l 87 (169)
++....+|+|.+ +. .+...|++++| .+..+++.=.|..-
T Consensus 88 ~~~~~vtv~f~~~~~~~~~d~~G~ii~G~~~~~~~~~e~W~f~r~ 132 (147)
T PF04280_consen 88 GNFDQVTVRFRSQQIDYVDDKDGEIIEGDPDKIQEFTEYWTFERD 132 (147)
T ss_dssp TTEEEEEEEEEEEEEEEEETTTCTCCCCSTTS-EEEEEEEEEEE-
T ss_pred CCEEEEEEEEEEEEEEEEECCCCcEeeCCCCCceEEEEEEEEEEe
Confidence 666677777743 33 45567999999 88888887777765
No 126
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=28.43 E-value=76 Score=28.64 Aligned_cols=79 Identities=14% Similarity=0.080 Sum_probs=53.3
Q ss_pred cCceee--CCeeEEEEEe---eee------eeccceEeeCCC--ceeEEEEEEEEEEec---------------------
Q psy11392 20 SHTKVF--PNVGLCMMLY---DIT------KIEDSVIIPGDG--ASHTKVEFRYVVFRP--------------------- 65 (169)
Q Consensus 20 yegKVi--~~vGLiV~V~---dI~------~I~eG~I~pgDG--~~~~~V~FraIvFrP--------------------- 65 (169)
..|+|. .+.|..|.+. ++. +++-+++.+-.- .++.++.+.++-+.|
T Consensus 21 V~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~~~pw~~~~ 100 (319)
T PTZ00248 21 VMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVSPEDIEACE 100 (319)
T ss_pred EEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecccchHHHHH
Confidence 345553 4559988884 332 345555543322 366788888888876
Q ss_pred ---CCCcEEEEEEEEEec-ceeEEE------e-CCCCCCccCCc
Q psy11392 66 ---FVSEIIIGKIRSCSK-EGVHDS------Q-SSNQPEQPISD 98 (169)
Q Consensus 66 ---f~GEVVeG~V~~vt~-~GiFV~------l-Gp~dGlIhISd 98 (169)
.+|.++.|+|.++.+ +|+++. . -..+++.|+++
T Consensus 101 e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~ 144 (319)
T PTZ00248 101 EKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALD 144 (319)
T ss_pred HhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHH
Confidence 579999999999955 999987 2 24567777663
No 127
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=27.93 E-value=1.9e+02 Score=19.24 Aligned_cols=35 Identities=17% Similarity=0.067 Sum_probs=27.1
Q ss_pred EEEEEEEEEEecCCCcEEEEEEEEEecceeEEEeC
Q psy11392 54 TKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDSQS 88 (169)
Q Consensus 54 ~~V~FraIvFrPf~GEVVeG~V~~vt~~GiFV~lG 88 (169)
+.+...+.......+..+.|++.++...|+.+.+.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~diS~~G~~~~~~ 42 (102)
T PF07238_consen 8 VPVNLPIRVILDPGGSSFQGTIVDISEGGCAFRSP 42 (102)
T ss_dssp EEEEEEEE-EEEETTEEEEEEEEEETTSEEEEEEC
T ss_pred EeccceEEEEEecCCcEEEEEEEEECccceEEEEC
Confidence 34444555567778888999999999999999983
No 128
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=27.14 E-value=36 Score=22.69 Aligned_cols=32 Identities=16% Similarity=0.069 Sum_probs=25.6
Q ss_pred EEEEEEEEEecceeEEEeCCCCCCccCCcccc
Q psy11392 70 IIIGKIRSCSKEGVHDSQSSNQPEQPISDSTV 101 (169)
Q Consensus 70 VVeG~V~~vt~~GiFV~lGp~dGlIhISd~s~ 101 (169)
=+.|+|.++++.-+.+++|++-=.+.+|..++
T Consensus 4 ~l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~ 35 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGVGYEVFVPSNTL 35 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTEEEEEEE-HHHH
T ss_pred EEEEEEEEEcCCEEEEEECCEEEEEEeCCchH
Confidence 37899999999999999998876677775544
No 129
>PF08592 DUF1772: Domain of unknown function (DUF1772); InterPro: IPR013901 This entry represents proteins of unknown function.
Probab=25.89 E-value=66 Score=23.71 Aligned_cols=27 Identities=30% Similarity=0.489 Sum_probs=23.6
Q ss_pred hhhhhhhhcchhhhhhhhHHHHHHhhh
Q psy11392 124 AIAPALRSLPRHLFLKAKKEIFEAVHK 150 (169)
Q Consensus 124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 (169)
.+.|+++++|...++++-+.++...++
T Consensus 9 ~~~P~l~~l~~~~~~~~~~~~~~~~~~ 35 (139)
T PF08592_consen 9 VVMPALLSLPPEEYLKQWQRFYRRGPR 35 (139)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHhHH
Confidence 468999999999999999999888744
No 130
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=25.20 E-value=1.2e+02 Score=19.30 Aligned_cols=19 Identities=16% Similarity=0.053 Sum_probs=17.1
Q ss_pred CCcEEEEEEEEEecceeEE
Q psy11392 67 VSEIIIGKIRSCSKEGVHD 85 (169)
Q Consensus 67 ~GEVVeG~V~~vt~~GiFV 85 (169)
.++.++|++..+++.|..+
T Consensus 11 ~~~~~~G~~~gId~~G~L~ 29 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDDGALL 29 (48)
T ss_dssp TSCEEEEEEEEEETTSEEE
T ss_pred CCeEEEEEEEEECCCCEEE
Confidence 6888999999999999875
No 131
>TIGR00080 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt.
Probab=24.69 E-value=22 Score=28.77 Aligned_cols=22 Identities=27% Similarity=0.369 Sum_probs=17.6
Q ss_pred hhhhhhhhhhhhcchhhhhhhh
Q psy11392 120 FLMGAIAPALRSLPRHLFLKAK 141 (169)
Q Consensus 120 ~~~~~~~~~~~~~~~~~~~~~~ 141 (169)
..--.+.-|++++||+.|+...
T Consensus 20 v~~~~v~~a~~~v~R~~f~~~~ 41 (215)
T TIGR00080 20 IKSKRVIDALLSVPREEFVPEH 41 (215)
T ss_pred cCCHHHHHHHHhCChhhhCCch
Confidence 3445778899999999999753
No 132
>PF04491 Pox_T4_N: Poxvirus T4 protein, N terminus; InterPro: IPR007580 Poxvirus T4 protein is thought to be secreted or retained in the endoplasmic reticulum if the protein also contains an additional C-terminal region (IPR007579 from INTERPRO). M-T4 of myxoma virus (O55698 from SWISSPROT) is thought to protect infected lymphocytes from apoptosis and modulate the inflammatory response to virus infection [].
Probab=24.01 E-value=1e+02 Score=20.56 Aligned_cols=25 Identities=28% Similarity=0.638 Sum_probs=18.5
Q ss_pred CeeEEEEEeeee---------eeccceEeeCCCc
Q psy11392 27 NVGLCMMLYDIT---------KIEDSVIIPGDGA 51 (169)
Q Consensus 27 ~vGLiV~V~dI~---------~I~eG~I~pgDG~ 51 (169)
++||||-+.|.. +.+.|.|..|+|+
T Consensus 5 ~IglCI~~k~f~~~~t~C~~~~~~GGLItegNGf 38 (46)
T PF04491_consen 5 KIGLCIQVKDFKSSRTGCHRPQGPGGLITEGNGF 38 (46)
T ss_pred EEEEEEEeeeEEeecCCcccccCCCcEEeeCCcE
Confidence 469999987765 5677777777764
No 133
>COG1206 Gid NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]
Probab=23.41 E-value=29 Score=32.41 Aligned_cols=82 Identities=20% Similarity=0.252 Sum_probs=56.3
Q ss_pred cEEEEEEEEEecceeEE-EeCCCC------------------------CCccCCccccc-------------cccceecc
Q psy11392 69 EIIIGKIRSCSKEGVHD-SQSSNQ------------------------PEQPISDSTVK-------------DILKYFAE 110 (169)
Q Consensus 69 EVVeG~V~~vt~~GiFV-~lGp~d------------------------GlIhISd~s~~-------------e~i~~~~~ 110 (169)
||+.++|+.+-+.|+-| -.||+. .+||...+.+| +||+|=.|
T Consensus 117 ~vireEvt~iP~dg~~vIATGPLTs~~La~~i~~ltG~d~l~FyDAaAPIi~~dSIdmd~~~~~sRYdKg~a~YiNCPmt 196 (439)
T COG1206 117 EVIREEVTEIPPDGITVIATGPLTSDALAEKIKELTGEDYLYFYDAAAPIIEFDSIDMDKAYLKSRYDKGEADYINCPMT 196 (439)
T ss_pred EEEccccccCCCCCcEEEecCCCCCHHHHHHHHHhhCCceEEeecccCceeeccccchHHHHhhhccccccchhhcCCCC
Confidence 67888888887667764 447752 34454434332 99999999
Q ss_pred cCCCcchhhhhhhhhhhhhhhcchhhhhhhhHHHHHHhhhhhhhhhh
Q psy11392 111 KDKPDPVRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKYEMIAEE 157 (169)
Q Consensus 111 ~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (169)
|+|-.+..+-|..|= ..|-+-|-|. ..||..--.|.+|+.
T Consensus 197 kEey~~F~eaL~~ae-----~~~~k~fEk~--~~FegCmPIE~mA~r 236 (439)
T COG1206 197 KEEYLAFYEALIEAE-----KAPLKDFEKE--KYFEGCMPIEVMAER 236 (439)
T ss_pred HHHHHHHHHHHHhcc-----cCChhhhccc--ccccccCcHHHHHhh
Confidence 999988888776553 3344445443 578888888888864
No 134
>KOG4078|consensus
Probab=21.72 E-value=1.1e+02 Score=25.29 Aligned_cols=31 Identities=16% Similarity=0.199 Sum_probs=27.7
Q ss_pred EEEEEecCCCcEEEEEEEEEecceeEEEeCC
Q psy11392 59 RYVVFRPFVSEIIIGKIRSCSKEGVHDSQSS 89 (169)
Q Consensus 59 raIvFrPf~GEVVeG~V~~vt~~GiFV~lGp 89 (169)
+++-..|++|.+|.|+|-.+.+.-.|++.|.
T Consensus 74 kl~qlg~a~gklV~GkIfhiV~~DlYIDFG~ 104 (173)
T KOG4078|consen 74 KLMQLGDAKGKLVIGKIFHIVEEDLYIDFGG 104 (173)
T ss_pred ccccccCcCCcEEEeeeeeeeccceEEecCC
Confidence 3456778999999999999999999999986
No 135
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=21.15 E-value=2.1e+02 Score=19.80 Aligned_cols=22 Identities=9% Similarity=0.068 Sum_probs=20.5
Q ss_pred EEEEEEEEecceeEEEeCCCCC
Q psy11392 71 IIGKIRSCSKEGVHDSQSSNQP 92 (169)
Q Consensus 71 VeG~V~~vt~~GiFV~lGp~dG 92 (169)
+.|+|.++.++-+-|++..+++
T Consensus 16 ~~G~V~kv~eNSVIVdIT~m~~ 37 (57)
T PF09953_consen 16 FTGIVEKVYENSVIVDITIMEN 37 (57)
T ss_pred cEEEEEEEecCcEEEEEEecCC
Confidence 7999999999999999988876
No 136
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=20.80 E-value=79 Score=28.12 Aligned_cols=27 Identities=19% Similarity=0.112 Sum_probs=24.5
Q ss_pred ecCCCcEEEEEEEEEecceeEEEeCCC
Q psy11392 64 RPFVSEIIIGKIRSCSKEGVHDSQSSN 90 (169)
Q Consensus 64 rPf~GEVVeG~V~~vt~~GiFV~lGp~ 90 (169)
.|..||+-+|.|.+..+.|.+|++|--
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~~ 128 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIGKD 128 (272)
T ss_pred CccceeecceEEEEecCCceEEEecCC
Confidence 468999999999999999999999954
Done!