Query psy4846
Match_columns 279
No_of_seqs 223 out of 1608
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 19:12:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4846.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4846hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00358 3_prime_RNase VacB a 100.0 1.5E-45 3.3E-50 369.7 25.2 213 3-248 414-654 (654)
2 PRK11642 exoribonuclease R; Pr 100.0 2.2E-45 4.9E-50 373.8 25.9 215 3-250 480-727 (813)
3 TIGR02063 RNase_R ribonuclease 100.0 6.7E-45 1.5E-49 368.4 25.4 213 3-248 466-709 (709)
4 PRK05054 exoribonuclease II; P 100.0 1.2E-43 2.7E-48 354.7 23.3 213 3-248 411-644 (644)
5 TIGR02062 RNase_B exoribonucle 100.0 4.2E-43 9.2E-48 350.4 22.8 210 3-246 407-638 (639)
6 COG0557 VacB Exoribonuclease R 100.0 3.2E-43 7E-48 355.6 22.1 214 3-249 466-705 (706)
7 KOG2102|consensus 100.0 9.7E-36 2.1E-40 305.9 18.4 224 2-257 690-936 (941)
8 COG4776 Rnb Exoribonuclease II 100.0 2E-28 4.4E-33 228.4 10.1 214 2-247 410-643 (645)
9 PF00773 RNB: RNB domain CAUTI 99.8 2.6E-21 5.6E-26 179.6 4.8 84 3-95 224-325 (325)
10 cd04471 S1_RNase_R S1_RNase_R: 99.3 1.5E-11 3.3E-16 91.4 9.6 77 169-248 5-83 (83)
11 cd04460 S1_RpoE S1_RpoE: RpoE, 98.8 3.3E-08 7.2E-13 76.4 8.3 79 169-252 3-88 (99)
12 cd05686 S1_pNO40 S1_pNO40: pNO 98.7 4.1E-08 8.8E-13 71.7 7.3 67 168-247 6-72 (73)
13 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.7 3.1E-08 6.8E-13 71.2 5.6 67 168-247 3-69 (69)
14 cd05689 S1_RPS1_repeat_ec4 S1_ 98.6 1.2E-07 2.6E-12 68.6 7.0 66 168-245 6-71 (72)
15 cd05708 S1_Rrp5_repeat_sc12 S1 98.6 1.4E-07 3.1E-12 68.7 7.4 71 168-250 5-75 (77)
16 cd05698 S1_Rrp5_repeat_hs6_sc5 98.6 8.3E-08 1.8E-12 69.0 6.0 66 169-247 4-69 (70)
17 PRK07252 hypothetical protein; 98.6 1.5E-07 3.3E-12 75.5 7.9 75 168-255 6-80 (120)
18 cd05690 S1_RPS1_repeat_ec5 S1_ 98.6 1E-07 2.2E-12 68.2 5.7 66 169-246 4-69 (69)
19 cd05706 S1_Rrp5_repeat_sc10 S1 98.6 2E-07 4.4E-12 67.6 7.4 67 168-247 6-72 (73)
20 cd05703 S1_Rrp5_repeat_hs12_sc 98.6 1.6E-07 3.5E-12 68.6 6.1 70 168-248 3-72 (73)
21 cd05707 S1_Rrp5_repeat_sc11 S1 98.6 1.3E-07 2.7E-12 67.8 5.2 65 169-246 4-68 (68)
22 cd05684 S1_DHX8_helicase S1_DH 98.5 3.3E-07 7.1E-12 67.7 7.4 68 169-249 4-73 (79)
23 cd05705 S1_Rrp5_repeat_hs14 S1 98.5 1.9E-07 4.2E-12 68.5 5.8 70 167-246 5-74 (74)
24 TIGR00448 rpoE DNA-directed RN 98.5 3E-07 6.4E-12 78.7 7.3 86 161-252 78-170 (179)
25 PRK08582 hypothetical protein; 98.5 6.3E-07 1.4E-11 73.7 8.6 70 167-250 7-76 (139)
26 PTZ00248 eukaryotic translatio 98.5 1.8E-07 3.8E-12 86.5 5.4 86 169-272 21-107 (319)
27 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.5 4.1E-07 9E-12 66.0 6.3 64 171-247 7-71 (71)
28 cd04452 S1_IF2_alpha S1_IF2_al 98.5 5.9E-07 1.3E-11 65.5 6.9 70 167-248 5-75 (76)
29 cd04461 S1_Rrp5_repeat_hs8_sc7 98.5 3.3E-07 7.2E-12 68.3 5.7 66 169-247 18-83 (83)
30 PF00575 S1: S1 RNA binding do 98.4 5E-07 1.1E-11 65.5 6.0 67 168-247 7-73 (74)
31 cd05685 S1_Tex S1_Tex: The C-t 98.4 3.5E-07 7.6E-12 64.7 4.9 65 169-246 4-68 (68)
32 COG1098 VacB Predicted RNA bin 98.4 2.2E-07 4.8E-12 73.8 2.9 68 168-249 8-75 (129)
33 COG0539 RpsA Ribosomal protein 98.3 5.3E-07 1.1E-11 88.5 5.4 83 170-272 197-279 (541)
34 PHA02945 interferon resistance 98.3 3.1E-06 6.8E-11 63.4 7.9 68 169-250 15-84 (88)
35 cd05691 S1_RPS1_repeat_ec6 S1_ 98.3 1.9E-06 4.1E-11 62.1 6.7 68 169-249 4-71 (73)
36 cd05692 S1_RPS1_repeat_hs4 S1_ 98.3 1.9E-06 4.2E-11 60.9 6.1 65 169-247 4-68 (69)
37 PRK05807 hypothetical protein; 98.3 3.2E-06 6.9E-11 69.3 7.9 69 167-250 7-75 (136)
38 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.3 1.8E-06 3.9E-11 61.8 5.6 63 169-246 4-66 (66)
39 cd04473 S1_RecJ_like S1_RecJ_l 98.3 2.9E-06 6.2E-11 62.6 6.8 59 168-248 19-77 (77)
40 PLN00207 polyribonucleotide nu 98.3 3.8E-06 8.2E-11 86.8 10.0 65 171-249 760-824 (891)
41 cd04472 S1_PNPase S1_PNPase: P 98.3 2.2E-06 4.7E-11 60.8 5.9 65 169-247 4-68 (68)
42 PRK03987 translation initiatio 98.2 2.6E-06 5.7E-11 77.1 6.9 72 166-249 9-81 (262)
43 COG1095 RPB7 DNA-directed RNA 98.2 5.4E-06 1.2E-10 70.5 8.0 79 168-251 84-169 (183)
44 cd05688 S1_RPS1_repeat_ec3 S1_ 98.2 4.6E-06 1E-10 59.0 6.2 65 168-246 4-68 (68)
45 PRK08059 general stress protei 98.2 4.8E-06 1E-10 67.0 6.7 71 168-251 10-80 (123)
46 COG0539 RpsA Ribosomal protein 98.2 2.4E-06 5.2E-11 83.9 5.8 71 167-250 279-349 (541)
47 cd05694 S1_Rrp5_repeat_hs2_sc2 98.1 1.2E-05 2.5E-10 59.0 7.4 63 169-249 8-70 (74)
48 cd00164 S1_like S1_like: Ribos 98.1 9.4E-06 2E-10 56.2 6.5 64 170-246 2-65 (65)
49 PRK08563 DNA-directed RNA poly 98.1 2.4E-05 5.2E-10 67.3 9.5 85 162-252 79-170 (187)
50 PRK07899 rpsA 30S ribosomal pr 98.1 1.3E-05 2.9E-10 78.5 8.5 71 166-249 294-364 (486)
51 cd05704 S1_Rrp5_repeat_hs13 S1 98.1 8.7E-06 1.9E-10 59.2 5.4 65 168-247 6-71 (72)
52 smart00316 S1 Ribosomal protei 98.1 1.3E-05 2.9E-10 56.4 6.3 67 168-247 5-71 (72)
53 PRK13806 rpsA 30S ribosomal pr 98.0 7.5E-06 1.6E-10 80.6 6.2 88 167-272 294-381 (491)
54 cd05687 S1_RPS1_repeat_ec1_hs1 98.0 2.2E-05 4.8E-10 56.3 6.0 66 169-247 4-69 (70)
55 cd05693 S1_Rrp5_repeat_hs1_sc1 98.0 1.1E-05 2.4E-10 62.7 4.7 78 168-249 6-96 (100)
56 PRK12269 bifunctional cytidyla 98.0 1.2E-05 2.6E-10 83.6 6.2 73 166-250 666-738 (863)
57 PRK07899 rpsA 30S ribosomal pr 97.9 1.9E-05 4.1E-10 77.4 6.4 66 170-249 213-278 (486)
58 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 97.9 2.2E-05 4.7E-10 58.8 5.1 76 166-251 7-82 (86)
59 PRK12269 bifunctional cytidyla 97.8 4.1E-05 8.9E-10 79.7 7.3 75 166-250 753-827 (863)
60 PRK07400 30S ribosomal protein 97.8 4.9E-05 1.1E-09 70.8 7.1 70 167-250 198-267 (318)
61 COG1093 SUI2 Translation initi 97.8 1.7E-05 3.6E-10 70.8 3.6 69 170-250 16-85 (269)
62 PRK06299 rpsA 30S ribosomal pr 97.8 4.1E-05 8.8E-10 76.5 6.5 89 166-272 374-462 (565)
63 PRK13806 rpsA 30S ribosomal pr 97.7 5E-05 1.1E-09 74.8 6.3 72 166-250 380-451 (491)
64 TIGR00717 rpsA ribosomal prote 97.7 6.8E-05 1.5E-09 74.0 6.6 72 166-249 360-431 (516)
65 PRK06676 rpsA 30S ribosomal pr 97.7 9.5E-05 2.1E-09 70.5 7.1 72 166-250 278-349 (390)
66 cd04465 S1_RPS1_repeat_ec2_hs2 97.7 0.00012 2.7E-09 52.0 6.0 63 169-247 4-66 (67)
67 COG2183 Tex Transcriptional ac 97.7 6.4E-05 1.4E-09 76.2 5.8 75 168-255 661-735 (780)
68 PRK11824 polynucleotide phosph 97.6 0.00014 3E-09 74.5 7.7 70 166-249 622-691 (693)
69 PRK06676 rpsA 30S ribosomal pr 97.6 0.00015 3.1E-09 69.3 7.2 83 170-272 197-279 (390)
70 TIGR00717 rpsA ribosomal prote 97.6 0.00017 3.7E-09 71.2 6.9 70 166-248 447-516 (516)
71 TIGR02696 pppGpp_PNP guanosine 97.5 0.00011 2.4E-09 74.6 5.6 72 165-246 647-718 (719)
72 PRK00087 4-hydroxy-3-methylbut 97.5 0.00025 5.4E-09 72.1 7.4 72 167-251 564-635 (647)
73 cd05702 S1_Rrp5_repeat_hs11_sc 97.5 0.0002 4.4E-09 51.4 5.0 60 169-239 4-63 (70)
74 PRK06299 rpsA 30S ribosomal pr 97.5 0.00023 5.1E-09 71.1 6.6 84 169-272 205-288 (565)
75 PRK00087 4-hydroxy-3-methylbut 97.3 0.00036 7.8E-09 71.0 6.3 86 167-272 479-564 (647)
76 cd04454 S1_Rrp4_like S1_Rrp4_l 97.3 0.0012 2.7E-08 48.8 7.0 72 166-251 7-78 (82)
77 PHA02858 EIF2a-like PKR inhibi 97.2 0.00056 1.2E-08 50.9 4.5 75 157-247 9-85 (86)
78 PTZ00162 DNA-directed RNA poly 97.2 0.005 1.1E-07 52.6 10.8 85 161-250 78-166 (176)
79 cd04453 S1_RNase_E S1_RNase_E: 97.1 0.0019 4.2E-08 48.8 6.9 70 168-245 10-81 (88)
80 TIGR03591 polynuc_phos polyrib 97.1 0.00057 1.2E-08 69.9 5.2 67 165-245 618-684 (684)
81 PRK07400 30S ribosomal protein 97.0 0.00087 1.9E-08 62.5 5.2 85 170-272 36-120 (318)
82 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.0 0.0036 7.9E-08 47.4 7.6 68 169-242 5-75 (88)
83 cd04455 S1_NusA S1_NusA: N-uti 96.8 0.0039 8.6E-08 44.4 5.8 59 168-246 6-66 (67)
84 PRK09202 nusA transcription el 96.3 0.048 1E-06 53.5 11.4 62 170-251 139-202 (470)
85 PRK09521 exosome complex RNA-b 96.2 0.0083 1.8E-07 51.7 5.3 71 166-251 65-144 (189)
86 COG1185 Pnp Polyribonucleotide 96.2 0.0069 1.5E-07 61.0 5.1 69 167-249 621-689 (692)
87 PRK12442 translation initiatio 96.1 0.059 1.3E-06 40.5 8.7 66 169-251 9-75 (87)
88 PRK04163 exosome complex RNA-b 95.9 0.021 4.6E-07 50.9 6.5 76 166-251 64-139 (235)
89 COG2996 Predicted RNA-bindinin 95.2 0.045 9.8E-07 49.5 6.0 63 166-250 156-218 (287)
90 cd05699 S1_Rrp5_repeat_hs7 S1_ 94.5 0.07 1.5E-06 38.8 4.3 68 168-247 3-71 (72)
91 PRK12327 nusA transcription el 94.3 0.55 1.2E-05 44.6 11.2 62 170-251 139-202 (362)
92 TIGR01953 NusA transcription t 93.3 1.1 2.4E-05 42.3 11.2 62 170-251 136-200 (341)
93 TIGR00008 infA translation ini 91.5 0.95 2.1E-05 32.6 6.4 60 169-245 7-67 (68)
94 KOG1070|consensus 91.0 0.16 3.6E-06 54.9 2.9 70 168-250 602-671 (1710)
95 KOG1067|consensus 89.6 0.86 1.9E-05 45.4 6.3 60 170-242 673-732 (760)
96 KOG3298|consensus 87.9 2 4.4E-05 36.0 6.6 75 161-242 78-155 (170)
97 cd05791 S1_CSL4 S1_CSL4: CSL4, 87.7 1.4 3E-05 33.4 5.2 71 168-250 9-87 (92)
98 KOG1070|consensus 87.5 1.6 3.5E-05 47.7 7.1 73 169-254 1166-1238(1710)
99 COG1107 Archaea-specific RecJ- 84.9 0.81 1.7E-05 45.7 3.2 63 170-251 127-189 (715)
100 COG0361 InfA Translation initi 84.9 6.1 0.00013 29.0 7.0 64 169-249 9-73 (75)
101 TIGR00757 RNaseEG ribonuclease 84.7 2.9 6.3E-05 40.5 6.8 78 168-247 28-110 (414)
102 PRK12328 nusA transcription el 83.5 14 0.0003 35.4 10.7 61 170-250 143-207 (374)
103 PRK12329 nusA transcription el 81.9 21 0.00047 34.8 11.4 63 170-250 157-226 (449)
104 PF08292 RNA_pol_Rbc25: RNA po 80.1 14 0.00031 29.6 8.1 60 170-232 8-72 (122)
105 PF13509 S1_2: S1 domain; PDB: 79.4 10 0.00022 26.3 6.3 46 170-234 6-51 (61)
106 CHL00010 infA translation init 79.1 16 0.00035 26.7 7.6 29 220-250 46-74 (78)
107 PRK00276 infA translation init 78.0 16 0.00035 26.2 7.2 25 220-246 46-70 (72)
108 KOG2916|consensus 76.5 1.5 3.2E-05 39.7 1.6 66 172-249 23-89 (304)
109 PRK04012 translation initiatio 74.8 17 0.00038 28.1 7.0 65 167-249 21-86 (100)
110 PRK09937 stationary phase/star 73.6 28 0.00061 25.2 7.5 47 171-232 4-53 (74)
111 COG1097 RRP4 RNA-binding prote 67.6 21 0.00045 32.0 6.8 73 168-250 67-139 (239)
112 cd05790 S1_Rrp40 S1_Rrp40: Rrp 67.5 30 0.00065 25.9 6.7 67 169-250 10-76 (86)
113 cd05793 S1_IF1A S1_IF1A: Trans 66.2 30 0.00065 25.3 6.4 61 171-249 4-65 (77)
114 cd05701 S1_Rrp5_repeat_hs10 S1 61.4 21 0.00045 25.4 4.4 57 170-238 5-61 (69)
115 PRK14998 cold shock-like prote 59.3 65 0.0014 23.3 7.4 47 171-232 4-53 (73)
116 TIGR00523 eIF-1A eukaryotic/ar 57.9 66 0.0014 24.8 7.2 73 160-249 12-85 (99)
117 PRK10811 rne ribonuclease E; R 56.1 30 0.00065 37.1 6.5 75 168-244 41-117 (1068)
118 PTZ00329 eukaryotic translatio 55.9 59 0.0013 27.2 7.0 63 170-250 35-98 (155)
119 PRK09507 cspE cold shock prote 54.4 51 0.0011 23.4 5.7 48 170-232 5-55 (69)
120 PF01835 A2M_N: MG2 domain; I 52.4 36 0.00077 25.3 5.0 33 218-250 8-45 (99)
121 PRK11712 ribonuclease G; Provi 52.4 41 0.00088 33.4 6.5 78 169-247 42-123 (489)
122 PRK06763 F0F1 ATP synthase sub 51.9 29 0.00064 30.2 4.7 44 168-230 41-84 (213)
123 PRK15464 cold shock-like prote 51.2 41 0.00088 24.2 4.8 48 170-232 6-56 (70)
124 smart00652 eIF1a eukaryotic tr 49.4 1.1E+02 0.0023 22.8 6.9 62 170-249 8-70 (83)
125 KOG1856|consensus 49.3 15 0.00032 39.9 3.0 68 169-249 989-1059(1299)
126 cd04456 S1_IF1A_like S1_IF1A_l 48.3 98 0.0021 22.7 6.5 62 171-250 4-67 (78)
127 PRK10943 cold shock-like prote 46.3 1E+02 0.0023 21.8 6.8 48 170-232 5-55 (69)
128 PRK10354 RNA chaperone/anti-te 46.2 57 0.0012 23.2 4.9 48 170-232 6-56 (70)
129 PLN00208 translation initiatio 45.6 1.1E+02 0.0024 25.4 7.0 63 170-250 35-98 (145)
130 cd04458 CSP_CDS Cold-Shock Pro 44.5 1E+02 0.0022 21.1 6.2 47 171-232 3-52 (65)
131 PRK09890 cold shock protein Cs 43.5 74 0.0016 22.6 5.2 48 170-232 6-56 (70)
132 PF10447 EXOSC1: Exosome compo 43.2 28 0.0006 25.9 2.9 56 169-232 8-80 (82)
133 TIGR02381 cspD cold shock doma 40.6 1.3E+02 0.0028 21.2 6.3 47 171-232 4-53 (68)
134 PRK15463 cold shock-like prote 40.2 95 0.002 22.2 5.3 49 170-232 6-56 (70)
135 PRK11570 peptidyl-prolyl cis-t 40.2 2.5E+02 0.0054 24.4 10.4 22 257-278 154-175 (206)
136 COG2139 RPL21A Ribosomal prote 38.8 1.3E+02 0.0029 23.1 6.0 59 135-196 27-86 (98)
137 COG1096 Predicted RNA-binding 37.6 1.2E+02 0.0027 26.1 6.3 66 168-250 67-143 (188)
138 PF01176 eIF-1a: Translation i 36.5 1.5E+02 0.0032 20.7 5.9 56 171-244 7-63 (65)
139 PF00313 CSD: 'Cold-shock' DNA 35.5 1.5E+02 0.0032 20.3 5.9 47 171-232 3-52 (66)
140 PF02599 CsrA: Global regulato 34.5 92 0.002 21.3 4.2 30 218-251 9-38 (54)
141 cd00210 PTS_IIA_glc PTS_IIA, P 32.4 2E+02 0.0044 23.0 6.6 30 168-198 41-72 (124)
142 PF03459 TOBE: TOBE domain; I 31.9 1.1E+02 0.0025 20.5 4.5 14 219-232 45-58 (64)
143 cd05700 S1_Rrp5_repeat_hs9 S1_ 30.0 2E+02 0.0043 20.3 5.5 28 218-247 38-65 (65)
144 TIGR00830 PTBA PTS system, glu 29.8 2.4E+02 0.0052 22.5 6.6 31 167-198 40-72 (121)
145 cd04508 TUDOR Tudor domains ar 27.0 60 0.0013 20.6 2.2 32 167-198 13-45 (48)
146 PF08696 Dna2: DNA replication 26.9 2.4E+02 0.0053 24.4 6.7 13 84-96 96-108 (209)
147 COG2106 Uncharacterized conser 25.2 1.6E+02 0.0034 27.0 5.2 61 170-259 110-171 (272)
148 COG0141 HisD Histidinol dehydr 24.3 1.1E+02 0.0024 29.8 4.3 41 36-78 329-376 (425)
149 smart00333 TUDOR Tudor domain. 24.1 85 0.0019 20.6 2.7 33 166-198 16-49 (57)
150 PRK01712 carbon storage regula 23.0 2.1E+02 0.0044 20.4 4.4 30 218-251 9-38 (64)
151 COG0572 Udk Uridine kinase [Nu 22.7 16 0.00034 32.4 -1.6 22 68-89 170-191 (218)
152 COG1278 CspC Cold shock protei 22.0 2.8E+02 0.0061 19.8 5.0 47 171-232 4-53 (67)
153 PF12949 HeH: HeH/LEM domain; 21.4 1.2E+02 0.0027 18.7 2.7 32 12-43 1-33 (35)
154 PF14444 S1-like: S1-like 20.9 1.4E+02 0.0031 20.8 3.2 15 218-232 31-45 (58)
155 PF10246 MRP-S35: Mitochondria 20.8 3.1E+02 0.0067 21.4 5.3 44 169-232 27-72 (104)
156 PRK09439 PTS system glucose-sp 20.5 3.5E+02 0.0076 22.9 6.2 31 167-198 62-94 (169)
No 1
>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=100.00 E-value=1.5e-45 Score=369.65 Aligned_cols=213 Identities=24% Similarity=0.384 Sum_probs=187.0
Q ss_pred eeEEeeCCCCCccCHHHHHHHHHHcCCcccCC-----CHHHHHHHHHhh-------------------ccccccCcCCCC
Q psy4846 3 NAMLRRHPVPPPANFEPLLHAARRQGFELSVG-----TGKELATSLDAA-------------------AVYFSSGMLQQS 58 (279)
Q Consensus 3 ~al~R~H~~P~~~~~~~l~~~~~~~g~~~~~~-----~~~~l~~~L~~~-------------------A~Y~~~~~~~~~ 58 (279)
+++||+|++|+++++++|.++++.+|+.++.. ++.+++..|..+ |+| +++
T Consensus 414 p~iyR~h~~p~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~llr~m~~A~y------~~~ 487 (654)
T TIGR00358 414 PGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENVTTLDGACWLREVKDRPEYEILVTRLLRSLSQAEY------SPE 487 (654)
T ss_pred CeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCcCCCChHHHHHHHHHhhCCCHHHHHHHHHHHhhccccc------CCC
Confidence 58999999999999999999999999986432 355666665543 556 468
Q ss_pred CccccccCCCCccccccCccccchHHHHHHHHHHHcCCCCCC-CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4846 59 DFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYP-SLLDKKASTALCYNLNYRNRQAQYAGRASVALHTHLF 137 (279)
Q Consensus 59 ~~~H~gL~~~~YthfTSPIRRY~DlivHR~L~a~l~~~~~~~-~~~~~~~l~~~~~~~n~~~r~a~~aer~~~~~~~~~~ 137 (279)
|.+|||||++.|||||||||||+||+|||||+++|.+....+ ...+.+.+..+|.+||.++++|++|||++.++|.+.|
T Consensus 488 ~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~a~l~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~y 567 (654)
T TIGR00358 488 PLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTERYQPQDELLQIAEHCSDTERRARDAERDVADWLKCRY 567 (654)
T ss_pred CCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999997653211 1245677999999999999999999999999999999
Q ss_pred Hhhccc-eeeEEEEEeecchhhhhcCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEee
Q psy4846 138 FRSRVQ-DEDGYVLYVRKNALQILIPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSC 216 (279)
Q Consensus 138 l~~~~~-~~~g~V~~~~~~~~~~~~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~ 216 (279)
|+++++ .++|.|+ +|+++|+||.|+++++||+||+++ +++++|.||+.++.+.+
T Consensus 568 l~~~iG~~~~g~I~------------------------~v~~~GifV~L~~~~veGlV~~s~-l~~d~y~~d~~~~~l~g 622 (654)
T TIGR00358 568 LLDKVGTEFSGEIS------------------------SVTRFGMFVRLDDNGIDGLIHIST-LHNDYYVFDQEKMALIG 622 (654)
T ss_pred hhhCCCcEEEEEEE------------------------eEEcCcEEEEecCCceEEEEEeEe-CCCcceEEeccccEEEe
Confidence 999975 4888888 999999999999999999999998 88899999999999988
Q ss_pred c--CeEecCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 217 G--SVVFHSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 217 ~--~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
. +..|++||+|+|+|. ++|+.+++|+|+++
T Consensus 623 ~~~~~~~~lGD~V~Vki~--~vd~~~~~I~f~l~ 654 (654)
T TIGR00358 623 KGTGKVYRIGDRVTVKLT--EVNMETRSIIFELV 654 (654)
T ss_pred ccCCcEECCCCEEEEEEE--EEecccCeEEEEEC
Confidence 6 578999999999998 99999999999873
No 2
>PRK11642 exoribonuclease R; Provisional
Probab=100.00 E-value=2.2e-45 Score=373.80 Aligned_cols=215 Identities=21% Similarity=0.326 Sum_probs=188.1
Q ss_pred eeEEeeCCCCCccCHHHHHHHHHHcCCcccCC---CHHHHHHHHHhh-------------------ccccccCcCCCCCc
Q psy4846 3 NAMLRRHPVPPPANFEPLLHAARRQGFELSVG---TGKELATSLDAA-------------------AVYFSSGMLQQSDF 60 (279)
Q Consensus 3 ~al~R~H~~P~~~~~~~l~~~~~~~g~~~~~~---~~~~l~~~L~~~-------------------A~Y~~~~~~~~~~~ 60 (279)
++|||+|++|+++++++|.+++..+|+.++.. +++.++.+|+.+ |.| ++++.
T Consensus 480 p~lyR~H~~P~~ekl~~l~~~l~~lG~~l~~~~~~~~~~~~~ll~~~~~~~~~~~l~~~llRsm~~A~Y------~~~~~ 553 (813)
T PRK11642 480 PALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIY------DPENR 553 (813)
T ss_pred CEEEEeCCCCCHHHHHHHHHHHHHcCCcccCCCCCCHHHHHHHHHHHhCCcHHHHHHHHHHHhcccccc------CCCCC
Confidence 68999999999999999999999999988643 356676666543 666 46899
Q ss_pred cccccCCCCccccccCccccchHHHHHHHHHHHcCCCC----C---CC-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4846 61 HHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADAT----Y---PS-LLDKKASTALCYNLNYRNRQAQYAGRASVAL 132 (279)
Q Consensus 61 ~H~gL~~~~YthfTSPIRRY~DlivHR~L~a~l~~~~~----~---~~-~~~~~~l~~~~~~~n~~~r~a~~aer~~~~~ 132 (279)
||||||+++||||||||||||||+|||+|+++|.+... + .. ....+.+..+|++||.++++|..|||++.+|
T Consensus 554 gHfGLa~~~YtHFTSPIRRY~DLivHR~Lk~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~s~~er~A~~aeR~~~~~ 633 (813)
T PRK11642 554 GHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEATRDVADW 633 (813)
T ss_pred CccccccccccccCchhhhhHHHHHHHHHHHHHhCCCCcccccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999965321 0 00 1123568999999999999999999999999
Q ss_pred HHHHHHhhccce-eeEEEEEeecchhhhhcCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCC
Q psy4846 133 HTHLFFRSRVQD-EDGYVLYVRKNALQILIPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKE 211 (279)
Q Consensus 133 ~~~~~l~~~~~~-~~g~V~~~~~~~~~~~~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~ 211 (279)
+.+.||++++++ |+|.|+ +|+++|+||.|+++++||+||+++ ++++||.|++..
T Consensus 634 ~~~~~m~~~iGe~f~G~Is------------------------~V~~fGifVeL~~~~vEGlV~vs~-L~~d~y~~d~~~ 688 (813)
T PRK11642 634 LKCDFMLDQVGNVFKGVIS------------------------SVTGFGFFVRLDDLFIDGLVHVSS-LDNDYYRFDQVG 688 (813)
T ss_pred HHHhhhhccCCcEEEEEEE------------------------EeecCceEEEECCCCeeeeEEEee-cCCcceEecchh
Confidence 999999998764 888888 999999999999989999999998 888999999999
Q ss_pred ceEeec--CeEecCCCeEEEEEEeccccCCCCeEEEEEecC
Q psy4846 212 QSQSCG--SVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVRP 250 (279)
Q Consensus 212 ~~l~~~--~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~~ 250 (279)
+.+++. +..|++||+|+|+|. ++|..+++|+|++++.
T Consensus 689 ~~L~g~~~~~~~~lGD~V~VkV~--~vD~~~rkI~f~l~~~ 727 (813)
T PRK11642 689 QRLIGESSGQTYRLGDRVEVRVE--AVNMDERKIDFSLISS 727 (813)
T ss_pred eEEecccCCcEECCCCEEEEEEE--EeecCCCeEEEEEecc
Confidence 999986 578999999999998 9999999999999854
No 3
>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=100.00 E-value=6.7e-45 Score=368.44 Aligned_cols=213 Identities=23% Similarity=0.349 Sum_probs=187.4
Q ss_pred eeEEeeCCCCCccCHHHHHHHHHHcCCcccC-----CCHHHHHHHHHhh-------------------ccccccCcCCCC
Q psy4846 3 NAMLRRHPVPPPANFEPLLHAARRQGFELSV-----GTGKELATSLDAA-------------------AVYFSSGMLQQS 58 (279)
Q Consensus 3 ~al~R~H~~P~~~~~~~l~~~~~~~g~~~~~-----~~~~~l~~~L~~~-------------------A~Y~~~~~~~~~ 58 (279)
+++||+|++|+++++++|.++++.+|++++. .++++++.+|+.+ |.| +++
T Consensus 466 p~iyR~h~~P~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~llr~m~~A~y------~~~ 539 (709)
T TIGR02063 466 PFIYRVHERPSEEKLQNLREFLKTLGITLKGGTSDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKY------SPE 539 (709)
T ss_pred CeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCCCCCCHHHHHHHHHHhhCCcHHHHHHHHHHHHhcCccc------CCC
Confidence 5799999999999999999999999998754 2467777776554 555 468
Q ss_pred CccccccCCCCccccccCccccchHHHHHHHHHHHcCCCCCC--C--cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4846 59 DFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYP--S--LLDKKASTALCYNLNYRNRQAQYAGRASVALHT 134 (279)
Q Consensus 59 ~~~H~gL~~~~YthfTSPIRRY~DlivHR~L~a~l~~~~~~~--~--~~~~~~l~~~~~~~n~~~r~a~~aer~~~~~~~ 134 (279)
+.+|||||+++|||||||||||+||+|||||+++|.+....+ . ..+...+..+|.+||.++++|++|||++.++|.
T Consensus 540 ~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~ 619 (709)
T TIGR02063 540 NIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKK 619 (709)
T ss_pred CCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCCCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999997653211 1 234567999999999999999999999999999
Q ss_pred HHHHhhccc-eeeEEEEEeecchhhhhcCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCce
Q psy4846 135 HLFFRSRVQ-DEDGYVLYVRKNALQILIPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQS 213 (279)
Q Consensus 135 ~~~l~~~~~-~~~g~V~~~~~~~~~~~~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~ 213 (279)
+.||+.+++ .++|.|+ +|+++|+||.|+++|+||+||+++ +++++|.|++..+.
T Consensus 620 ~~yl~~~iG~~~~g~V~------------------------~v~~fGifV~L~~~~~eGlvhis~-l~~d~~~~d~~~~~ 674 (709)
T TIGR02063 620 AEYMSEKIGEEFEGVIS------------------------GVTSFGLFVELENNTIEGLVHIST-LKDDYYVFDEKGLA 674 (709)
T ss_pred HHhhhccCCcEEEEEEE------------------------EEEeCCEEEEecCCceEEEEEeee-cCCCcEEEcccceE
Confidence 999999875 4888887 999999999999999999999998 88899999999999
Q ss_pred Eeec--CeEecCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 214 QSCG--SVVFHSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 214 l~~~--~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
+.+. +..|++||.|+|+|. ++|..+++|.|+++
T Consensus 675 l~g~~~~~~~~lGd~V~Vkv~--~vd~~~~~I~~~l~ 709 (709)
T TIGR02063 675 LVGERTGKVFRLGDRVKVRVV--KADLDTGKIDFELV 709 (709)
T ss_pred EEeccCCcEECCCCEEEEEEE--EEecccCeEEEEEC
Confidence 9886 578999999999998 99999999999873
No 4
>PRK05054 exoribonuclease II; Provisional
Probab=100.00 E-value=1.2e-43 Score=354.73 Aligned_cols=213 Identities=18% Similarity=0.270 Sum_probs=175.0
Q ss_pred eeEEeeCCCCCccCHHHHHHHHHHcCCcccCCC---HHHHHHHHHhh------------ccccccCcCCCCCccccccCC
Q psy4846 3 NAMLRRHPVPPPANFEPLLHAARRQGFELSVGT---GKELATSLDAA------------AVYFSSGMLQQSDFHHYGLAT 67 (279)
Q Consensus 3 ~al~R~H~~P~~~~~~~l~~~~~~~g~~~~~~~---~~~l~~~L~~~------------A~Y~~~~~~~~~~~~H~gL~~ 67 (279)
++|||+|++|+++++++|.++++.+|++++..+ ...++..++.+ -+++..+.+++++.||||||+
T Consensus 411 p~iyRvH~~P~~~~l~~l~~~~~~~g~~~~~~~~~~l~~~~~~~~~l~~~~~~~l~~~llr~~~~a~ys~~~~gHfgL~~ 490 (644)
T PRK05054 411 FGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEGFCKLRRELDAQPTGYLDSRIRRFQSFAEISTEPGPHFGLGL 490 (644)
T ss_pred CEEEECCCCCCHHHHHHHHHHHHHCCCCcCCCcccChHHHHHHHHHHhcchHHHHHHHHHHHHhceecCCCCcCcccccc
Confidence 589999999999999999999999999886542 22332222211 122233444679999999999
Q ss_pred CCccccccCccccchHHHHHHHHHHHcCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc---e
Q psy4846 68 PIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNLNYRNRQAQYAGRASVALHTHLFFRSRVQ---D 144 (279)
Q Consensus 68 ~~YthfTSPIRRY~DlivHR~L~a~l~~~~~~~~~~~~~~l~~~~~~~n~~~r~a~~aer~~~~~~~~~~l~~~~~---~ 144 (279)
++|||||||||||+||+|||||+++|.+++.. ..+.++|.++|+++++|++|||++.+++++.||+++++ +
T Consensus 491 ~~YthfTSPIRRY~DLivHR~L~a~l~~~~~~------~~~~~~~~~~s~~er~a~~aer~~~~~~~~~y~~~~~G~~~~ 564 (644)
T PRK05054 491 EAYATWTSPIRKYGDMINHRLLKAVIKGETAE------RPQDEITVQLAERRRLNRMAERDVGDWLYARYLKDKAGTDTR 564 (644)
T ss_pred ccccccCChhhhhHHHHHHHHHHHHHcCCCCC------ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeE
Confidence 99999999999999999999999999775431 13678999999999999999999999999999999974 6
Q ss_pred eeEEEEEeecchhhhhcCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCC--ceeeecCCceEeec-CeEe
Q psy4846 145 EDGYVLYVRKNALQILIPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSV--SWTYNEKEQSQSCG-SVVF 221 (279)
Q Consensus 145 ~~g~V~~~~~~~~~~~~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d--~~~~~~~~~~l~~~-~~~~ 221 (279)
|+|+|+ +|+++|+||.|+++|+||+||++. ++++ +|.|+..+..+... ++.|
T Consensus 565 f~g~I~------------------------~v~~~G~fV~l~~~~veglV~~~~-l~~~~~~y~~~~~~~~~~~~~~~~~ 619 (644)
T PRK05054 565 FAAEII------------------------DISRGGMRVRLLENGAVAFIPASF-LHAVRDELVCNQENGTVQIKGETVY 619 (644)
T ss_pred EEEEEE------------------------eeecCcEEEEEeCCceEEEEEccc-cCCCccceEEccccceEEEeCCEEE
Confidence 899988 999999999999999999999998 6655 45555444433333 4789
Q ss_pred cCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 222 HSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 222 ~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
++||+|+|+|. ++|+.+++|+|.++
T Consensus 620 ~lGd~V~V~v~--~vd~~~~~i~~~~~ 644 (644)
T PRK05054 620 KLGDVIDVTLA--EVRMETRSIIARPV 644 (644)
T ss_pred cCCCEEEEEEE--EEccccCeEEEEEC
Confidence 99999999998 99999999999874
No 5
>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=100.00 E-value=4.2e-43 Score=350.39 Aligned_cols=210 Identities=19% Similarity=0.274 Sum_probs=177.4
Q ss_pred eeEEeeCCCCCccCHHHHHHHHHHcCCcccCC---CHHHHHHHHHhh------------ccccccCcCCCCCccccccCC
Q psy4846 3 NAMLRRHPVPPPANFEPLLHAARRQGFELSVG---TGKELATSLDAA------------AVYFSSGMLQQSDFHHYGLAT 67 (279)
Q Consensus 3 ~al~R~H~~P~~~~~~~l~~~~~~~g~~~~~~---~~~~l~~~L~~~------------A~Y~~~~~~~~~~~~H~gL~~ 67 (279)
++|||+|++|+++++++|.++++.+|++++.. +...++..++.+ .+|+..+.+++++.+|||||+
T Consensus 407 p~iyR~H~~P~~~~l~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~r~~~~a~ys~~~~~HfgL~~ 486 (639)
T TIGR02062 407 FGIYNTHAGFDPANAENVVALLKTNGLHVDAEELATLDGFCKLRRELDAQETGYLDSRIRRYQSFAEISTEPGPHFGLGL 486 (639)
T ss_pred CeEEecCCCCCHHHHHHHHHHHHHcCCCCCcccccCHHHHHHHHHHhhcchHHHHHHHHHHHhhhcccCCCCcCcchhcc
Confidence 58999999999999999999999999988643 233333332221 445555666789999999999
Q ss_pred CCccccccCccccchHHHHHHHHHHHcCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc---e
Q psy4846 68 PIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNLNYRNRQAQYAGRASVALHTHLFFRSRVQ---D 144 (279)
Q Consensus 68 ~~YthfTSPIRRY~DlivHR~L~a~l~~~~~~~~~~~~~~l~~~~~~~n~~~r~a~~aer~~~~~~~~~~l~~~~~---~ 144 (279)
+.|||||||||||+||+|||||+++|.+... + ..+.++|.+++++++.|+.|||++.+|+++.||+++++ .
T Consensus 487 ~~YthfTSPIRRY~DLivHR~L~~~l~~~~~-~-----~~~~~~~~~~s~~er~a~~aeR~~~~~~~~~yl~~~~g~~~~ 560 (639)
T TIGR02062 487 EAYATWTSPIRKYGDMINHRLLKAVIKGETA-T-----RPQEDITVQLAERRRLNRIAERDVADWLYARFLADKAAKNTR 560 (639)
T ss_pred ccccccCChhhhhHHHHHHHHHHHHHcCCCC-C-----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcE
Confidence 9999999999999999999999999976542 1 13578899999999999999999999999999999974 4
Q ss_pred eeEEEEEeecchhhhhcCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCC--CceeeecCCc--eEeecCeE
Q psy4846 145 EDGYVLYVRKNALQILIPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPS--VSWTYNEKEQ--SQSCGSVV 220 (279)
Q Consensus 145 ~~g~V~~~~~~~~~~~~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~--d~~~~~~~~~--~l~~~~~~ 220 (279)
|+|+|+ +++.+|+||.|++.|++|+||+.+ +++ ++|.|+.... .+.+. ++
T Consensus 561 f~g~I~------------------------~v~~~g~~v~l~~~~~~g~v~~~~-l~~~~~~~~~~~~~~~~~l~g~-~~ 614 (639)
T TIGR02062 561 FAAEIV------------------------DISRGGMRVRLLENGAIAFIPAAF-LHANREELVCNQENGTVQIKGE-TV 614 (639)
T ss_pred EEEEEE------------------------eeeCCcEEEEEecCceEEEEEhhh-cCCCCcceEEcccccEEEEecc-EE
Confidence 899888 999999999999999999999998 655 6788888765 44433 58
Q ss_pred ecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 221 FHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 221 ~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
|++||+|+|+|. ++|..+++|+|.
T Consensus 615 ~~lgd~v~V~v~--~vd~~~~~i~~~ 638 (639)
T TIGR02062 615 YKIGDVIDVVLT--EVRMETRSIIAR 638 (639)
T ss_pred EecCCEEEEEEE--EeccccCcEeee
Confidence 999999999998 999999999986
No 6
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=100.00 E-value=3.2e-43 Score=355.64 Aligned_cols=214 Identities=28% Similarity=0.458 Sum_probs=190.3
Q ss_pred eeEEeeCCCCCccCHHHHHHHHHHcCCcccCCC----HHHHHHHHHhh-------------------ccccccCcCCCCC
Q psy4846 3 NAMLRRHPVPPPANFEPLLHAARRQGFELSVGT----GKELATSLDAA-------------------AVYFSSGMLQQSD 59 (279)
Q Consensus 3 ~al~R~H~~P~~~~~~~l~~~~~~~g~~~~~~~----~~~l~~~L~~~-------------------A~Y~~~~~~~~~~ 59 (279)
+.+||+|+.|+.++++.|++++..+|+.+.... ++.++..++.. |.| ++.+
T Consensus 466 ~~~~R~h~~P~~ek~~~l~~~l~~lg~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~lRsm~~a~Y------s~~~ 539 (706)
T COG0557 466 PLLYRTHERPSTEKLQSLREFLQNLGLVLPLGGSKPQPQDYQILLETVKGRPLEAVLQTLLLRSMKQAEY------SPDN 539 (706)
T ss_pred CcceeCCCCCCHHHHHHHHHHHHHcCceecCCCCcCCHHHHHHHHhhccCChHHHHHHHHHHHhhhcCee------cCCC
Confidence 459999999999999999999999999987442 55666666554 555 5689
Q ss_pred ccccccCCCCccccccCccccchHHHHHHHHHHHcCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy4846 60 FHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNLNYRNRQAQYAGRASVALHTHLFFR 139 (279)
Q Consensus 60 ~~H~gL~~~~YthfTSPIRRY~DlivHR~L~a~l~~~~~~~~~~~~~~l~~~~~~~n~~~r~a~~aer~~~~~~~~~~l~ 139 (279)
.||||||+++|||||||||||+||||||||+++|.+........+...+.++|.++|.++|+|..|+|++.++|.+.||+
T Consensus 540 ~~HfgL~~~~YtHFTSPIRRY~DLivHR~L~~~l~~~~~~~~~~~~~~l~~i~~~~s~~er~a~~aer~~~~~~~~~~m~ 619 (706)
T COG0557 540 VGHFGLALDYYTHFTSPIRRYPDLIVHRQLKALLSGEPIPEKKTSEEELDELAAHISSAERRAQEAERDVIDLLKAEYMK 619 (706)
T ss_pred CCceeccccchhccCCchhhchHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999998754432211347899999999999999999999999999999999
Q ss_pred hccc-eeeEEEEEeecchhhhhcCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeec-
Q psy4846 140 SRVQ-DEDGYVLYVRKNALQILIPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCG- 217 (279)
Q Consensus 140 ~~~~-~~~g~V~~~~~~~~~~~~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~- 217 (279)
++++ +|+|+|+ +|+.+|+||.|+++++||+||++. +++++|.|++..+.+.+.
T Consensus 620 ~~vg~~f~g~V~------------------------~v~~~g~~V~l~~~~ieglV~~s~-L~~d~y~~~~~~~~l~~~~ 674 (706)
T COG0557 620 KRVGEEFDGVVT------------------------GVTSFGFFVELPELGLEGLVHISS-LPDDYYHFDERGQALVGEK 674 (706)
T ss_pred HhcCCEEEEEEE------------------------EEEeccEEEEecccccccceEccc-CCCceeeeccccceeeccc
Confidence 9986 6999998 999999999999999999999998 888999999999888886
Q ss_pred -CeEecCCCeEEEEEEeccccCCCCeEEEEEec
Q psy4846 218 -SVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVR 249 (279)
Q Consensus 218 -~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~ 249 (279)
+..+++||.|+|++. +++...++|+|++++
T Consensus 675 ~~~~~~lgd~v~v~v~--~v~~~~~~i~~~~v~ 705 (706)
T COG0557 675 SGKVYRLGDEVKVKVT--SVDLDERKIDFELVE 705 (706)
T ss_pred cccccccCCEEEEEEE--EEcccccceEEEecC
Confidence 668999999999998 999999999999875
No 7
>KOG2102|consensus
Probab=100.00 E-value=9.7e-36 Score=305.90 Aligned_cols=224 Identities=44% Similarity=0.728 Sum_probs=185.0
Q ss_pred ceeEEeeCCCCCccCHHHHHHHHHHcCCcccCCCHHHHHHHHHhh----------------------ccccccCcCCCCC
Q psy4846 2 DNAMLRRHPVPPPANFEPLLHAARRQGFELSVGTGKELATSLDAA----------------------AVYFSSGMLQQSD 59 (279)
Q Consensus 2 ~~al~R~H~~P~~~~~~~l~~~~~~~g~~~~~~~~~~l~~~L~~~----------------------A~Y~~~~~~~~~~ 59 (279)
+.++||.||.|....++.+.++|..+|++++.+++++|+.+|+++ |+|||+|...+..
T Consensus 690 ~~alLR~hp~P~~~~~~~~~~~~~~~g~~ld~sS~~~L~~Sl~r~~~~~~p~~~~~l~~l~~r~m~~A~yf~sg~~~~~~ 769 (941)
T KOG2102|consen 690 SLALLRRHPSPPPENFKPLVSLCLELGFNLDTSSSKSLADSLDRIRDDDKPYLNTLLRILATRSMTRAVYFCSGSSDTPQ 769 (941)
T ss_pred chhhhccCCCCccccccHHHHHHHHcCCCccccchHHHhhhHhhhcCCchHHHHHHHHHHHhhhhhceeEEeecccCcch
Confidence 578999999999999999999999999999999999998888765 9999999878889
Q ss_pred ccccccCCCCccccccCccccchHHHHHHHHHHHcCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy4846 60 FHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNLNYRNRQAQYAGRASVALHTHLFFR 139 (279)
Q Consensus 60 ~~H~gL~~~~YthfTSPIRRY~DlivHR~L~a~l~~~~~~~~~~~~~~l~~~~~~~n~~~r~a~~aer~~~~~~~~~~l~ 139 (279)
++|||||++.|||||||||||+||+|||||++...... +...+...+..+|.+||.+.+.|+.|++++.++|.+.|++
T Consensus 770 ~~HygLa~p~YTHFTsPiRRY~DIivHrqL~~~~~~~~--~~~~~~~~l~~i~~~~N~r~~~a~~a~~~S~~l~~~~~~k 847 (941)
T KOG2102|consen 770 FHHYGLASPLYTHFTSPIRRYADIIVHRQLAAAFLERS--PTAPDRPNLSSLAANCNERKKAAKKAQEASTELYLCEYLK 847 (941)
T ss_pred hhchhhcccchhhccCcccccchHHHHHHHHHHhhccC--ccccccccHHHHHhhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 99999999999999999999999999999995333222 2223445899999999999999999999999999999999
Q ss_pred hccceeeEEEEEeecchhhhhcCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCe
Q psy4846 140 SRVQDEDGYVLYVRKNALQILIPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSV 219 (279)
Q Consensus 140 ~~~~~~~g~V~~~~~~~~~~~~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~ 219 (279)
+.....+|+|+ +|.++|+.|++|+||+||.|++....+...+..++.. ..
T Consensus 848 ~~~~~~~a~v~------------------------~V~~~~~~v~ipe~G~e~~v~l~~~~~~~~~~~~~~~------~~ 897 (941)
T KOG2102|consen 848 DKQVLEEAVVL------------------------FVRPNGIDVVIPEYGLEGRVYLDLLKPSQTFFLDDEV------SL 897 (941)
T ss_pred hcccccceEEE------------------------EEecCceEEEEcccCceEEEEecccCCccceeecccc------cc
Confidence 98555677777 9999999999999999999999731111112221111 12
Q ss_pred EecCCCeEEEEEEeccccCCCCeEEEEEec-CCccCccc
Q psy4846 220 VFHSFDPVTVQLSLDRSNVQHEKLVLRLVR-PVIEGFSV 257 (279)
Q Consensus 220 ~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~-~~~~~~~~ 257 (279)
.+...|.|.+++.++..++...+|.+.++. |...+.++
T Consensus 898 ~~~~~~~v~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~v 936 (941)
T KOG2102|consen 898 RFEESDPVVVRIKLDKLVPQPDRLRIELVSEPSLKSSNV 936 (941)
T ss_pred cccccCCceeeecccccccCcceEEEEeccccccccccc
Confidence 278889999998878889999999999988 54444443
No 8
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=99.95 E-value=2e-28 Score=228.38 Aligned_cols=214 Identities=20% Similarity=0.266 Sum_probs=164.9
Q ss_pred ceeEEeeCCCCCccCHHHHHHHHHHcCCcccCCC------HHHHHHHHHhh---------ccccccCcCCCCCccccccC
Q psy4846 2 DNAMLRRHPVPPPANFEPLLHAARRQGFELSVGT------GKELATSLDAA---------AVYFSSGMLQQSDFHHYGLA 66 (279)
Q Consensus 2 ~~al~R~H~~P~~~~~~~l~~~~~~~g~~~~~~~------~~~l~~~L~~~---------A~Y~~~~~~~~~~~~H~gL~ 66 (279)
-+++|-+|..-++..++....++...|...+... -.+|.+.|+.. -+|.+.++++.++.+|||||
T Consensus 410 gfGI~N~HsGFd~~~~e~a~~~l~~~~~~~~~e~l~Tl~Gfc~lRr~l~~~~t~yld~RiRrfqsfae~~t~p~PHFglG 489 (645)
T COG4776 410 GFGIYNVHSGFDPANAEAAAALLKTNGLNVDAEELLTLEGFCKLRRELDAQPTGYLDSRIRRFQSFAEISTEPGPHFGLG 489 (645)
T ss_pred CcceeeccccCCHHHHHHHHHHHHhcCcCCCHHHHhhhHHHHHHHHHhhccccchHHHHHHHHHhHHhhccCcCcccccc
Confidence 4689999999999999999999999999776542 14455555544 66777788899999999999
Q ss_pred CCCccccccCccccchHHHHHHHHHHHcCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc---
Q psy4846 67 TPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNLNYRNRQAQYAGRASVALHTHLFFRSRVQ--- 143 (279)
Q Consensus 67 ~~~YthfTSPIRRY~DlivHR~L~a~l~~~~~~~~~~~~~~l~~~~~~~n~~~r~a~~aer~~~~~~~~~~l~~~~~--- 143 (279)
++.|++||||||+|.|+|+||+|++.+.++.... .-+.+..++.++.|..+.|||+.-+|.+++||+.+.+
T Consensus 490 l~~YATWTSPIRKY~DMiNHRLlKavi~~~~~~k------Pqedi~v~lae~Rr~nrmaERdv~DWLY~r~L~~k~~~~~ 563 (645)
T COG4776 490 LEAYATWTSPIRKYGDMINHRLLKAVIKGETAEK------PQEDITVQLAERRRLNRMAERDVADWLYARFLADKAGTNT 563 (645)
T ss_pred chheeeccchhhhhhhHHHHHHHHHHHcCCCcCC------CchHHHHHHHHHHHhhhhhhhhhHHHHHHHHhccccccCc
Confidence 9999999999999999999999999998764321 1245566778888999999999999999999999864
Q ss_pred eeeEEEEEeecchhhhhcCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEccc-CCCCCceeeecCCceEeec-CeEe
Q psy4846 144 DEDGYVLYVRKNALQILIPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRC-DSPSVSWTYNEKEQSQSCG-SVVF 221 (279)
Q Consensus 144 ~~~g~V~~~~~~~~~~~~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~-~~~~d~~~~~~~~~~l~~~-~~~~ 221 (279)
.|.+.|. .|...|+.|.|-+.|.-.+|+-.- ....+...++.+..++.-. ..+|
T Consensus 564 ~F~AEI~------------------------Di~R~G~RvrLleNGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Y 619 (645)
T COG4776 564 RFAAEIQ------------------------DISRGGMRVRLLENGAIAFIPAPLIHANREELVCNQENGTVQIKGETVY 619 (645)
T ss_pred hhhhhhh------------------------hhccCceEEEeccCCcceecchhhhccchhheEecCCCceEEEccEEEE
Confidence 3777776 444444444444444444443322 1112678899888887655 6789
Q ss_pred cCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 222 HSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 222 ~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
++||.|+|++. +|+.+.+.|.-.+
T Consensus 620 k~~D~i~V~l~--eVr~etRsii~~p 643 (645)
T COG4776 620 KVGDVIDVTLA--EVRMETRSIIARP 643 (645)
T ss_pred eeccEEEEEeH--HHHHhhhhhhccc
Confidence 99999999988 9998888776543
No 9
>PF00773 RNB: RNB domain CAUTION: The Prosite pattern does not correspond to this Pfam.; InterPro: IPR001900 This entry represents the catalytic domain of ribonuclease II []. It includes characterised and related sequences to exoribonuclease II (RNase II) and ribonuclease R, a bacterial 3' --> 5' exoribonuclease homologous to RNase II [,,].; GO: 0003723 RNA binding, 0004540 ribonuclease activity; PDB: 2R7D_A 2R7F_A 2ID0_D 2IX1_A 2IX0_A 2VNU_D 2WP8_J.
Probab=99.83 E-value=2.6e-21 Score=179.57 Aligned_cols=84 Identities=40% Similarity=0.648 Sum_probs=57.9
Q ss_pred eeEEeeCCCCCccCHHHHHHHHHHcCCcccCCC---------------HHHHHHHHHhh---ccccccCcCCCCCccccc
Q psy4846 3 NAMLRRHPVPPPANFEPLLHAARRQGFELSVGT---------------GKELATSLDAA---AVYFSSGMLQQSDFHHYG 64 (279)
Q Consensus 3 ~al~R~H~~P~~~~~~~l~~~~~~~g~~~~~~~---------------~~~l~~~L~~~---A~Y~~~~~~~~~~~~H~g 64 (279)
+++||+|+.|+..+++++.+.+ +++++... ...+...+.+. |+| ++++.+|||
T Consensus 224 p~iyR~~~~p~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~a~y------~~~p~~H~~ 294 (325)
T PF00773_consen 224 PAIYRVQPEPDPERLEELLKLL---KLDLDETKSLTLQNLLQAENPPNSLALRYLLLKTLPPAEY------STEPSGHFG 294 (325)
T ss_dssp TSEEEEB-SSSCCCHHHHHHHH---T---STCHHHCHHCHHCCCCTTSSHHHHHHHHCCC--EEE------ESSGC-BTT
T ss_pred CceeeeCCCCCHHHHHHHHHHh---cCCCCCcchhhHHHHHHhcCChHHHHHHHHHHHhhccccc------ccCCCccee
Confidence 6899999999999999999888 33332211 12222222222 777 468899999
Q ss_pred cCCCCccccccCccccchHHHHHHHHHHHcC
Q psy4846 65 LATPIYTHFTSPIRRYADIIVHRLLAACIGA 95 (279)
Q Consensus 65 L~~~~YthfTSPIRRY~DlivHR~L~a~l~~ 95 (279)
||++.|||||||||||+||+|||||+++|.+
T Consensus 295 L~l~~Yt~~TSPlRRY~Dl~~hrql~~~L~~ 325 (325)
T PF00773_consen 295 LGLPAYTHFTSPLRRYADLVVHRQLKAALRK 325 (325)
T ss_dssp TTBSS-B--S-TTTBHHHHHHHHHHHHHHH-
T ss_pred eeccccccccChhhhhHHHHHHHHHHHHhhC
Confidence 9999999999999999999999999999863
No 10
>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=99.31 E-value=1.5e-11 Score=91.37 Aligned_cols=77 Identities=21% Similarity=0.283 Sum_probs=68.2
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeec--CeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCG--SVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~--~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
++|.|++|+++|+||.|+.+|++|+||+++ ++.++|.||+..+.+.+. +..|++||.|+|+|. ++|.++++|.|+
T Consensus 5 ~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~-l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~--~vd~~~~~i~~~ 81 (83)
T cd04471 5 FDGVISGVTSFGLFVELDNLTVEGLVHVST-LGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVV--RVDLDRRKIDFE 81 (83)
T ss_pred EEEEEEeEEeeeEEEEecCCCEEEEEEEEe-cCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEE--EeccccCEEEEE
Confidence 456667999999999999999999999998 777789999998888764 578999999999998 999999999998
Q ss_pred Ee
Q psy4846 247 LV 248 (279)
Q Consensus 247 lv 248 (279)
+.
T Consensus 82 l~ 83 (83)
T cd04471 82 LV 83 (83)
T ss_pred EC
Confidence 63
No 11
>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=98.78 E-value=3.3e-08 Score=76.41 Aligned_cols=79 Identities=18% Similarity=0.191 Sum_probs=66.5
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeec--CeEecCCCeEEEEEEeccccCCC-----C
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCG--SVVFHSFDPVTVQLSLDRSNVQH-----E 241 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~--~~~~~lGD~V~VkV~~~~vd~~~-----~ 241 (279)
+.|.|++|.++|+||.+. +++|+|++++ ++.+++.+++..+.+.+. +..|++||.|+|+|. ++|.+. .
T Consensus 3 v~g~V~~i~~~GifV~l~--~v~G~v~~~~-l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~--~vd~~~~~~~~~ 77 (99)
T cd04460 3 VEGEVVEVVDFGAFVRIG--PVDGLLHISQ-IMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIV--AVSLKERRPRES 77 (99)
T ss_pred EEEEEEEEEeccEEEEEc--CeEEEEEEEE-ccCCceEechhheeecccCcCCEECCCCEEEEEEE--EEeHHHCcCCCc
Confidence 456677999999999997 5999999998 777889999988888876 578999999999998 888763 5
Q ss_pred eEEEEEecCCc
Q psy4846 242 KLVLRLVRPVI 252 (279)
Q Consensus 242 ~I~~~lv~~~~ 252 (279)
+|.+++.++..
T Consensus 78 ~i~ls~k~~~~ 88 (99)
T cd04460 78 KIGLTMRQPGL 88 (99)
T ss_pred eEEEEEecCCC
Confidence 89999987643
No 12
>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=98.74 E-value=4.1e-08 Score=71.66 Aligned_cols=67 Identities=21% Similarity=0.137 Sum_probs=52.0
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.++|.|+++.++|+||.+++++++|+||+++ +..+ .++ ..+..|++||.|+|+|. ++|..+ ++.|++
T Consensus 6 ~~~g~V~~i~~fG~fv~l~~~~~eGlvh~se-l~~~--~~~-------~~~~~~~~Gd~v~vkv~--~vd~~~-ki~ls~ 72 (73)
T cd05686 6 IFKGEVASVTEYGAFVKIPGCRKQGLVHKSH-MSSC--RVD-------DPSEVVDVGEKVWVKVI--GREMKD-KMKLSL 72 (73)
T ss_pred EEEEEEEEEEeeeEEEEECCCCeEEEEEchh-hCCC--ccc-------CHhhEECCCCEEEEEEE--EECCCC-cEEEEe
Confidence 3466677999999999998777899999998 4322 111 12457999999999998 999876 888876
No 13
>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=98.70 E-value=3.1e-08 Score=71.22 Aligned_cols=67 Identities=15% Similarity=0.148 Sum_probs=54.1
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.++|.|++|.++|++|.+++ +++|+||.++ +.++++. .....|++||.|+|+|. ++|..+++|.|+|
T Consensus 3 ~v~g~V~~v~~~Gv~V~l~~-~v~g~i~~~~-l~~~~~~---------~~~~~~~~Gd~i~~~V~--~id~~~~~i~ls~ 69 (69)
T cd05697 3 VVKGTIRKLRPSGIFVKLSD-HIKGLVPPMH-LADVRLK---------HPEKKFKPGLKVKCRVL--SVEPERKRLVLTL 69 (69)
T ss_pred EEEEEEEEEeccEEEEEecC-CcEEEEEHHH-CCCcccc---------CHHHcCCCCCEEEEEEE--EEECCCCEEEEEC
Confidence 35677889999999999987 7999999987 4333221 11357999999999998 9999999999875
No 14
>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=98.63 E-value=1.2e-07 Score=68.60 Aligned_cols=66 Identities=18% Similarity=0.138 Sum_probs=51.2
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
.+.|.|.+++++|+||.|++ +++|++|.++ ++ + ..... ..+..|++||.|+|+|. ++|..+++|.+
T Consensus 6 ~~~g~V~~i~~~G~fv~l~~-~~~Gl~~~~~-l~--~---~~~~~---~~~~~~~~Gd~v~v~v~--~id~~~~~i~~ 71 (72)
T cd05689 6 RLFGKVTNLTDYGCFVELEE-GVEGLVHVSE-MD--W---TNKNI---HPSKVVSLGDEVEVMVL--DIDEERRRISL 71 (72)
T ss_pred EEEEEEEEEEeeEEEEEcCC-CCEEEEEEEe-cc--C---ccccc---CcccEeCCCCEEEEEEE--EeeCCcCEEeC
Confidence 35667779999999999987 7999999997 42 1 11110 12467999999999998 99999999876
No 15
>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=98.63 E-value=1.4e-07 Score=68.73 Aligned_cols=71 Identities=18% Similarity=0.146 Sum_probs=57.3
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.+.|.|++++++|+||.+.+.+++|++|.++ ++.++ .. .....|++||.|+|+|. ++|.+.+++.|++
T Consensus 5 ~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~-l~~~~-~~--------~~~~~~~~Gd~v~v~i~--~vd~~~~~i~ls~ 72 (77)
T cd05708 5 KIDGTVRRVEDYGVFIDIDGTNVSGLCHKSE-ISDNR-VA--------DASKLFRVGDKVRAKVL--KIDAEKKRISLGL 72 (77)
T ss_pred EEEEEEEEEEcceEEEEECCCCeEEEEEHHH-CCCCc-cC--------CHhHeecCCCEEEEEEE--EEeCCCCEEEEEE
Confidence 3567777999999999998778999999998 53332 11 12457999999999998 9999999999998
Q ss_pred ecC
Q psy4846 248 VRP 250 (279)
Q Consensus 248 v~~ 250 (279)
...
T Consensus 73 k~~ 75 (77)
T cd05708 73 KAS 75 (77)
T ss_pred Eee
Confidence 864
No 16
>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=98.62 E-value=8.3e-08 Score=69.00 Aligned_cols=66 Identities=15% Similarity=0.164 Sum_probs=53.8
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
+.|.|+++.++|++|.+++ +++|+||.++ +..++ ..++ ...+++||.|+|+|. ++|+.++++.|++
T Consensus 4 ~~g~V~~v~~~G~~V~l~~-~~~gli~~s~-l~~~~-~~~~--------~~~~~~G~~i~v~v~--~~d~~~~~i~ls~ 69 (70)
T cd05698 4 THGTIVKVKPNGCIVSFYN-NVKGFLPKSE-LSEAF-IKDP--------EEHFRVGQVVKVKVL--SCDPEQQRLLLSC 69 (70)
T ss_pred EEEEEEEEecCcEEEEECC-CCEEEEEHHH-cChhh-cCCH--------HHcccCCCEEEEEEE--EEcCCCCEEEEEe
Confidence 4677789999999999987 7999999998 53332 2222 346899999999998 9999999999986
No 17
>PRK07252 hypothetical protein; Provisional
Probab=98.62 E-value=1.5e-07 Score=75.49 Aligned_cols=75 Identities=13% Similarity=0.027 Sum_probs=58.9
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.+.|.|++|.++|+||.++. +++|+||+++ ++.+++. .....|++||.|+|+|. ++|.+.++|.|++
T Consensus 6 iv~G~V~~V~~~G~fVei~~-~~~Gllhise-Ls~~~~~---------~~~~~~~vGD~V~VkI~--~iD~~~~ri~lSl 72 (120)
T PRK07252 6 KLKGTITGIKPYGAFVALEN-GTTGLIHISE-IKTGFID---------NIHQLLKVGEEVLVQVV--DFDEYTGKASLSL 72 (120)
T ss_pred EEEEEEEEEeCcEEEEEECC-CCEEEEEHHH-cCCcccc---------ChhhccCCCCEEEEEEE--EEeCCCCEEEEEE
Confidence 34677779999999999987 7999999998 5433321 11457999999999998 9999999999999
Q ss_pred ecCCccCc
Q psy4846 248 VRPVIEGF 255 (279)
Q Consensus 248 v~~~~~~~ 255 (279)
......+.
T Consensus 73 k~~~~~~~ 80 (120)
T PRK07252 73 RTLEEEKQ 80 (120)
T ss_pred eecccCcc
Confidence 87544333
No 18
>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=98.60 E-value=1e-07 Score=68.25 Aligned_cols=66 Identities=12% Similarity=0.229 Sum_probs=51.5
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+.|.|.+++++|+||.|+. +++|+||.++ ++ |.. ........|++||.|+|+|. ++|.++++|.|+
T Consensus 4 ~~g~V~~i~~~G~fv~l~~-~~~Glv~~~~-l~-----~~~---~~~~~~~~~~~G~~v~v~v~--~id~~~~~i~l~ 69 (69)
T cd05690 4 VSGKIKSITDFGIFVGLDG-GIDGLVHISD-IS-----WTQ---RVRHPSEIYKKGQEVEAVVL--NIDVERERISLG 69 (69)
T ss_pred EEEEEEEEEeeeEEEEeCC-CCEEEEEHHH-CC-----Ccc---ccCChhhEECCCCEEEEEEE--EEECCcCEEeCC
Confidence 4677779999999999987 8999999998 42 111 11112457999999999998 999999999863
No 19
>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=98.59 E-value=2e-07 Score=67.60 Aligned_cols=67 Identities=19% Similarity=0.175 Sum_probs=54.2
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.+.|.|+++.++|++|.|+. +++|+||.++ +++++ +.. ....|++||.|+++|. ++|..+++|.|++
T Consensus 6 iv~g~V~~v~~~gi~v~l~~-~~~g~v~~s~-l~~~~---~~~------~~~~~~~Gd~v~~~V~--~~d~~~~~i~ls~ 72 (73)
T cd05706 6 ILPGRVTKVNDRYVLVQLGN-KVTGPSFITD-ALDDY---SEA------LPYKFKKNDIVRACVL--SVDVPNKKIALSL 72 (73)
T ss_pred EEEEEEEEEeCCeEEEEeCC-CcEEEEEhhh-ccCcc---ccc------cccccCCCCEEEEEEE--EEeCCCCEEEEEE
Confidence 45677789999999999988 7999999998 54332 111 1356999999999998 9999999999986
No 20
>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=98.56 E-value=1.6e-07 Score=68.62 Aligned_cols=70 Identities=16% Similarity=0.128 Sum_probs=55.0
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.+.|+|..+.++|++|.|.+ +++|+|++++ ++.+ ... .......|++||.|+++|. ++|+++++|.|++
T Consensus 3 ~V~g~V~~i~~~g~~V~l~~-~i~G~i~~~~-ls~~-~~~------~~~~~~~~~vG~~v~~kV~--~id~~~~~i~Ls~ 71 (73)
T cd05703 3 EVTGFVNNVSKEFVWLTISP-DVKGRIPLLD-LSDD-VSV------LEHPEKKFPIGQALKAKVV--GVDKEHKLLRLSA 71 (73)
T ss_pred EEEEEEEEEeCCEEEEEeCC-CcEEEEEHHH-cCCc-ccc------ccCHHHhCCCCCEEEEEEE--EEeCCCCEEEEEe
Confidence 35788889999999999987 8999999997 4211 000 1111457999999999998 9999999999997
Q ss_pred e
Q psy4846 248 V 248 (279)
Q Consensus 248 v 248 (279)
.
T Consensus 72 k 72 (73)
T cd05703 72 R 72 (73)
T ss_pred c
Confidence 4
No 21
>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=98.55 E-value=1.3e-07 Score=67.84 Aligned_cols=65 Identities=9% Similarity=0.127 Sum_probs=52.4
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+.|.|++|.++|++|.++. +++|+||.++ +++++.. .....|++||.|+|+|. ++|+.+++|.|+
T Consensus 4 v~g~V~~v~~~Gv~V~l~~-~~~G~v~~s~-l~~~~~~---------~~~~~~~~Gd~v~~~v~--~~d~~~~~i~ls 68 (68)
T cd05707 4 VRGFVKNIANNGVFVTLGR-GVDARVRVSE-LSDSYLK---------DWKKRFKVGQLVKGKIV--SIDPDNGRIEMT 68 (68)
T ss_pred EEEEEEEEECccEEEEeCC-CCEEEEEHHH-CCchhhc---------CHhhccCCCCEEEEEEE--EEeCCCCEEecC
Confidence 4677789999999999987 7999999997 5433221 11457999999999998 999999998764
No 22
>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=98.54 E-value=3.3e-07 Score=67.67 Aligned_cols=68 Identities=15% Similarity=0.062 Sum_probs=53.2
Q ss_pred CcceEEEEEeCeEEEEecCc--ceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKY--GLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~--giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+.|.|+++.++|+||.|.+. +++|++|.++ ++.+++ +......|++||.|+|+|. ++| ++++.|+
T Consensus 4 ~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~-l~~~~~--------~~~~~~~~~~Gd~v~v~v~--~vd--~~~i~~s 70 (79)
T cd05684 4 YKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQ-LSFEGR--------VANPSDVVKRGQKVKVKVI--SIQ--NGKISLS 70 (79)
T ss_pred EEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHh-ccCCCC--------cCChhheeCCCCEEEEEEE--EEe--CCEEEEE
Confidence 45667799999999999865 7999999998 543322 0111457999999999988 888 8899999
Q ss_pred Eec
Q psy4846 247 LVR 249 (279)
Q Consensus 247 lv~ 249 (279)
+..
T Consensus 71 ~k~ 73 (79)
T cd05684 71 MKD 73 (79)
T ss_pred EEe
Confidence 865
No 23
>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=98.53 E-value=1.9e-07 Score=68.47 Aligned_cols=70 Identities=14% Similarity=0.127 Sum_probs=53.0
Q ss_pred cCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 167 QDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 167 ~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+.+.|+|.+++++|+||.|.. +++|+||+++ +..+++. ++. .-...|++||.|+++|. ++|.++++|.|+
T Consensus 5 ~~V~g~V~~i~~~G~fV~l~~-~v~G~v~~~~-ls~~~~~-~~~-----~~~~~~~~G~~v~~kVl--~id~~~~~i~LS 74 (74)
T cd05705 5 QLLRGYVSSVTKQGVFFRLSS-SIVGRVLFQN-VTKYFVS-DPS-----LYNKYLPEGKLLTAKVL--SVNSEKNLVELS 74 (74)
T ss_pred CEEEEEEEEEeCCcEEEEeCC-CCEEEEEHHH-ccCcccc-Chh-----hHhcccCCCCEEEEEEE--EEECCCCEEecC
Confidence 446788889999999999976 8999999887 3212110 110 01357999999999998 999999998874
No 24
>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=98.51 E-value=3e-07 Score=78.74 Aligned_cols=86 Identities=15% Similarity=0.181 Sum_probs=71.0
Q ss_pred cCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeec--CeEecCCCeEEEEEEecccc-
Q psy4846 161 IPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCG--SVVFHSFDPVTVQLSLDRSN- 237 (279)
Q Consensus 161 ~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~--~~~~~lGD~V~VkV~~~~vd- 237 (279)
.|+ ....++|.|++++++|+||.+ . .++|.++.++ +..+.+.||+.+..+.+. +..|++||.|+|+|. +++
T Consensus 78 ~p~-~gEvv~G~V~~v~~~GifV~l-g-~~~gi~~~~~-l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~--~v~~ 151 (179)
T TIGR00448 78 KPE-LGEIVEGEVIEIVEFGAFVSL-G-PFDGLFHVSQ-VTDDYCYYDPKESALIGKETKKVLDEGDKVRARIV--ALSL 151 (179)
T ss_pred ecc-CCCEEEEEEEEEEeeEEEEEe-C-CceEEEEcHH-hCCCceEEccccceEEEccCCeEEcCCCEEEEEEE--EEEc
Confidence 455 344679999999999999999 3 5999999998 666788999988888775 578999999999998 776
Q ss_pred ----CCCCeEEEEEecCCc
Q psy4846 238 ----VQHEKLVLRLVRPVI 252 (279)
Q Consensus 238 ----~~~~~I~~~lv~~~~ 252 (279)
+...+|.+++.+|..
T Consensus 152 ~~~~~~~~~I~lt~k~~~L 170 (179)
T TIGR00448 152 KDRRPEGSKIGLTMRQPLL 170 (179)
T ss_pred cCCCCCcceEEEEeccCcC
Confidence 567889999988743
No 25
>PRK08582 hypothetical protein; Provisional
Probab=98.49 E-value=6.3e-07 Score=73.72 Aligned_cols=70 Identities=14% Similarity=0.108 Sum_probs=55.4
Q ss_pred cCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 167 QDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 167 ~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+.+.|.|++|+++|+||.|+. +++|+||+++ +..+++ .+ ....|++||.|+|+|. ++|. .++|.|+
T Consensus 7 ~iv~G~V~~I~~fG~fV~L~~-~~~GlVhiSe-ls~~~v-~~--------~~~~l~vGD~VkvkV~--~id~-~gkI~LS 72 (139)
T PRK08582 7 SKLQGKVTGITNFGAFVELPE-GKTGLVHISE-VADNYV-KD--------INDHLKVGDEVEVKVL--NVED-DGKIGLS 72 (139)
T ss_pred CEEEEEEEEEECCeEEEEECC-CCEEEEEeec-cCcccc-cc--------cccccCCCCEEEEEEE--EECC-CCcEEEE
Confidence 345677779999999999987 8999999998 543322 11 1357999999999998 8886 5899999
Q ss_pred EecC
Q psy4846 247 LVRP 250 (279)
Q Consensus 247 lv~~ 250 (279)
+...
T Consensus 73 lk~~ 76 (139)
T PRK08582 73 IKKA 76 (139)
T ss_pred EEec
Confidence 9864
No 26
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.48 E-value=1.8e-07 Score=86.50 Aligned_cols=86 Identities=14% Similarity=0.094 Sum_probs=66.4
Q ss_pred CcceEEEEEeCeEEEEecCc-ceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKY-GLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~-giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
+.|.|+.|.++|+||.|.+| |++|+||+++ + +|.. .......+++||.|.|+|. ++|.++++|.|++
T Consensus 21 V~g~V~~I~d~GafV~L~EY~gvEGlIhiSE-l-----S~~r----i~~i~d~vkvGd~v~vkVl--~VD~ekg~IdLS~ 88 (319)
T PTZ00248 21 VMVKVVRITEMGAYVSLLEYDDIEGMILMSE-L-----SKRR----IRSINKLIRVGRHEVVVVL--RVDKEKGYIDLSK 88 (319)
T ss_pred EEEEEEEEeCCeEEEEecCCCCcEEEEEHHH-h-----cccc----cCCHHHhcCCCCEEEEEEE--EEeCCCCEEEEEe
Confidence 46777799999999999988 8999999998 3 2211 1112457999999999998 9999999999999
Q ss_pred ecCCccCcccCccccccchhhhccc
Q psy4846 248 VRPVIEGFSVSSAGEQGEEKMEEGE 272 (279)
Q Consensus 248 v~~~~~~~~~~~~~~~~~~~~~~~~ 272 (279)
++- .+.+|+....+-..|+
T Consensus 89 K~v------~~~pw~~~~e~~~~g~ 107 (319)
T PTZ00248 89 KRV------SPEDIEACEEKFSKSK 107 (319)
T ss_pred eec------ccchHHHHHHhCcCCC
Confidence 872 2336666666666664
No 27
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.47 E-value=4.1e-07 Score=66.04 Aligned_cols=64 Identities=14% Similarity=0.033 Sum_probs=51.2
Q ss_pred ceEEEE-EeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 171 GYVLYV-RKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 171 g~V~~V-~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
|.|+++ .++|++|.|++ |++|+||.++ ++.+... .....|++||.|+++|. ++|+.+++|.+++
T Consensus 7 g~V~~v~~~~G~~V~l~~-gv~G~i~~s~-l~~~~~~---------~~~~~~~vG~~v~~kV~--~id~~~~~i~lS~ 71 (71)
T cd05696 7 VKVTKVEPDLGAVFELKD-GLLGFVHISH-LSDDKVP---------SDTGPFKAGTTHKARII--GYSPMDGLLQLSL 71 (71)
T ss_pred eEEEEEccCceEEEEeCC-CCEEEEEHHH-CCcchhc---------CcccccCCCCEEEEEEE--EEeCCCCEEEEeC
Confidence 677898 69999999988 8999999987 4322110 11346999999999998 9999999999875
No 28
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=98.46 E-value=5.9e-07 Score=65.47 Aligned_cols=70 Identities=11% Similarity=0.012 Sum_probs=55.2
Q ss_pred cCCcceEEEEEeCeEEEEecCc-ceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 167 QDEDGYVLYVRKNALQILIPKY-GLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 167 ~~~~g~V~~V~~~Gi~V~Lp~~-giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
+.+.|.|+++.++|++|.+.++ +++|+||.++ +..+++.. ....|++||.|+|+|. ++|..++++.|
T Consensus 5 ~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~-l~~~~~~~---------~~~~~~~Gd~v~vkv~--~~d~~~~~i~l 72 (76)
T cd04452 5 ELVVVTVKSIADMGAYVSLLEYGNIEGMILLSE-LSRRRIRS---------IRKLVKVGRKEVVKVI--RVDKEKGYIDL 72 (76)
T ss_pred CEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHH-cCCcccCC---------HHHeeCCCCEEEEEEE--EEECCCCEEEE
Confidence 3456777899999999999765 5999999997 43232111 1457999999999988 99998999999
Q ss_pred EEe
Q psy4846 246 RLV 248 (279)
Q Consensus 246 ~lv 248 (279)
++.
T Consensus 73 s~k 75 (76)
T cd04452 73 SKK 75 (76)
T ss_pred EEc
Confidence 875
No 29
>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=98.46 E-value=3.3e-07 Score=68.34 Aligned_cols=66 Identities=20% Similarity=0.202 Sum_probs=52.5
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
+.|.|.+|.++|+||.+.. +++|+||.++ ++.+++. .....|++||.|+|+|. ++|.++++|.+++
T Consensus 18 ~~g~V~~v~~~G~fv~l~~-~~~g~v~~~e-l~~~~~~---------~~~~~~~~Gd~v~vkV~--~id~~~~~i~lsl 83 (83)
T cd04461 18 VHGYVRNITPYGVFVEFLG-GLTGLAPKSY-ISDEFVT---------DPSFGFKKGQSVTAKVT--SVDEEKQRFLLSL 83 (83)
T ss_pred EEEEEEEEeeceEEEEcCC-CCEEEEEHHH-CCccccc---------CHHHhcCCCCEEEEEEE--EEcCCCCEEEEeC
Confidence 3555669999999999987 7999999998 5333210 11457999999999998 9999999999875
No 30
>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=98.44 E-value=5e-07 Score=65.54 Aligned_cols=67 Identities=18% Similarity=0.167 Sum_probs=54.1
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.+.|.|.++.++|++|.+. .+++|+||.++ ++.+ +.+ .....|++||.|+|+|. ++|..++++.|++
T Consensus 7 iv~g~V~~v~~~g~~V~l~-~~~~g~ip~~~-l~~~---~~~------~~~~~~~~G~~v~v~v~--~vd~~~~~i~lS~ 73 (74)
T PF00575_consen 7 IVEGKVTSVEDFGVFVDLG-NGIEGFIPISE-LSDD---RID------DPSEVYKIGQTVRVKVI--KVDKEKGRIRLSL 73 (74)
T ss_dssp EEEEEEEEEETTEEEEEES-TSSEEEEEGGG-SSSS---EES------SSHGTCETTCEEEEEEE--EEETTTTEEEEES
T ss_pred EEEEEEEEEECCEEEEEEC-CcEEEEEEeeh-hcCc---ccc------ccccccCCCCEEEEEEE--EEECCCCeEEEEE
Confidence 3467777999999999999 69999999998 4322 111 12457999999999998 9999999999985
No 31
>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=98.43 E-value=3.5e-07 Score=64.65 Aligned_cols=65 Identities=17% Similarity=0.086 Sum_probs=51.4
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+.|.|+++.++|+||.+.. +.+|++|.++ ++++++. .....|++||.|+|+|. ++|..++++.|+
T Consensus 4 ~~g~V~~i~~~G~fv~l~~-~~~g~~~~~~-l~~~~~~---------~~~~~~~~Gd~v~v~i~--~vd~~~~~i~ls 68 (68)
T cd05685 4 LEGVVTNVTDFGAFVDIGV-KQDGLIHISK-MADRFVS---------HPSDVVSVGDIVEVKVI--SIDEERGRISLS 68 (68)
T ss_pred EEEEEEEEecccEEEEcCC-CCEEEEEHHH-CCCcccc---------CHHHhcCCCCEEEEEEE--EEECCCCEEecC
Confidence 4567779999999999976 6999999987 5433322 11346999999999998 999988998874
No 32
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=98.37 E-value=2.2e-07 Score=73.77 Aligned_cols=68 Identities=10% Similarity=0.082 Sum_probs=54.2
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.+.|.|++|+++|+||.|+. |-.|+||++. .... |+-| -...+++||.|+|+|. ++|- +++|.|++
T Consensus 8 ~l~GkItgI~~yGAFV~l~~-g~tGLVHISE-Ia~~-fVkd--------I~d~L~vG~eV~vKVl--~ide-~GKisLSI 73 (129)
T COG1098 8 KLKGKITGITPYGAFVELEG-GKTGLVHISE-IADG-FVKD--------IHDHLKVGQEVKVKVL--DIDE-NGKISLSI 73 (129)
T ss_pred eEEEEEEeeEecceEEEecC-CCcceEEehH-hhhh-hHHh--------HHHHhcCCCEEEEEEE--eecc-CCCcceeh
Confidence 35788889999999999998 8899999997 2111 2111 1457899999999998 8887 99999999
Q ss_pred ec
Q psy4846 248 VR 249 (279)
Q Consensus 248 v~ 249 (279)
..
T Consensus 74 r~ 75 (129)
T COG1098 74 RK 75 (129)
T ss_pred HH
Confidence 74
No 33
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.34 E-value=5.3e-07 Score=88.45 Aligned_cols=83 Identities=20% Similarity=0.226 Sum_probs=68.1
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEec
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVR 249 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~ 249 (279)
.|+|.+++++|+||.|- |++|+||+++ + +|. .+......+++||.|+|+|. ++|.++++|.|++++
T Consensus 197 ~G~V~~It~~GafVdig--GvdGLlHise-i-----S~~----rv~~P~~vvkvGd~VkvkVi--~~D~e~~RVsLSlK~ 262 (541)
T COG0539 197 EGVVKNITDYGAFVDIG--GVDGLLHISE-I-----SWK----RVDHPSEVVKVGDEVKVKVI--SLDEERGRVSLSLKQ 262 (541)
T ss_pred EEEEEEeecCcEEEEec--CeeeEEehhh-c-----ccc----ccCCHHHhcccCCEEEEEEE--EEccCCCeEEEEehh
Confidence 45566999999999997 6999999998 3 111 11223568999999999998 999999999999997
Q ss_pred CCccCcccCccccccchhhhccc
Q psy4846 250 PVIEGFSVSSAGEQGEEKMEEGE 272 (279)
Q Consensus 250 ~~~~~~~~~~~~~~~~~~~~~~~ 272 (279)
+.+.+|+....+...|+
T Consensus 263 ------l~~dPw~~i~~~~~~g~ 279 (541)
T COG0539 263 ------LEEDPWEGIEKKYPVGD 279 (541)
T ss_pred ------cccCcHHHHhhhcCCCC
Confidence 66778999888888887
No 34
>PHA02945 interferon resistance protein; Provisional
Probab=98.33 E-value=3.1e-06 Score=63.39 Aligned_cols=68 Identities=18% Similarity=0.070 Sum_probs=53.9
Q ss_pred CcceEEEEEeCeEEEEecCc-ceeEEEEcccC-CCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKY-GLEGTLFLRCD-SPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~-giEG~V~l~~~-~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+-|+|.. .++|+||.|++| |+||+||.+.. .. +.|. .. ...+ .|++|.++|. ++|+.++.|++|
T Consensus 15 vigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva-~~wv--------K~-rd~l-~GqkvV~KVi--rVd~~kg~IDlS 80 (88)
T PHA02945 15 LKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHM-NRYF--------KY-RDKL-VGKTVKVKVI--RVDYTKGYIDVN 80 (88)
T ss_pred EEEEEEe-cCceEEEEecccCCcEEEEEeehhhhc-cceE--------ee-eeEe-cCCEEEEEEE--EECCCCCEEEeE
Confidence 3677778 999999999999 99999999840 11 2222 11 3356 9999999998 999999999999
Q ss_pred EecC
Q psy4846 247 LVRP 250 (279)
Q Consensus 247 lv~~ 250 (279)
|++-
T Consensus 81 lK~V 84 (88)
T PHA02945 81 YKRM 84 (88)
T ss_pred eeEc
Confidence 9864
No 35
>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=98.33 E-value=1.9e-06 Score=62.10 Aligned_cols=68 Identities=18% Similarity=0.168 Sum_probs=54.9
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
+.|.|+++.++|++|.+.. +++|+||.++ +..+++. .....|++||.|+++|. ++|..++++.|++.
T Consensus 4 v~g~V~~v~~~g~~v~l~~-~~~g~i~~~~-~~~~~~~---------~~~~~~~~Gd~v~~~v~--~~d~~~~~i~ls~k 70 (73)
T cd05691 4 VTGKVTEVDAKGATVKLGD-GVEGFLRAAE-LSRDRVE---------DATERFKVGDEVEAKIT--NVDRKNRKISLSIK 70 (73)
T ss_pred EEEEEEEEECCeEEEEeCC-CCEEEEEHHH-CCCcccc---------CHHHccCCCCEEEEEEE--EEeCCCCEEEEEEE
Confidence 4677889999999999976 6999999997 4333211 11456899999999998 99999999999987
Q ss_pred c
Q psy4846 249 R 249 (279)
Q Consensus 249 ~ 249 (279)
.
T Consensus 71 ~ 71 (73)
T cd05691 71 A 71 (73)
T ss_pred E
Confidence 5
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=98.30 E-value=1.9e-06 Score=60.90 Aligned_cols=65 Identities=14% Similarity=0.183 Sum_probs=51.2
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
+.|.|.++.++|++|.+.. +.+|++|.++ ++.++ ..+ ....|++||.|+|+|. ++|. .+++.+++
T Consensus 4 ~~g~V~~i~~~g~~v~i~~-~~~g~l~~~~-l~~~~-~~~--------~~~~~~~Gd~v~v~v~--~~~~-~~~i~ls~ 68 (69)
T cd05692 4 VEGTVTRLKPFGAFVELGG-GISGLVHISQ-IAHKR-VKD--------VKDVLKEGDKVKVKVL--SIDA-RGRISLSI 68 (69)
T ss_pred EEEEEEEEEeeeEEEEECC-CCEEEEEhHH-cCCcc-cCC--------HHHccCCCCEEEEEEE--EECC-CCcEEEEE
Confidence 4677779999999999986 7999999987 43332 111 1356899999999987 8888 88999886
No 37
>PRK05807 hypothetical protein; Provisional
Probab=98.29 E-value=3.2e-06 Score=69.30 Aligned_cols=69 Identities=13% Similarity=0.144 Sum_probs=53.8
Q ss_pred cCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 167 QDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 167 ~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+.+.|.|++|+++|+||.|+ +.+|+||+++ +..++ ..+. ...|++||.|+|+|. ++|. .++|.|+
T Consensus 7 ~vv~G~Vt~i~~~GafV~L~--~~~Glvhise-is~~~-v~~~--------~~~~kvGd~V~VkV~--~id~-~gkI~LS 71 (136)
T PRK05807 7 SILEGTVVNITNFGAFVEVE--GKTGLVHISE-VADTY-VKDI--------REHLKEQDKVKVKVI--SIDD-NGKISLS 71 (136)
T ss_pred CEEEEEEEEEECCeEEEEEC--CEEEEEEhhh-ccccc-ccCc--------cccCCCCCEEEEEEE--EECC-CCcEEEE
Confidence 44577777999999999994 6899999998 43332 2111 346899999999988 8887 7999999
Q ss_pred EecC
Q psy4846 247 LVRP 250 (279)
Q Consensus 247 lv~~ 250 (279)
+...
T Consensus 72 lk~~ 75 (136)
T PRK05807 72 IKQA 75 (136)
T ss_pred EEec
Confidence 9763
No 38
>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=98.28 E-value=1.8e-06 Score=61.81 Aligned_cols=63 Identities=13% Similarity=0.066 Sum_probs=50.8
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
++|.|+.+.++|++|.|.+ +++|+|+.++ +..+. . ....|++||.|+++|. .+|+.+++|.|+
T Consensus 4 V~g~V~~i~~~G~~v~l~~-~v~g~v~~~~-l~~~~-------~----~~~~~~~G~~i~~kVi--~id~~~~~i~LS 66 (66)
T cd05695 4 VNARVKKVLSNGLILDFLS-SFTGTVDFLH-LDPEK-------S----SKSTYKEGQKVRARIL--YVDPSTKVVGLS 66 (66)
T ss_pred EEEEEEEEeCCcEEEEEcC-CceEEEEHHH-cCCcc-------C----cccCcCCCCEEEEEEE--EEeCCCCEEecC
Confidence 5788889999999999987 8999999987 32111 0 0346999999999998 999999988764
No 39
>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=98.28 E-value=2.9e-06 Score=62.56 Aligned_cols=59 Identities=19% Similarity=0.077 Sum_probs=49.5
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.++|.|.+++++|+||.+.+ +.+|++|.++ . ...|++||.|+|+|. ++ .++++|+|++
T Consensus 19 ~~~g~V~~i~~~G~fV~l~~-~~~Glv~~se-~-----------------~~~~~iGd~v~v~I~--~i-~e~~~i~l~~ 76 (77)
T cd04473 19 LYKGKVNGVAKYGVFVDLND-HVRGLIHRSN-L-----------------LRDYEVGDEVIVQVT--DI-PENGNIDLIP 76 (77)
T ss_pred EEEEEEEeEecceEEEEECC-CcEEEEEchh-c-----------------cCcCCCCCEEEEEEE--EE-CCCCcEEEEE
Confidence 34666669999999999987 6999999986 2 235899999999998 88 7899999987
Q ss_pred e
Q psy4846 248 V 248 (279)
Q Consensus 248 v 248 (279)
+
T Consensus 77 ~ 77 (77)
T cd04473 77 V 77 (77)
T ss_pred C
Confidence 4
No 40
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.27 E-value=3.8e-06 Score=86.83 Aligned_cols=65 Identities=18% Similarity=0.075 Sum_probs=52.8
Q ss_pred ceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEec
Q psy4846 171 GYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVR 249 (279)
Q Consensus 171 g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~ 249 (279)
|.|++|.++|+||.|.. |+||+||+++ +..+++.+. ...|++||.|+|+|. ++|. +++|.|+++.
T Consensus 760 g~V~~I~~FGaFVeL~~-g~EGLVHISe-Ls~~rv~~~---------~dv~kvGD~V~VkVi--~ID~-~grI~LSlK~ 824 (891)
T PLN00207 760 CEIKSIAPYGAFVEIAP-GREGLCHISE-LSSNWLAKP---------EDAFKVGDRIDVKLI--EVND-KGQLRLSRRA 824 (891)
T ss_pred cEEEEEeccEEEEEeCC-CCEEEEEhhh-cCCccccCH---------HHhcCCCCEEEEEEE--EECC-CCcEEEEEec
Confidence 45669999999999976 7999999998 543333221 357999999999998 9997 7899999975
No 41
>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=98.27 E-value=2.2e-06 Score=60.76 Aligned_cols=65 Identities=15% Similarity=0.130 Sum_probs=50.7
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
+.|.|..+.++|++|.++. +.+|+++.++ ++.+++. .....|++||.|+|+|. ++|+ .+++.|++
T Consensus 4 ~~g~V~~v~~~G~~v~l~~-~~~g~l~~~~-l~~~~~~---------~~~~~~~~Gd~v~v~v~--~~d~-~~~i~ls~ 68 (68)
T cd04472 4 YEGKVVKIKDFGAFVEILP-GKDGLVHISE-LSDERVE---------KVEDVLKVGDEVKVKVI--EVDD-RGRISLSR 68 (68)
T ss_pred EEEEEEEEEEeEEEEEeCC-CCEEEEEhHH-cCCcccc---------CHHHccCCCCEEEEEEE--EECC-CCcEEeeC
Confidence 4566779999999999986 6999999987 4323210 11357999999999988 8998 88998873
No 42
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.23 E-value=2.6e-06 Score=77.13 Aligned_cols=72 Identities=18% Similarity=0.094 Sum_probs=59.1
Q ss_pred ccCCcceEEEEEeCeEEEEecCc-ceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKY-GLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLV 244 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~-giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~ 244 (279)
...+.|.|++|.++|+||.|.+| |++|+||+++ +..+++.. ....+++||.|.|+|. ++|..+++|.
T Consensus 9 GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSE-ls~~~i~~---------i~~~~kvGd~V~vkVi--~VD~~k~~I~ 76 (262)
T PRK03987 9 GELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISE-VASGWVKN---------IRDHVKEGQKVVCKVI--RVDPRKGHID 76 (262)
T ss_pred CCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHH-cCcccccC---------HHHhCCCCCEEEEEEE--EEecccCeEE
Confidence 34567888899999999999998 8999999998 43333211 1347899999999998 9999999999
Q ss_pred EEEec
Q psy4846 245 LRLVR 249 (279)
Q Consensus 245 ~~lv~ 249 (279)
|++..
T Consensus 77 LSlK~ 81 (262)
T PRK03987 77 LSLKR 81 (262)
T ss_pred EEEEe
Confidence 99985
No 43
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.21 E-value=5.4e-06 Score=70.47 Aligned_cols=79 Identities=19% Similarity=0.176 Sum_probs=66.7
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeec--CeEecCCCeEEEEEEeccccC-----CC
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCG--SVVFHSFDPVTVQLSLDRSNV-----QH 240 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~--~~~~~lGD~V~VkV~~~~vd~-----~~ 240 (279)
.++|.|+.+.++|+||.+- .++|+||.+. .++|++.||+....+++. ++.++.||.|++||. .++. ..
T Consensus 84 VV~GeVv~~~~~G~fV~ig--p~dglvh~sq-i~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv--~~s~~~~~~~~ 158 (183)
T COG1095 84 VVEGEVVEVVEFGAFVRIG--PLDGLVHVSQ-IMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIV--GVSLKSRRPRE 158 (183)
T ss_pred EEEEEEEEEeecceEEEec--cccccccHhh-ccCcccccCcccceeeecccceEEecCCEEEEEEE--EEecccCcccc
Confidence 3699999999999999997 6899999998 788899999999998886 568999999999997 4333 33
Q ss_pred CeEEEEEecCC
Q psy4846 241 EKLVLRLVRPV 251 (279)
Q Consensus 241 ~~I~~~lv~~~ 251 (279)
-+|.+.+.+|.
T Consensus 159 ~~I~lTmrq~~ 169 (183)
T COG1095 159 SKIGLTMRQPG 169 (183)
T ss_pred ceEEEEecccc
Confidence 67888888764
No 44
>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=98.19 E-value=4.6e-06 Score=58.97 Aligned_cols=65 Identities=17% Similarity=0.149 Sum_probs=50.3
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
.+.|.|+++.++|++|.+. +++|++|.++ +... + ....+..|++||.|+|+|. ++|..++++.|+
T Consensus 4 ~~~g~V~~v~~~g~~v~l~--~~~g~l~~~e-~~~~---~------~~~~~~~~~~Gd~v~v~i~--~vd~~~~~i~ls 68 (68)
T cd05688 4 VVEGTVKSITDFGAFVDLG--GVDGLLHISD-MSWG---R------VKHPSEVVNVGDEVEVKVL--KIDKERKRISLG 68 (68)
T ss_pred EEEEEEEEEEeeeEEEEEC--CeEEEEEhHH-CCCc---c------ccCHhHEECCCCEEEEEEE--EEECCCCEEecC
Confidence 3467777999999999996 6999999987 4211 1 1112457999999999998 999999998874
No 45
>PRK08059 general stress protein 13; Validated
Probab=98.18 E-value=4.8e-06 Score=67.02 Aligned_cols=71 Identities=11% Similarity=0.044 Sum_probs=56.5
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.+.|.|+++.++|++|.+.. +++|+||.++ ++.++ ..+ ....|++||.|+|+|. ++|...+++.|++
T Consensus 10 iv~G~V~~i~~~G~fV~i~~-~~~Gli~~se-l~~~~-~~~--------~~~~~~vGD~I~vkI~--~id~~~~~i~lsl 76 (123)
T PRK08059 10 VVTGKVTGIQPYGAFVALDE-ETQGLVHISE-ITHGF-VKD--------IHDFLSVGDEVKVKVL--SVDEEKGKISLSI 76 (123)
T ss_pred EEEEEEEEEecceEEEEECC-CCEEEEEHHH-CCccc-ccC--------HHHcCCCCCEEEEEEE--EEECCCCeEEEEE
Confidence 34666779999999999986 8999999998 54332 111 1347899999999998 9999999999999
Q ss_pred ecCC
Q psy4846 248 VRPV 251 (279)
Q Consensus 248 v~~~ 251 (279)
.+..
T Consensus 77 k~~~ 80 (123)
T PRK08059 77 RATE 80 (123)
T ss_pred EEcc
Confidence 8753
No 46
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.17 E-value=2.4e-06 Score=83.89 Aligned_cols=71 Identities=21% Similarity=0.271 Sum_probs=59.4
Q ss_pred cCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 167 QDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 167 ~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
..+.|+|+.++++|+||.+.. |+||+||+++ + .|..... .+..+++||.|.|+|. ++|+++++|.++
T Consensus 279 ~~v~G~Vt~i~~~GafVei~~-GvEGlvhvSE-i---sw~~~~~------P~evv~~Gq~V~V~Vl--~id~e~rRIsL~ 345 (541)
T COG0539 279 DKVEGKVTNLTDYGAFVEIEE-GVEGLVHVSE-I---SWTKKNV------PSEVVKVGQEVEVKVL--DIDPERRRISLG 345 (541)
T ss_pred CEEEEEEEEeecCcEEEEecC-Cccceeechh-h---cccccCC------HHHhcccCCEEEEEEE--eeCchhceEEee
Confidence 457999999999999999988 9999999997 2 1222111 3568999999999999 999999999999
Q ss_pred EecC
Q psy4846 247 LVRP 250 (279)
Q Consensus 247 lv~~ 250 (279)
+.+.
T Consensus 346 iKq~ 349 (541)
T COG0539 346 LKQL 349 (541)
T ss_pred ehhh
Confidence 9974
No 47
>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=98.13 E-value=1.2e-05 Score=59.01 Aligned_cols=63 Identities=13% Similarity=-0.016 Sum_probs=53.1
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
+.|.|.+|.++|++|.+..-|++|+++.++ .. + ...+++||.|.++|. ++|..++++.+++.
T Consensus 8 v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~-~~-----~----------~~~~~~Gq~v~~~V~--~vd~~~~~v~ls~k 69 (74)
T cd05694 8 LSGCVSSVEDHGYILDIGIPGTTGFLPKKD-AG-----N----------FSKLKVGQLLLCVVE--KVKDDGRVVSLSAD 69 (74)
T ss_pred EEEEEEEEeCCEEEEEeCCCCcEEEEEHHH-CC-----c----------ccccCCCCEEEEEEE--EEECCCCEEEEEEe
Confidence 578888999999999995338999999987 31 1 146899999999998 99999999999987
Q ss_pred c
Q psy4846 249 R 249 (279)
Q Consensus 249 ~ 249 (279)
.
T Consensus 70 ~ 70 (74)
T cd05694 70 P 70 (74)
T ss_pred e
Confidence 5
No 48
>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=98.12 E-value=9.4e-06 Score=56.17 Aligned_cols=64 Identities=20% Similarity=0.241 Sum_probs=49.8
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
.|.|..+.++|++|.+.. +++|+++.++ ...+++ ......|++||.|+|+|. ++|..++++.++
T Consensus 2 ~g~V~~v~~~g~~v~l~~-~~~g~~~~~~-~~~~~~---------~~~~~~~~~G~~v~~~v~--~~d~~~~~i~ls 65 (65)
T cd00164 2 TGKVVSITKFGVFVELED-GVEGLVHISE-LSDKFV---------KDPSEVFKVGDEVEVKVL--EVDPEKGRISLS 65 (65)
T ss_pred EEEEEEEEeeeEEEEecC-CCEEEEEHHH-CCCccc---------cCHhhEeCCCCEEEEEEE--EEcCCcCEEecC
Confidence 467779999999999985 7999999987 432322 011457999999999998 899888888764
No 49
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.08 E-value=2.4e-05 Score=67.30 Aligned_cols=85 Identities=18% Similarity=0.184 Sum_probs=69.1
Q ss_pred CCCcccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeec--CeEecCCCeEEEEEEeccccCC
Q psy4846 162 PKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCG--SVVFHSFDPVTVQLSLDRSNVQ 239 (279)
Q Consensus 162 p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~--~~~~~lGD~V~VkV~~~~vd~~ 239 (279)
|+ ....++|.|+++.++|++|.+. .++|+++.++ ++.+.+.||+.+....+. +..+++||.|+|+|. +++..
T Consensus 79 P~-~GEVv~g~V~~v~~~Gi~V~lg--~~~g~v~~~~-l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~--~v~~~ 152 (187)
T PRK08563 79 PE-LQEVVEGEVVEVVEFGAFVRIG--PVDGLLHISQ-IMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIV--AVSLK 152 (187)
T ss_pred cc-CCCEEEEEEEEEEccEEEEEEe--CceEEEEcHH-cCCCceEEccccceEEEccCCeEEcCCCEEEEEEE--EEEcc
Confidence 44 3456799999999999999996 4899999998 666778999988888765 568999999999998 77764
Q ss_pred C-----CeEEEEEecCCc
Q psy4846 240 H-----EKLVLRLVRPVI 252 (279)
Q Consensus 240 ~-----~~I~~~lv~~~~ 252 (279)
. .+|.+++.++..
T Consensus 153 ~~~~~~~~I~ls~~~~~L 170 (187)
T PRK08563 153 ERRPRGSKIGLTMRQPGL 170 (187)
T ss_pred cCCCCCCEEEEEecCCCC
Confidence 3 378888887643
No 50
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.06 E-value=1.3e-05 Score=78.50 Aligned_cols=71 Identities=17% Similarity=0.146 Sum_probs=58.7
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
.+.+.|.|+++.++|+||.|++ |++|+||.++ ++.+.+. .....|++||.|+|+|. ++|.++++|.|
T Consensus 294 G~vv~G~V~~I~~fGvFVeL~~-gieGLvh~Se-Ls~~~v~---------~~~~~~kvGd~V~VkIi--~ID~e~rrI~L 360 (486)
T PRK07899 294 GQIVPGKVTKLVPFGAFVRVEE-GIEGLVHISE-LAERHVE---------VPEQVVQVGDEVFVKVI--DIDLERRRISL 360 (486)
T ss_pred CCEEEEEEEEEeccEEEEEeCC-CcEEEEEHHH-cCccccc---------CccceeCCCCEEEEEEE--EEECCCCEEEE
Confidence 3457999999999999999987 8999999997 5333221 12457999999999998 99999999999
Q ss_pred EEec
Q psy4846 246 RLVR 249 (279)
Q Consensus 246 ~lv~ 249 (279)
+++.
T Consensus 361 SlK~ 364 (486)
T PRK07899 361 SLKQ 364 (486)
T ss_pred EEEE
Confidence 9975
No 51
>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=98.06 E-value=8.7e-06 Score=59.19 Aligned_cols=65 Identities=22% Similarity=0.161 Sum_probs=48.9
Q ss_pred CCcceEEEEEe-CeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 168 DEDGYVLYVRK-NALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 168 ~~~g~V~~V~~-~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
.+.|.|+.+.+ +|++|.++. +.+|++|+++ ..++ |... ....|++||.|+|+|. +++. ++|.|+
T Consensus 6 iv~G~V~~i~~~~g~~v~l~~-~~~Glvhis~-~s~~---~~~~------~~~~~~~Gd~v~~kV~--~~~~--~~i~LS 70 (72)
T cd05704 6 VTLGMVTKVIPHSGLTVQLPF-GKTGLVSIFH-LSDS---YTEN------PLEGFKPGKIVRCCIL--SKKD--GKYQLS 70 (72)
T ss_pred EEEEEEEEeeCCcEEEEECCC-CCEEEEEHHH-hcCc---ccCC------HHHhCCCCCEEEEEEE--EecC--CEEEEE
Confidence 34677779986 899999987 8999999997 3222 1111 1346899999999998 7763 789888
Q ss_pred E
Q psy4846 247 L 247 (279)
Q Consensus 247 l 247 (279)
+
T Consensus 71 l 71 (72)
T cd05704 71 L 71 (72)
T ss_pred e
Confidence 6
No 52
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.05 E-value=1.3e-05 Score=56.43 Aligned_cols=67 Identities=16% Similarity=0.168 Sum_probs=52.4
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.+.|.|.+++++|++|.+.. +++|+++.++ ++..+ .. .....|++||.|+|+|. +++..++++.+++
T Consensus 5 ~v~g~V~~v~~~g~~v~i~~-~~~g~l~~~~-~~~~~---~~------~~~~~~~~G~~v~~~V~--~~~~~~~~i~ls~ 71 (72)
T smart00316 5 VVEGTVTEITPFGAFVDLGN-GVEGLIPISE-LSDKR---VK------DPEEVLKVGDEVKVKVL--SVDEEKGRIILSL 71 (72)
T ss_pred EEEEEEEEEEccEEEEEeCC-CCEEEEEHHH-CCccc---cC------CHHHeecCCCEEEEEEE--EEeCCCCEEEEEe
Confidence 34677779999999999986 7999999987 43221 00 01346999999999998 9998889999886
No 53
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.04 E-value=7.5e-06 Score=80.57 Aligned_cols=88 Identities=16% Similarity=0.186 Sum_probs=65.4
Q ss_pred cCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 167 QDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 167 ~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+.+.|.|+++.++|+||.+.. |++|+||+++ ++ |.. ........|++||.|+|+|. ++|+++++|.++
T Consensus 294 ~~v~G~V~~v~~~G~fV~l~~-gv~Glvh~se-ls-----~~~---~~~~~~~~~~~Gd~v~vkVl--~iD~e~~ri~Ls 361 (491)
T PRK13806 294 DKVTGKVVRLAPFGAFVEILP-GIEGLVHVSE-MS-----WTR---RVNKPEDVVAPGDAVAVKIK--DIDPAKRRISLS 361 (491)
T ss_pred CEEEEEEEEEeCceEEEEeCC-CcEEEEEHHH-cC-----ccc---ccCCHHHcCCCCCEEEEEEE--EEEccCCEEEEE
Confidence 456889999999999999976 8999999987 42 211 01111457999999999998 999999999999
Q ss_pred EecCCccCcccCccccccchhhhccc
Q psy4846 247 LVRPVIEGFSVSSAGEQGEEKMEEGE 272 (279)
Q Consensus 247 lv~~~~~~~~~~~~~~~~~~~~~~~~ 272 (279)
+.+. .+.+|+....+...|.
T Consensus 362 ~K~~------~~~p~~~~~~~~~vG~ 381 (491)
T PRK13806 362 LRDA------EGDPWADVAERFAPGT 381 (491)
T ss_pred Eeec------ccChhHHhhhhCCCCC
Confidence 9863 3345555555555553
No 54
>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=97.96 E-value=2.2e-05 Score=56.26 Aligned_cols=66 Identities=20% Similarity=0.136 Sum_probs=51.3
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
+.|.|..+.++|++|.|.. +.+|++|.++ +...+ . ......|++||.|+++|. ++|...++|.|++
T Consensus 4 v~g~V~~i~~~~~~v~l~~-~~~g~l~~~e-~~~~~-~--------~~~~~~~~~Gd~i~~~i~--~~~~~~~~i~lS~ 69 (70)
T cd05687 4 VKGTVVSVDDDEVLVDIGY-KSEGIIPISE-FSDDP-I--------ENGEDEVKVGDEVEVYVL--RVEDEEGNVVLSK 69 (70)
T ss_pred EEEEEEEEeCCEEEEEeCC-CceEEEEHHH-hCccc-c--------CCHhHcCCCCCEEEEEEE--EEECCCCeEEEEe
Confidence 4678889999999999965 7999999987 32111 0 011346899999999998 8888888999886
No 55
>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=97.96 E-value=1.1e-05 Score=62.67 Aligned_cols=78 Identities=18% Similarity=0.139 Sum_probs=55.6
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecC--------CceEee--cCeEecCCCeEEEEEEecccc
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEK--------EQSQSC--GSVVFHSFDPVTVQLSLDRSN 237 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~--------~~~l~~--~~~~~~lGD~V~VkV~~~~vd 237 (279)
.+.|.|..|.++|++|.||. |++|+|++++ ..+++-.+... ...... ....|++||.|+++|. ++|
T Consensus 6 vV~G~V~~v~~~gl~v~L~~-g~~G~v~~se-is~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi--~~d 81 (100)
T cd05693 6 LVLGQVKEITKLDLVISLPN-GLTGYVPITN-ISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVV--SLD 81 (100)
T ss_pred EEEEEEEEEcCCCEEEECCC-CcEEEEEHHH-hhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEE--Ecc
Confidence 35688889999999999997 9999999987 42221111000 000111 1356999999999998 899
Q ss_pred CC---CCeEEEEEec
Q psy4846 238 VQ---HEKLVLRLVR 249 (279)
Q Consensus 238 ~~---~~~I~~~lv~ 249 (279)
.. +++|.+++..
T Consensus 82 ~~~~~~~~i~LSlr~ 96 (100)
T cd05693 82 KSKSGKKRIELSLEP 96 (100)
T ss_pred CCcCCCcEEEEEecH
Confidence 87 7899999863
No 56
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.95 E-value=1.2e-05 Score=83.58 Aligned_cols=73 Identities=10% Similarity=0.110 Sum_probs=58.1
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
.+.++|+|++++++|+||.|.+ |++|+||.++ + +|..... .....|++||.|+|+|. ++|+++++|.|
T Consensus 666 G~~v~G~V~~i~~~G~fV~l~~-gV~GlIh~se-l-----s~~~~~~---~~~~~~kvGq~VkvkVl--~ID~e~rrI~L 733 (863)
T PRK12269 666 GARFTRRIVKVTNAGAFIEMEE-GIDGFLHVDD-L-----SWVKRTR---PADHELEVGKEIECMVI--ECDPQARRIRL 733 (863)
T ss_pred CCEEEEEEEEEecceEEEEeCC-CcEEEEEhHH-h-----hcccccc---chhhccCCCCEEEEEEE--EEeccCCEEEE
Confidence 3457899999999999999986 9999999987 3 2211100 01346999999999998 99999999999
Q ss_pred EEecC
Q psy4846 246 RLVRP 250 (279)
Q Consensus 246 ~lv~~ 250 (279)
++++.
T Consensus 734 S~K~l 738 (863)
T PRK12269 734 GVKQL 738 (863)
T ss_pred Eeccc
Confidence 99863
No 57
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.91 E-value=1.9e-05 Score=77.45 Aligned_cols=66 Identities=18% Similarity=0.218 Sum_probs=52.3
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEec
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVR 249 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~ 249 (279)
.|+|++++++|+||.|. |++|+||.++ +. |.. .......|++||.|+|+|. ++|..+++|.|+++.
T Consensus 213 ~G~V~~i~~~G~FVdlg--gv~Glv~~Se-ls-----~~~----v~~~~~~~kvGd~V~vkVl--~iD~e~~rI~LSlK~ 278 (486)
T PRK07899 213 KGVVSSIVNFGAFVDLG--GVDGLVHVSE-LS-----WKH----IDHPSEVVEVGQEVTVEVL--DVDMDRERVSLSLKA 278 (486)
T ss_pred EEEEEEEECCeEEEEEC--CEEEEEEHHH-CC-----Ccc----cCCHHHhcCCCCEEEEEEE--EEECCCCEEEEEEee
Confidence 55556999999999995 7999999998 42 111 1111356899999999998 999999999999986
No 58
>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=97.90 E-value=2.2e-05 Score=58.78 Aligned_cols=76 Identities=12% Similarity=-0.033 Sum_probs=55.4
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
.+.+.|.|+++.++|++|.+.. +.+|++|.++ +..+.. +.. .......+++||.|+++|. +++.. +++.|
T Consensus 7 GdiV~g~V~~i~~~g~~v~i~~-~~~G~l~~se-~~~~~~--~~~---~~~~~~~l~vGd~i~~~V~--~~~~~-~~i~L 76 (86)
T cd05789 7 GDVVIGRVTEVGFKRWKVDINS-PYDAVLPLSE-VNLPRT--DED---ELNMRSYLDEGDLIVAEVQ--SVDSD-GSVSL 76 (86)
T ss_pred CCEEEEEEEEECCCEEEEECCC-CeEEEEEHHH-ccCCCC--ccc---hHHHHhhCCCCCEEEEEEE--EECCC-CCEEE
Confidence 3456788889999999999975 8999999987 321100 000 0001346899999999998 88775 89999
Q ss_pred EEecCC
Q psy4846 246 RLVRPV 251 (279)
Q Consensus 246 ~lv~~~ 251 (279)
++..++
T Consensus 77 S~~~~~ 82 (86)
T cd05789 77 HTRSLK 82 (86)
T ss_pred EeCccc
Confidence 998764
No 59
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.82 E-value=4.1e-05 Score=79.72 Aligned_cols=75 Identities=17% Similarity=0.147 Sum_probs=60.1
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
.+.++|.|++++++|+||.|++ |++|+||+++ +++++ ..+... ....|++||.|+|+|. ++|+.+++|.|
T Consensus 753 G~iV~GkV~~v~~~GvFVeL~~-gVeGlI~~s~-lsdd~-~~~~~~-----~~~~f~vGD~V~v~Vl--~iD~~~rkI~L 822 (863)
T PRK12269 753 GSTVEGEVSSVTDFGIFVRVPG-GVEGLVRKQH-LVENR-DGDPGE-----ALRKYAVGDRVKAVIV--DMNVKDRKVAF 822 (863)
T ss_pred CCEEEEEEEEEecCeEEEEcCC-CeEEEEEHHH-cCCcc-cccchh-----hccccCCCCEEEEEEE--EEEcCCCEEEE
Confidence 4567999999999999999998 8999999998 54332 111100 1357999999999998 99999999999
Q ss_pred EEecC
Q psy4846 246 RLVRP 250 (279)
Q Consensus 246 ~lv~~ 250 (279)
++...
T Consensus 823 Slk~~ 827 (863)
T PRK12269 823 SVRDY 827 (863)
T ss_pred EEech
Confidence 99854
No 60
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.81 E-value=4.9e-05 Score=70.82 Aligned_cols=70 Identities=19% Similarity=0.158 Sum_probs=56.9
Q ss_pred cCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 167 QDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 167 ~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+.+.|.|++|+++|+||.+. |++|+||.++ ++.++ .. .....|++||.|+|+|. ++|..+++|.|+
T Consensus 198 ~vv~G~V~~I~~~G~fV~i~--gv~Gllhise-ls~~~---~~------~~~~~~~vGd~VkvkVl--~iD~e~~rI~LS 263 (318)
T PRK07400 198 EVVVGTVRGIKPYGAFIDIG--GVSGLLHISE-ISHEH---IE------TPHSVFNVNDEMKVMII--DLDAERGRISLS 263 (318)
T ss_pred CEEEEEEEEEECCeEEEEEC--CEEEEEEHHH-ccccc---cc------ChhhccCCCCEEEEEEE--EEeCCCCEEEEE
Confidence 45799999999999999995 8999999998 42221 11 12457999999999998 999999999999
Q ss_pred EecC
Q psy4846 247 LVRP 250 (279)
Q Consensus 247 lv~~ 250 (279)
+...
T Consensus 264 ~K~l 267 (318)
T PRK07400 264 TKQL 267 (318)
T ss_pred Eecc
Confidence 9864
No 61
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.80 E-value=1.7e-05 Score=70.82 Aligned_cols=69 Identities=17% Similarity=0.094 Sum_probs=56.2
Q ss_pred cceEEEEEeCeEEEEecCcc-eeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 170 DGYVLYVRKNALQILIPKYG-LEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~g-iEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
-|+|..|.++|+||.|.+|+ +||+||++. ....| . ..-...++.|++|-++|. +||+.++.|++||.
T Consensus 16 v~tV~~V~~~GAyv~L~EY~g~Eg~ihiSE-vas~w-V--------knIrd~vkegqkvV~kVl--rVd~~rg~IDLSlk 83 (269)
T COG1093 16 VGTVKQVADYGAYVELDEYPGKEGFIHISE-VASGW-V--------KNIRDYVKEGQKVVAKVL--RVDPKRGHIDLSLK 83 (269)
T ss_pred EEEEEEeeccccEEEeeccCCeeeeEEHHH-HHHHH-H--------HHHHHHhhcCCeEEEEEE--EEcCCCCeEeeehh
Confidence 47788999999999999998 999999997 21111 1 011457899999999998 99999999999998
Q ss_pred cC
Q psy4846 249 RP 250 (279)
Q Consensus 249 ~~ 250 (279)
.-
T Consensus 84 rV 85 (269)
T COG1093 84 RV 85 (269)
T ss_pred hC
Confidence 64
No 62
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.78 E-value=4.1e-05 Score=76.54 Aligned_cols=89 Identities=15% Similarity=0.152 Sum_probs=64.9
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
.+.+.|.|++++++|+||.|++ +++|+||+++ ++. .+.. ......|++||.|+|+|. .+|..+++|.|
T Consensus 374 G~~v~g~V~~v~~~G~fV~l~~-~v~g~i~~s~-l~~---~~~~-----~~~~~~~~~Gd~v~v~Il--~vd~~~~~i~l 441 (565)
T PRK06299 374 GDVVEGKVKNITDFGAFVGLEG-GIDGLVHLSD-ISW---DKKG-----EEAVELYKKGDEVEAVVL--KVDVEKERISL 441 (565)
T ss_pred CCEEEEEEEEEecceEEEECCC-CCEEEEEHHH-cCc---cccc-----cChHhhCCCCCEEEEEEE--EEeCCCCEEEE
Confidence 4567888999999999999987 8999999998 431 1110 011457999999999998 99999999999
Q ss_pred EEecCCccCcccCccccccchhhhccc
Q psy4846 246 RLVRPVIEGFSVSSAGEQGEEKMEEGE 272 (279)
Q Consensus 246 ~lv~~~~~~~~~~~~~~~~~~~~~~~~ 272 (279)
++.... ..++.+......+|+
T Consensus 442 s~k~~~------~~p~~~~~~~~~~G~ 462 (565)
T PRK06299 442 GIKQLE------EDPFEEFAKKHKKGS 462 (565)
T ss_pred EEehhh------cCchhHHHhhcCCCC
Confidence 998632 234444444445554
No 63
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.74 E-value=5e-05 Score=74.78 Aligned_cols=72 Identities=17% Similarity=0.105 Sum_probs=58.3
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
.+.+.|.|++++++|+||.+.+ |++|+||.++ ++ ++.. ......+++||.|+|+|. ++|+++++|.|
T Consensus 380 G~~v~G~V~~i~~~G~FV~l~~-gv~Gli~~se-~s-----~~~~----~~~~~~~~~Gd~v~~~V~--~id~e~~ri~L 446 (491)
T PRK13806 380 GTTVTGTVEKRAQFGLFVNLAP-GVTGLLPASV-IS-----RAGK----PATYEKLKPGDSVTLVVE--EIDTAKRKISL 446 (491)
T ss_pred CCEEEEEEEEEecCceEEEcCC-CcEEEEEHHH-cC-----cccc----cchhhcCCCCCEEEEEEE--EEeCCCCEEEE
Confidence 3567999999999999999987 9999999987 32 1111 111357899999999998 99999999999
Q ss_pred EEecC
Q psy4846 246 RLVRP 250 (279)
Q Consensus 246 ~lv~~ 250 (279)
++...
T Consensus 447 s~~~~ 451 (491)
T PRK13806 447 APAGA 451 (491)
T ss_pred Eeehh
Confidence 99853
No 64
>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=97.70 E-value=6.8e-05 Score=74.04 Aligned_cols=72 Identities=10% Similarity=0.225 Sum_probs=58.3
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
.+.+.|.|++++++|+||.+.. |++|+||+++ ++ |.+... .....|++||.|.|+|. .+|..+++|.+
T Consensus 360 G~~v~g~V~~v~~~G~fV~l~~-~v~glv~~s~-ls---~~~~~~-----~~~~~~~~G~~V~~~Vl--~vd~~~~~i~l 427 (516)
T TIGR00717 360 GDRVTGKIKKITDFGAFVELEG-GIDGLIHLSD-IS---WDKDGR-----EADHLYKKGDEIEAVVL--AVDKEKKRISL 427 (516)
T ss_pred CCEEEEEEEEEecceEEEECCC-CCEEEEEHHH-Cc---CcccCC-----CHhHccCCCCEEEEEEE--EEeCcCCEEEE
Confidence 4567899999999999999986 8999999988 42 222111 11357999999999998 99999999999
Q ss_pred EEec
Q psy4846 246 RLVR 249 (279)
Q Consensus 246 ~lv~ 249 (279)
++..
T Consensus 428 s~K~ 431 (516)
T TIGR00717 428 GVKQ 431 (516)
T ss_pred eecc
Confidence 9986
No 65
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.69 E-value=9.5e-05 Score=70.53 Aligned_cols=72 Identities=15% Similarity=0.135 Sum_probs=57.9
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
...+.|.|+++.++|+||.+++ |++|++|.++ ++... .......|++||.|+|+|. ++|.++++|.|
T Consensus 278 G~~v~g~V~~i~~~G~fV~l~~-gi~Glv~~se-~~~~~---------~~~~~~~~~~Gd~v~v~V~--~id~e~~~i~l 344 (390)
T PRK06676 278 GDVIEGTVKRLTDFGAFVEVLP-GVEGLVHISQ-ISHKH---------IATPSEVLEEGQEVKVKVL--EVNEEEKRISL 344 (390)
T ss_pred CcEEEEEEEEEeCceEEEEECC-CCeEEEEhHH-cCccc---------cCChhhccCCCCEEEEEEE--EEECCCCEEEE
Confidence 3457999999999999999976 8999999987 42111 1111456999999999998 99999999999
Q ss_pred EEecC
Q psy4846 246 RLVRP 250 (279)
Q Consensus 246 ~lv~~ 250 (279)
++...
T Consensus 345 s~k~~ 349 (390)
T PRK06676 345 SIKAL 349 (390)
T ss_pred EEEec
Confidence 99864
No 66
>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=97.69 E-value=0.00012 Score=52.05 Aligned_cols=63 Identities=16% Similarity=0.072 Sum_probs=48.1
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
+.|.|+.+.++|++|.+ + |++|+||.+. +...+ .. ...-.+||.++|+|. ++|...++|.++.
T Consensus 4 v~g~V~~v~~~G~~v~l-~-g~~gfip~s~-~~~~~---~~--------~~~~~vG~~i~~~i~--~vd~~~~~i~lS~ 66 (67)
T cd04465 4 VEGKVTEKVKGGLIVDI-E-GVRAFLPASQ-VDLRP---VE--------DLDEYVGKELKFKII--EIDRERNNIVLSR 66 (67)
T ss_pred EEEEEEEEECCeEEEEE-C-CEEEEEEHHH-CCCcc---cC--------ChHHhCCCEEEEEEE--EEeCCCCEEEEEc
Confidence 46778899999999999 4 8999999987 32111 00 111148999999998 9999899999875
No 67
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.67 E-value=6.4e-05 Score=76.21 Aligned_cols=75 Identities=16% Similarity=0.099 Sum_probs=63.4
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.+.|+|.+|.++|+||.|-- ..+|+||++. +. +.|.++| ..++++||.|+|+|. ++|..+++|.+++
T Consensus 661 ~leg~Vrnv~~fgafVdIgv-~qDglvHis~-ls-~~fv~~P--------~~vv~vGdiV~v~V~--~vD~~r~rI~Lsm 727 (780)
T COG2183 661 ILEGTVRNVVDFGAFVDIGV-HQDGLVHISQ-LS-DKFVKDP--------NEVVKVGDIVKVKVI--EVDTARKRIALSM 727 (780)
T ss_pred EEEEEEEEeeeccceEEecc-ccceeeeHHH-hh-hhhcCCh--------HHhcccCCEEEEEEE--EEecccCeeeeEe
Confidence 45899999999999999965 7889999997 32 4455555 347899999999998 9999999999999
Q ss_pred ecCCccCc
Q psy4846 248 VRPVIEGF 255 (279)
Q Consensus 248 v~~~~~~~ 255 (279)
..+..++.
T Consensus 728 r~~~~~~~ 735 (780)
T COG2183 728 RLDEEEGK 735 (780)
T ss_pred eccCCccc
Confidence 99887766
No 68
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.63 E-value=0.00014 Score=74.50 Aligned_cols=70 Identities=14% Similarity=0.071 Sum_probs=55.7
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
...+.|.|++|.++|+||.|.. +.+|+||+++ ++.+++ ......|++||.|+|+|. ++|.. ++|.|
T Consensus 622 G~v~~G~V~~I~~fGafVei~~-~~~GllhiSe-ls~~~v---------~~~~~v~kvGD~V~VkV~--~iD~~-grI~L 687 (693)
T PRK11824 622 GEIYEGKVVRIVDFGAFVEILP-GKDGLVHISE-IADERV---------EKVEDVLKEGDEVKVKVL--EIDKR-GRIRL 687 (693)
T ss_pred CeEEEEEEEEEECCeEEEEECC-CCEEEEEeee-ccCccc---------cCccceeCCCCEEEEEEE--EECCC-CcEEE
Confidence 3456888889999999999986 8999999998 432221 112467999999999998 99986 99999
Q ss_pred EEec
Q psy4846 246 RLVR 249 (279)
Q Consensus 246 ~lv~ 249 (279)
+++.
T Consensus 688 S~k~ 691 (693)
T PRK11824 688 SRKA 691 (693)
T ss_pred EEEe
Confidence 9864
No 69
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.61 E-value=0.00015 Score=69.28 Aligned_cols=83 Identities=23% Similarity=0.229 Sum_probs=59.6
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEec
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVR 249 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~ 249 (279)
.|.|+++.++|+||.+. +++|+||.++ ++.. +.. .....|++||.|+|+|. .+|..+++|.+++.+
T Consensus 197 ~g~V~~v~~~G~fV~l~--~v~g~v~~se-ls~~---~~~------~~~~~~~vGd~i~~~Vl--~vd~~~~~i~lS~k~ 262 (390)
T PRK06676 197 EGTVARLTDFGAFVDIG--GVDGLVHISE-LSHE---RVE------KPSEVVSVGQEVEVKVL--SIDWETERISLSLKD 262 (390)
T ss_pred EEEEEEEecceEEEEeC--CeEEEEEHHH-cCcc---ccC------CHHHhcCCCCEEEEEEE--EEeCCCCEEEEEEee
Confidence 44555999999999995 7999999997 4211 110 11346899999999998 999999999999986
Q ss_pred CCccCcccCccccccchhhhccc
Q psy4846 250 PVIEGFSVSSAGEQGEEKMEEGE 272 (279)
Q Consensus 250 ~~~~~~~~~~~~~~~~~~~~~~~ 272 (279)
.. +.+++....+.+.|+
T Consensus 263 ~~------~~~~~~~~~~~~~G~ 279 (390)
T PRK06676 263 TL------PGPWEGVEEKLPEGD 279 (390)
T ss_pred cc------cCccccchhhhcCCc
Confidence 32 234554455566664
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=97.55 E-value=0.00017 Score=71.24 Aligned_cols=70 Identities=16% Similarity=0.125 Sum_probs=57.1
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
.+.+.|.|++++++|+||.+.+ +++|+||.++ ++.++ .. .....|++||.|+|+|. ++|.++++|.|
T Consensus 447 G~~v~g~V~~v~~~G~fV~l~~-~~~Glv~~s~-l~~~~---~~------~~~~~~~~Gd~v~~~V~--~id~~~~~i~l 513 (516)
T TIGR00717 447 GSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSE-LSENR---DE------DKTDEIKVGDEVEAKVV--DIDKKNRKVSL 513 (516)
T ss_pred ceEEEEEEEEEecceEEEEcCC-CeEEEEEHHH-cCccc---cc------cccccCCCCCEEEEEEE--EEeCCCCEEEE
Confidence 4467999999999999999987 8999999998 43221 11 12457999999999998 99999999999
Q ss_pred EEe
Q psy4846 246 RLV 248 (279)
Q Consensus 246 ~lv 248 (279)
+++
T Consensus 514 s~k 516 (516)
T TIGR00717 514 SVK 516 (516)
T ss_pred EEC
Confidence 874
No 71
>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=97.54 E-value=0.00011 Score=74.59 Aligned_cols=72 Identities=14% Similarity=0.056 Sum_probs=52.7
Q ss_pred cccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEE
Q psy4846 165 RVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLV 244 (279)
Q Consensus 165 ~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~ 244 (279)
..+.+.|.|++|.++|+||.|.. |++|+||+++ +. .++|... .......+++||.|+|+|. ++|. +++|.
T Consensus 647 vG~i~~GkV~~I~dfGaFVel~~-G~eGLvHISe-is--dls~~~r---v~~~~dv~kvGd~V~VKVl--~ID~-~gKI~ 716 (719)
T TIGR02696 647 VGERFLGTVVKTTAFGAFVSLLP-GKDGLLHISQ-IR--KLAGGKR---VENVEDVLSVGQKIQVEIA--DIDD-RGKLS 716 (719)
T ss_pred CCCEEEEEEEEEECceEEEEecC-CceEEEEhhh-cc--ccccccC---cCCHHHcCCCCCEEEEEEE--EECC-CCCee
Confidence 34556888999999999999975 8999999996 31 1112111 1111457999999999998 8984 77887
Q ss_pred EE
Q psy4846 245 LR 246 (279)
Q Consensus 245 ~~ 246 (279)
|+
T Consensus 717 L~ 718 (719)
T TIGR02696 717 LV 718 (719)
T ss_pred ec
Confidence 75
No 72
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.49 E-value=0.00025 Score=72.13 Aligned_cols=72 Identities=10% Similarity=0.074 Sum_probs=58.4
Q ss_pred cCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 167 QDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 167 ~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
..+.|.|+++.++|+||.+.+ +++|++|.++ ++.+. .......|++||.|+|+|. ++|.++++|.|+
T Consensus 564 ~~v~g~V~~i~~~G~fV~l~~-~i~Gli~~se-l~~~~---------~~~~~~~~kvGd~V~vkV~--~id~e~~rI~ls 630 (647)
T PRK00087 564 SIVLGKVVRIAPFGAFVELEP-GVDGLVHISQ-ISWKR---------IDKPEDVLSEGEEVKAKIL--EVDPEEKRIRLS 630 (647)
T ss_pred eEEEEEEEEEECCeEEEEECC-CCEEEEEhhh-cCccc---------cCCHhhcCCCCCEEEEEEE--EEeCCCCEEEEE
Confidence 357899999999999999976 8999999987 42211 1111457999999999998 999999999999
Q ss_pred EecCC
Q psy4846 247 LVRPV 251 (279)
Q Consensus 247 lv~~~ 251 (279)
+....
T Consensus 631 lk~~~ 635 (647)
T PRK00087 631 IKEVE 635 (647)
T ss_pred Eeecc
Confidence 98753
No 73
>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=97.49 E-value=0.0002 Score=51.42 Aligned_cols=60 Identities=8% Similarity=0.091 Sum_probs=44.3
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCC
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQ 239 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~ 239 (279)
+.|.|+.+.++|++|.++. +++|+++.++ ...+ |... ......|++||.|+++|. ++|..
T Consensus 4 V~g~V~~i~~~gi~v~l~~-~i~g~i~~~~-i~~~---~~~~----~~~~~~~~~Gd~i~~kVl--~~d~~ 63 (70)
T cd05702 4 VKAKVKSVKPTQLNVQLAD-NVHGRIHVSE-VFDE---WPDG----KNPLSKFKIGQKIKARVI--GGHDA 63 (70)
T ss_pred EEEEEEEEECCcEEEEeCC-CcEEEEEHHH-hccc---cccc----cChhHhCCCCCEEEEEEE--EEeCc
Confidence 4688889999999999987 8999999987 3212 1000 011346899999999998 77764
No 74
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.45 E-value=0.00023 Score=71.12 Aligned_cols=84 Identities=19% Similarity=0.217 Sum_probs=61.2
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
+.|.|+.+.++|+||.+. |++|+||.++ + .|+. .......|++||.|+|+|. .+|.++++|.+++.
T Consensus 205 v~g~V~~v~~~G~~V~i~--g~~glv~~se-~-----s~~~----~~~~~~~~kvG~~v~v~V~--~~d~~~~~i~lS~k 270 (565)
T PRK06299 205 VEGVVKNITDYGAFVDLG--GVDGLLHITD-I-----SWKR----VNHPSEVVNVGDEVKVKVL--KFDKEKKRVSLGLK 270 (565)
T ss_pred EEEEEEEEeCCeEEEEEC--CEEEEEEHHH-h-----cccc----cCCHhhcCCCCCEEEEEEE--EEeCCCCeEEEEEE
Confidence 356666999999999996 8999999987 3 2221 1111456999999999998 89999999999998
Q ss_pred cCCccCcccCccccccchhhhccc
Q psy4846 249 RPVIEGFSVSSAGEQGEEKMEEGE 272 (279)
Q Consensus 249 ~~~~~~~~~~~~~~~~~~~~~~~~ 272 (279)
.. .+-+|+....+...|+
T Consensus 271 ~~------~~~p~~~~~~~~~~G~ 288 (565)
T PRK06299 271 QL------GEDPWEAIEKKYPVGS 288 (565)
T ss_pred ec------ccChhHHHHhhCCCCC
Confidence 52 1224555555555565
No 75
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.33 E-value=0.00036 Score=70.99 Aligned_cols=86 Identities=24% Similarity=0.251 Sum_probs=62.8
Q ss_pred cCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 167 QDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 167 ~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+.+.|.|.++.++|+||.+ . |++|+||.++ +. |.+.. .....|++||.|+|+|. ++|+.+++|.++
T Consensus 479 ~iV~g~V~~v~~~G~fV~l-~-gv~Gll~~se-ls---~~~~~------~~~~~~~vGd~V~vkV~--~id~~~~~I~lS 544 (647)
T PRK00087 479 DVVEGEVKRLTDFGAFVDI-G-GVDGLLHVSE-IS---WGRVE------KPSDVLKVGDEIKVYIL--DIDKENKKLSLS 544 (647)
T ss_pred CEEEEEEEEEeCCcEEEEE-C-CEEEEEEHHH-cC---ccccC------CHHHhcCCCCEEEEEEE--EEECCCCEEEEE
Confidence 4557778899999999999 3 8999999987 42 11111 11346899999999998 999999999999
Q ss_pred EecCCccCcccCccccccchhhhccc
Q psy4846 247 LVRPVIEGFSVSSAGEQGEEKMEEGE 272 (279)
Q Consensus 247 lv~~~~~~~~~~~~~~~~~~~~~~~~ 272 (279)
++.. .+.+|+....+.+.|+
T Consensus 545 ~K~~------~~~p~~~~~~~~~~G~ 564 (647)
T PRK00087 545 LKKL------LPDPWENVEEKYPVGS 564 (647)
T ss_pred eecc------ccChhhhhhhhccCCe
Confidence 9863 2334555455555554
No 76
>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=97.26 E-value=0.0012 Score=48.76 Aligned_cols=72 Identities=11% Similarity=-0.071 Sum_probs=54.5
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
...+.|.|+++.+++++|.+.. +.+|.++.++ ...++ .. .....+++||.|.++|. +++.. +++.|
T Consensus 7 GdiV~G~V~~v~~~~~~V~i~~-~~~g~l~~~~-~~~~~----~~-----~~~~~~~~GD~i~~~V~--~~~~~-~~i~L 72 (82)
T cd04454 7 GDIVIGIVTEVNSRFWKVDILS-RGTARLEDSS-ATEKD----KK-----EIRKSLQPGDLILAKVI--SLGDD-MNVLL 72 (82)
T ss_pred CCEEEEEEEEEcCCEEEEEeCC-CceEEeechh-ccCcc----hH-----HHHhcCCCCCEEEEEEE--EeCCC-CCEEE
Confidence 3456788899999999999964 7999999987 32110 00 01346899999999998 88876 88999
Q ss_pred EEecCC
Q psy4846 246 RLVRPV 251 (279)
Q Consensus 246 ~lv~~~ 251 (279)
++.++.
T Consensus 73 S~~~~~ 78 (82)
T cd04454 73 TTADNE 78 (82)
T ss_pred EECCCC
Confidence 998753
No 77
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=97.22 E-value=0.00056 Score=50.89 Aligned_cols=75 Identities=15% Similarity=0.231 Sum_probs=55.2
Q ss_pred hhhhcCCCcccCCcceEEEEEeCeEEEEecCcceeEEEE-cccCCCCCceeeecCCceEeec-CeEecCCCeEEEEEEec
Q psy4846 157 LQILIPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLF-LRCDSPSVSWTYNEKEQSQSCG-SVVFHSFDPVTVQLSLD 234 (279)
Q Consensus 157 ~~~~~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~-l~~~~~~d~~~~~~~~~~l~~~-~~~~~lGD~V~VkV~~~ 234 (279)
|-+-||..+.... .|+.+.+.|++|.|.+|++||+|- .++ +. .+ .... ++.+ +|-.+.|+|.
T Consensus 9 fcy~~P~v~dvv~--~Vv~i~d~~~YV~LleY~iegmIl~~se-ls-------r~---rirsi~kll-VGk~e~v~Vi-- 72 (86)
T PHA02858 9 FCYVFPNINEVTK--GIVFVKDNIFYVKLIDYGLEALIVNYVN-VN-------AD---RAEKLKKKL-VGKTINVQVI-- 72 (86)
T ss_pred EEEecCCCCeEEE--EEEEEeccEEEEEEecCccceEEecHHH-Hh-------HH---HHHhhhhhh-cCCeeEEEEE--
Confidence 3455677555443 678999999999999999999986 544 11 00 0111 3456 9999999998
Q ss_pred cccCCCCeEEEEE
Q psy4846 235 RSNVQHEKLVLRL 247 (279)
Q Consensus 235 ~vd~~~~~I~~~l 247 (279)
++|.+++-|+++.
T Consensus 73 RVDk~KGYIDLs~ 85 (86)
T PHA02858 73 RTDKLKGYIDVRH 85 (86)
T ss_pred EECCCCCEEEeEc
Confidence 9999999999985
No 78
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.19 E-value=0.005 Score=52.62 Aligned_cols=85 Identities=13% Similarity=0.065 Sum_probs=60.3
Q ss_pred cCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCc--eEeec--CeEecCCCeEEEEEEeccc
Q psy4846 161 IPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQ--SQSCG--SVVFHSFDPVTVQLSLDRS 236 (279)
Q Consensus 161 ~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~--~l~~~--~~~~~lGD~V~VkV~~~~v 236 (279)
.|+. .-.++|.|++++++|++|.+- .++++|+.+. +|++ +.||+... ..... +..++.||.|++||...+.
T Consensus 78 rPf~-gEVv~g~V~~v~~~G~~v~~G--p~~ifI~~~~-l~~~-~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~ 152 (176)
T PTZ00162 78 KPFK-DEVLDAIVTDVNKLGFFAQAG--PLKAFVSRSA-IPPD-FVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRY 152 (176)
T ss_pred ecCC-CCEEEEEEEEEecceEEEEee--CeEEEEcHHH-CCCc-cEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEe
Confidence 4552 234699999999999999995 4679999887 7655 78887554 23322 5789999999999983333
Q ss_pred cCCCCeEEEEEecC
Q psy4846 237 NVQHEKLVLRLVRP 250 (279)
Q Consensus 237 d~~~~~I~~~lv~~ 250 (279)
+...-.+..++.+|
T Consensus 153 ~~~~~~~i~T~~~~ 166 (176)
T PTZ00162 153 DASNLFAIATINSD 166 (176)
T ss_pred cCCCcEEEEEecCC
Confidence 44344455666665
No 79
>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=97.13 E-value=0.0019 Score=48.84 Aligned_cols=70 Identities=16% Similarity=0.069 Sum_probs=45.4
Q ss_pred CCcceEEEEEeC--eEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 168 DEDGYVLYVRKN--ALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 168 ~~~g~V~~V~~~--Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
.+.|.|+.+.++ |+||.|.+ |.+|++|+++ + .|..|+. .......+++||.|.|+|.-...+....++..
T Consensus 10 iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~se-i--s~~~~~~----v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt~ 81 (88)
T cd04453 10 IYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSD-I--LPAYFKK----HKKIAKLLKEGQEILVQVVKEPIGTKGPRLTT 81 (88)
T ss_pred EEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHH-c--Cchhccc----cCCHHHcCCCCCEEEEEEEEecCCCCCceEEE
Confidence 346777799996 99999987 8999999987 3 1101111 11113479999999999983333333333333
No 80
>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=97.12 E-value=0.00057 Score=69.89 Aligned_cols=67 Identities=15% Similarity=0.089 Sum_probs=51.2
Q ss_pred cccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEE
Q psy4846 165 RVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLV 244 (279)
Q Consensus 165 ~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~ 244 (279)
....+.|.|++|.++|+||.+.. |++|+||+++ +..+++. .....|++||.|+|+|. ++|. +++|.
T Consensus 618 ~G~i~~G~V~~I~~~GafVei~~-g~~GllHiSe-i~~~~v~---------~~~~~~kvGD~V~VkVi--~id~-~gki~ 683 (684)
T TIGR03591 618 VGKIYEGKVVRIMDFGAFVEILP-GKDGLVHISE-IANERVE---------KVEDVLKEGDEVKVKVL--EIDK-QGRIK 683 (684)
T ss_pred cCcEEEEEEEEEeCCEEEEEECC-CcEEEEEHHH-cCCCccc---------ChhhccCCCCEEEEEEE--EECC-CCCcc
Confidence 34556889999999999999976 7999999998 4322211 11457999999999998 8887 66665
Q ss_pred E
Q psy4846 245 L 245 (279)
Q Consensus 245 ~ 245 (279)
|
T Consensus 684 L 684 (684)
T TIGR03591 684 L 684 (684)
T ss_pred C
Confidence 3
No 81
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.05 E-value=0.00087 Score=62.50 Aligned_cols=85 Identities=14% Similarity=0.062 Sum_probs=61.1
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEec
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVR 249 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~ 249 (279)
.|+|+.+.++|++|.|. +..+|+++.++ .. +.+.. .....|++||.|+|.|. +++...+++.+++..
T Consensus 36 ~G~V~~i~~~g~~Vdig-~k~~g~lp~sE-is---~~~~~------~~~~~~~~G~~v~~~Vi--~~~~~~~~i~lS~k~ 102 (318)
T PRK07400 36 NGTVFSLEPRGALIDIG-AKTAAFMPIQE-MS---INRVE------GPEEVLQPNETREFFIL--SDENEDGQLTLSIRR 102 (318)
T ss_pred EEEEEEEECCEEEEEEC-CCeEEEEEHHH-hc---ccccc------CHHHccCCCCEEEEEEE--EEeCCCCeEEEehhh
Confidence 56666999999999994 57899999987 31 11111 01346899999999998 888888999999886
Q ss_pred CCccCcccCccccccchhhhccc
Q psy4846 250 PVIEGFSVSSAGEQGEEKMEEGE 272 (279)
Q Consensus 250 ~~~~~~~~~~~~~~~~~~~~~~~ 272 (279)
. ....+|+......+.|+
T Consensus 103 ~-----~~~~~w~~l~~~~~~~~ 120 (318)
T PRK07400 103 I-----EYMRAWERVRQLQKEDA 120 (318)
T ss_pred h-----hhhhHHHHHHHhccCCC
Confidence 3 12235666666666554
No 82
>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=97.03 E-value=0.0036 Score=47.35 Aligned_cols=68 Identities=15% Similarity=0.138 Sum_probs=49.3
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecC-Cc-eEeec-CeEecCCCeEEEEEEeccccCCCCe
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEK-EQ-SQSCG-SVVFHSFDPVTVQLSLDRSNVQHEK 242 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~-~~-~l~~~-~~~~~lGD~V~VkV~~~~vd~~~~~ 242 (279)
++|.|+.+++.|++|.+- .++++++-.. .|.+ +.|++. +. ....+ +..++.|+.|++||. .+..+.+.
T Consensus 5 i~g~V~~v~~~G~~v~~G--pl~~f~~~~~-ip~~-~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~--~v~~~~~~ 75 (88)
T cd04462 5 VDAIVTSVNKTGFFAEVG--PLSIFISRHL-IPSD-MEFDPNASPPCFTSNEDIVIKKDTEVRLKII--GTRVDATD 75 (88)
T ss_pred EEEEEEEEeccEEEEEEc--CceEEEEeee-cCcc-ceECCcCCCCeEeCCCcEEECCCCEEEEEEE--EEEEccCc
Confidence 367777999999999995 5788888876 6655 778773 22 22332 578999999999997 55544333
No 83
>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=96.80 E-value=0.0039 Score=44.40 Aligned_cols=59 Identities=12% Similarity=0.091 Sum_probs=44.6
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCC--CeEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQH--EKLVL 245 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~--~~I~~ 245 (279)
.++|+|.++.++|++|.+. +++|+++.++ .. .+..+++||+|+|.|. +++... .+|.+
T Consensus 6 iV~G~V~~~~~~~~~vdig--~~eg~lp~~e-~~---------------~~~~~~~Gd~v~v~v~--~v~~~~~~~~i~l 65 (67)
T cd04455 6 IVTGIVKRVDRGNVIVDLG--KVEAILPKKE-QI---------------PGESYRPGDRIKAYVL--EVRKTSKGPQIIL 65 (67)
T ss_pred EEEEEEEEEcCCCEEEEcC--CeEEEeeHHH-CC---------------CCCcCCCCCEEEEEEE--EEecCCCCCEEEE
Confidence 4578888999999999995 3899999887 21 1235799999999998 776543 45655
Q ss_pred E
Q psy4846 246 R 246 (279)
Q Consensus 246 ~ 246 (279)
|
T Consensus 66 S 66 (67)
T cd04455 66 S 66 (67)
T ss_pred e
Confidence 4
No 84
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.28 E-value=0.048 Score=53.53 Aligned_cols=62 Identities=16% Similarity=0.151 Sum_probs=50.1
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCC--eEEEEE
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHE--KLVLRL 247 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~--~I~~~l 247 (279)
.|+|.++.++|++|.|. |++|++|.++ . ..+..|++||+|+|.|. +++...+ +|.+|-
T Consensus 139 ~G~V~ri~~~giiVDLg--gvea~LP~sE-~---------------ip~E~~~~GdrIka~I~--~Vd~~~kg~qIilSR 198 (470)
T PRK09202 139 TGVVKRVERGNIIVDLG--RAEAILPRKE-Q---------------IPRENFRPGDRVRAYVY--EVRKEARGPQIILSR 198 (470)
T ss_pred EEEEEEEecCCEEEEEC--CeEEEecHHH-c---------------CCCccCCCCCEEEEEEE--EEecCCCCCeEEEEe
Confidence 45566999999999993 8999999886 2 12457899999999998 9988766 899888
Q ss_pred ecCC
Q psy4846 248 VRPV 251 (279)
Q Consensus 248 v~~~ 251 (279)
..|.
T Consensus 199 t~p~ 202 (470)
T PRK09202 199 THPE 202 (470)
T ss_pred CcHH
Confidence 7663
No 85
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=96.23 E-value=0.0083 Score=51.74 Aligned_cols=71 Identities=15% Similarity=0.032 Sum_probs=52.6
Q ss_pred ccCCcceEEEEEeCeEEEEecC---------cceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccc
Q psy4846 166 VQDEDGYVLYVRKNALQILIPK---------YGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRS 236 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~---------~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~v 236 (279)
...+.|.|+++.++|++|.|.. .+++|++|.++ .... +.. .-...|++||.|.++|. ++
T Consensus 65 GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~-i~~~---~~~------~~~~~~~~GD~V~akV~--~i 132 (189)
T PRK09521 65 GDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQ-VSDG---YVE------SLTDAFKIGDIVRAKVI--SY 132 (189)
T ss_pred CCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhH-cChh---hhh------hHHhccCCCCEEEEEEE--ec
Confidence 3456899999999999999853 26889999987 3111 000 01346899999999998 77
Q ss_pred cCCCCeEEEEEecCC
Q psy4846 237 NVQHEKLVLRLVRPV 251 (279)
Q Consensus 237 d~~~~~I~~~lv~~~ 251 (279)
+ +++.|++.++.
T Consensus 133 ~---~~i~LS~k~~~ 144 (189)
T PRK09521 133 T---DPLQLSTKGKD 144 (189)
T ss_pred C---CcEEEEEecCC
Confidence 7 68999998753
No 86
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.19 E-value=0.0069 Score=60.95 Aligned_cols=69 Identities=13% Similarity=0.117 Sum_probs=54.1
Q ss_pred cCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 167 QDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 167 ~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
+.+.|.|+.+.++|+||.|.. |-+|++|++. +... +...-+.++++||.|+|++. .+|. +++++++
T Consensus 621 ~iy~G~V~ri~~fGaFv~l~~-gkdgl~hiS~-~~~~---------rv~kv~dvlk~Gd~v~Vkv~--~iD~-~Gri~ls 686 (692)
T COG1185 621 EVYEGTVVRIVDFGAFVELLP-GKDGLVHISQ-LAKE---------RVEKVEDVLKEGDEVKVKVI--EIDK-QGRIRLS 686 (692)
T ss_pred cEEEEEEEEEeecceEEEecC-CcceeEEehh-hhhh---------hhhcccceeecCceEEEEEe--eecc-cCCccce
Confidence 346899999999999999987 8899999997 3211 11112568999999999998 8885 6889988
Q ss_pred Eec
Q psy4846 247 LVR 249 (279)
Q Consensus 247 lv~ 249 (279)
++.
T Consensus 687 ~~~ 689 (692)
T COG1185 687 IKA 689 (692)
T ss_pred ehh
Confidence 764
No 87
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=96.15 E-value=0.059 Score=40.53 Aligned_cols=66 Identities=18% Similarity=0.130 Sum_probs=47.1
Q ss_pred CcceEEEEEeCeEEE-EecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 169 EDGYVLYVRKNALQI-LIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V-~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
++|.|+.+.+++.|. .|.+ |.+-+.|++.. +.-....+.+||.|+|.+. .-|+.+++|.+..
T Consensus 9 ~~G~V~e~Lp~~~frV~Len-G~~vla~isGK--------------mR~~rIrIl~GD~V~VE~s--pYDltkGRIiyR~ 71 (87)
T PRK12442 9 LDGIVDEVLPDSRFRVTLEN-GVEVGAYASGR--------------MRKHRIRILAGDRVTLELS--PYDLTKGRINFRH 71 (87)
T ss_pred EEEEEEEECCCCEEEEEeCC-CCEEEEEeccc--------------eeeeeEEecCCCEEEEEEC--cccCCceeEEEEe
Confidence 456666887777765 5544 77777777641 1111346889999999998 8999999999999
Q ss_pred ecCC
Q psy4846 248 VRPV 251 (279)
Q Consensus 248 v~~~ 251 (279)
..+.
T Consensus 72 ~~~~ 75 (87)
T PRK12442 72 KDER 75 (87)
T ss_pred cCCC
Confidence 8654
No 88
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.90 E-value=0.021 Score=50.95 Aligned_cols=76 Identities=12% Similarity=-0.040 Sum_probs=54.8
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
...+-|.|++++.++++|.|.. +.+|++|+++ ....+...|... -...|++||.|.++|. +++.. +++.|
T Consensus 64 GDiViG~V~~i~~~~~~vdI~~-~~~g~L~~s~-i~~~~~~~d~~~-----~~~~~~~GDlV~akV~--~i~~~-~~~~L 133 (235)
T PRK04163 64 GDLVIGKVTDVTFSGWEVDINS-PYKAYLPVSE-VLGRPVNVEGTD-----LRKYLDIGDYIIAKVK--DVDRT-RDVVL 133 (235)
T ss_pred CCEEEEEEEEEeCceEEEEeCC-CceeEEEHHH-cCCCccccchhh-----hHhhCCCCCEEEEEEE--EECCC-CcEEE
Confidence 3457899999999999999976 6899999987 321111111111 1346999999999998 78764 45899
Q ss_pred EEecCC
Q psy4846 246 RLVRPV 251 (279)
Q Consensus 246 ~lv~~~ 251 (279)
++.++.
T Consensus 134 S~k~~~ 139 (235)
T PRK04163 134 TLKGKG 139 (235)
T ss_pred EEcCCC
Confidence 987753
No 89
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=95.21 E-value=0.045 Score=49.49 Aligned_cols=63 Identities=16% Similarity=0.072 Sum_probs=52.4
Q ss_pred ccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 166 VQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 166 ~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
.+.++|+|-++.+.|.||.+.+ +.-|+||-++ - -..+++|++++++|. .++. .++|.+
T Consensus 156 nq~v~~tVYr~~~~G~fv~~e~-~~~GfIh~sE-r-----------------~~~prlG~~l~~rVi--~~re-Dg~lnL 213 (287)
T COG2996 156 NQEVDATVYRLLESGTFVITEN-GYLGFIHKSE-R-----------------FAEPRLGERLTARVI--GVRE-DGKLNL 213 (287)
T ss_pred cCeeeeEEEEEeccceEEEEcC-CeEEEEcchh-h-----------------cccccCCceEEEEEE--EEcc-CCeeec
Confidence 4667888889999999999954 8899999876 1 135799999999998 8887 999999
Q ss_pred EEecC
Q psy4846 246 RLVRP 250 (279)
Q Consensus 246 ~lv~~ 250 (279)
++..-
T Consensus 214 Sl~p~ 218 (287)
T COG2996 214 SLRPR 218 (287)
T ss_pred ccccc
Confidence 98643
No 90
>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=94.50 E-value=0.07 Score=38.84 Aligned_cols=68 Identities=13% Similarity=0.016 Sum_probs=48.7
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeE-EEEEEeccccCCCCeEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPV-TVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V-~VkV~~~~vd~~~~~I~~~ 246 (279)
.++|.|+.-+++++.|.|.+.|+.|+++... +.+ .++ ..... -..+++||++ ++-|. +..++.|.++
T Consensus 3 lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~H-LsD-~~~--k~~~~----~~klrvG~~L~~~lvL----~~~~r~i~lt 70 (72)
T cd05699 3 LVDARVLKKTLNGLEVAILPEEIRAFLPTMH-LSD-HVS--NCPLL----WHCLQEGDTIPNLMCL----SNYKGRIILT 70 (72)
T ss_pred eEEEEEEEEcCCcEEEEecCCCcEEEEEccc-cCC-chh--hCHHH----HhhhhcCCCccceEEE----eccccEEEEe
Confidence 3578888999999999999999999998875 432 111 11000 2478999999 77664 6667777765
Q ss_pred E
Q psy4846 247 L 247 (279)
Q Consensus 247 l 247 (279)
.
T Consensus 71 ~ 71 (72)
T cd05699 71 K 71 (72)
T ss_pred c
Confidence 3
No 91
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=94.34 E-value=0.55 Score=44.62 Aligned_cols=62 Identities=11% Similarity=0.090 Sum_probs=45.8
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCC--CCeEEEEE
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQ--HEKLVLRL 247 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~--~~~I~~~l 247 (279)
+|+|.++.++|++|.+. +++|+++.++ . + .+..|++||+|+|.|. +++.. ..+|.+|.
T Consensus 139 ~G~V~~~~~~~~~Vdlg--~vEa~LP~~E-~--------------i-p~e~~~~Gd~Ika~V~--~V~~~~kgp~IivSR 198 (362)
T PRK12327 139 TGVVQRRDNRFVYVNLG--KIEAVLPPAE-Q--------------I-PGETYKHGDRIKVYVV--KVEKTTKGPQIFVSR 198 (362)
T ss_pred EEEEEEEeCCcEEEEeC--CeEEEecHHH-c--------------C-CCCCCCCCCEEEEEEE--EEecCCCCCeEEEEe
Confidence 34455899999999885 5999999765 1 1 1346899999999998 88743 44688877
Q ss_pred ecCC
Q psy4846 248 VRPV 251 (279)
Q Consensus 248 v~~~ 251 (279)
..|.
T Consensus 199 t~p~ 202 (362)
T PRK12327 199 THPG 202 (362)
T ss_pred CCHH
Confidence 6653
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=93.33 E-value=1.1 Score=42.29 Aligned_cols=62 Identities=18% Similarity=0.180 Sum_probs=46.3
Q ss_pred cceEEEEEeCe-EEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccC--CCCeEEEE
Q psy4846 170 DGYVLYVRKNA-LQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNV--QHEKLVLR 246 (279)
Q Consensus 170 ~g~V~~V~~~G-i~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~--~~~~I~~~ 246 (279)
+|+|.++.++| ++|.+. +++|+++.++ . . .+..|++||+|+|.|. +++. ...+|.+|
T Consensus 136 ~G~V~~v~~~g~v~VdiG--~~ea~LP~~E-~--------------i-p~E~~~~Gd~ik~~V~--~V~~~~kg~qIivS 195 (341)
T TIGR01953 136 SGTVKRVNRRGNLYVELG--KTEGILPKKE-Q--------------I-PGEKFRIGDRIKAYVY--EVRKTAKGPQIILS 195 (341)
T ss_pred EEEEEEEecCCcEEEEEC--CeEEEecHHH-c--------------C-CCcCCCCCCEEEEEEE--EEEcCCCCCeEEEE
Confidence 45555998888 588883 8999999876 2 0 1335899999999998 7774 45689988
Q ss_pred EecCC
Q psy4846 247 LVRPV 251 (279)
Q Consensus 247 lv~~~ 251 (279)
...|.
T Consensus 196 Rt~~~ 200 (341)
T TIGR01953 196 RTHPE 200 (341)
T ss_pred eCcHH
Confidence 87764
No 93
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=91.53 E-value=0.95 Score=32.58 Aligned_cols=60 Identities=18% Similarity=0.130 Sum_probs=41.2
Q ss_pred CcceEEEEEeCeEEE-EecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 169 EDGYVLYVRKNALQI-LIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V-~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
+.|.|+...+++.|- .+++ |.+-+.|++.. +......+.+||.|.|.+. .-|+.+++|.+
T Consensus 7 ~~G~V~e~L~~~~f~V~l~n-g~~vla~i~GK--------------mr~~rI~I~~GD~V~Ve~s--pyd~tkgrIi~ 67 (68)
T TIGR00008 7 MEGKVTESLPNAMFRVELEN-GHEVLAHISGK--------------IRMHYIRILPGDKVKVELS--PYDLTRGRITY 67 (68)
T ss_pred EEEEEEEECCCCEEEEEECC-CCEEEEEecCc--------------chhccEEECCCCEEEEEEC--cccCCcEeEEe
Confidence 355566777777654 5655 77777777641 1111345899999999987 78888888865
No 94
>KOG1070|consensus
Probab=91.01 E-value=0.16 Score=54.91 Aligned_cols=70 Identities=14% Similarity=0.177 Sum_probs=55.9
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.+-|++..+.++|.+|.++. |++|+.+.+. ..++ |.-+. ...|.+||.|.++|. ++|.++++|.+++
T Consensus 602 ~~~G~l~~~~~~g~~V~F~g-~lsGf~p~s~-~sd~-~v~~~--------~ehf~vGqTv~~~i~--nvd~ek~rm~l~~ 668 (1710)
T KOG1070|consen 602 ITKGTLCAIKENGAFVTFTG-GLSGFAPVSE-MSDD-FVLSD--------SEHFPVGQTVRAKIV--NVDDEKRRMPLGL 668 (1710)
T ss_pred eEEEEEeeeccCCeEEEecC-ccccccchhh-hhhh-hhcCh--------hhhcccccEEEEEEE--ecCchhceeehhh
Confidence 34788899999999999998 9999999876 3222 22111 346899999999998 9999999999988
Q ss_pred ecC
Q psy4846 248 VRP 250 (279)
Q Consensus 248 v~~ 250 (279)
...
T Consensus 669 r~s 671 (1710)
T KOG1070|consen 669 RAS 671 (1710)
T ss_pred hhh
Confidence 753
No 95
>KOG1067|consensus
Probab=89.64 E-value=0.86 Score=45.37 Aligned_cols=60 Identities=8% Similarity=-0.000 Sum_probs=45.2
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCe
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEK 242 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~ 242 (279)
+|+|+.+++.|++|.++. +.+|++|.+. +...+ +......+.+||.|+|+.. +.|+..+.
T Consensus 673 ~~tIt~~rd~G~~V~l~p-~~~~Llh~sq-L~~e~---------iakpsd~levGq~I~vk~i--e~d~~g~~ 732 (760)
T KOG1067|consen 673 TATITEIRDTGVMVELYP-MQQGLLHNSQ-LDQEK---------IAKPSDLLEVGQEIQVKYI--ERDPRGGI 732 (760)
T ss_pred EEEEeeecccceEEEecC-Cchhhccchh-ccccc---------ccChHHHHhhcceeEEEEE--eecCccce
Confidence 566779999999999988 9999999987 42111 1112345999999999988 88885443
No 96
>KOG3298|consensus
Probab=87.93 E-value=2 Score=36.03 Aligned_cols=75 Identities=17% Similarity=0.135 Sum_probs=47.8
Q ss_pred cCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCce--Eeec-CeEecCCCeEEEEEEecccc
Q psy4846 161 IPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQS--QSCG-SVVFHSFDPVTVQLSLDRSN 237 (279)
Q Consensus 161 ~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~--l~~~-~~~~~lGD~V~VkV~~~~vd 237 (279)
.|+ +...++|+|+.|.+.|+|+.+-. ++.++.--. .| +.|.|++.+.. .... ..+++.|+.|+++|. .+.
T Consensus 78 kpf-KGEVvdgvV~~Vnk~G~F~~~GP--l~~f~sshl-~p-pd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kii--gtr 150 (170)
T KOG3298|consen 78 KPF-KGEVVDGVVTKVNKMGVFARSGP--LEVFYSSHL-KP-PDYEFDPGENPPNFQTEDESVIQKGVEVRLKII--GTR 150 (170)
T ss_pred eec-CCcEEEEEEEEEeeeeEEEeccc--eEeeeeccc-CC-CCcccCCCCCCCcccccccceeeeCcEEEEEEE--EEE
Confidence 444 34457999999999999999864 444442211 22 34788875432 2333 337999999999998 444
Q ss_pred CCCCe
Q psy4846 238 VQHEK 242 (279)
Q Consensus 238 ~~~~~ 242 (279)
.....
T Consensus 151 ~~~~~ 155 (170)
T KOG3298|consen 151 VDETE 155 (170)
T ss_pred Eeeee
Confidence 43333
No 97
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=87.65 E-value=1.4 Score=33.40 Aligned_cols=71 Identities=11% Similarity=0.006 Sum_probs=47.3
Q ss_pred CCcceEEEEEeCeEEEEe--------cCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCC
Q psy4846 168 DEDGYVLYVRKNALQILI--------PKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQ 239 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~L--------p~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~ 239 (279)
.+-|.|+.++...+.|.| +. ...|.+|.++ .... ..++.++ ...|++||-|+.+|. +.+.
T Consensus 9 iVig~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~~d-v~~~--~~d~~~~-----~~~f~~GDiV~AkVi--s~~~- 76 (92)
T cd05791 9 IVIARVTRINPRFAKVDILCVGGRPLKE-SFRGVIRKED-IRAT--EKDKVEM-----YKCFRPGDIVRAKVI--SLGD- 76 (92)
T ss_pred EEEEEEEEEcCCEEEEEEEEecCeecCC-CcccEEEHHH-cccc--ccchHHH-----HhhcCCCCEEEEEEE--EcCC-
Confidence 456788899999999988 44 5678888876 2101 0011011 356899999999997 6553
Q ss_pred CCeEEEEEecC
Q psy4846 240 HEKLVLRLVRP 250 (279)
Q Consensus 240 ~~~I~~~lv~~ 250 (279)
.+.+.+++.++
T Consensus 77 ~~~~~Lst~~~ 87 (92)
T cd05791 77 ASSYYLSTAEN 87 (92)
T ss_pred CCCcEEEecCC
Confidence 35578887764
No 98
>KOG1070|consensus
Probab=87.53 E-value=1.6 Score=47.74 Aligned_cols=73 Identities=16% Similarity=0.126 Sum_probs=57.0
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
+.|+|..+..+|+|+.+.. ++++++++++ +. +.+.-.+ ...|..|+.|+.+|. +++...++|.++|.
T Consensus 1166 v~G~V~nv~~~glfi~ls~-~v~a~v~is~-~~-ds~~k~w--------~k~~~~gklv~~rv~--~ve~~s~riel~Lk 1232 (1710)
T KOG1070|consen 1166 VRGFVKNVETKGLFIALSR-KVEAFVPISG-LS-DSFEKEW--------EKHLPVGKLVTGRVL--SVEEDSKRIELSLK 1232 (1710)
T ss_pred eEEEEEEecCCcEEEEEcc-ceEEEEEccc-cc-cchhhhh--------hccCCccceeeeEEE--EeeccCceEEEEEe
Confidence 4788889999999999986 9999999887 31 1111111 457999999999998 99999999999998
Q ss_pred cCCccC
Q psy4846 249 RPVIEG 254 (279)
Q Consensus 249 ~~~~~~ 254 (279)
...+-|
T Consensus 1233 ~s~~~d 1238 (1710)
T KOG1070|consen 1233 NSDIKD 1238 (1710)
T ss_pred ccccCC
Confidence 754433
No 99
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=84.94 E-value=0.81 Score=45.75 Aligned_cols=63 Identities=19% Similarity=0.173 Sum_probs=51.3
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEec
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVR 249 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~ 249 (279)
.|+|.+|.++|+||.|.. -+.|++|-++ +. +...+.+||.+-|++. .+.+.++.|+|..+.
T Consensus 127 ~g~v~~v~~~GvFv~Ln~-~v~GL~~~~d-~~---------------~~~~~~vgdeiiV~v~--~vr~~~geidf~~~~ 187 (715)
T COG1107 127 KGIVSRVEKYGVFVELNS-HVRGLIHRRD-LG---------------GDPDYAVGDEIIVQVS--DVRPEKGEIDFEPVG 187 (715)
T ss_pred eccccchhhhcceeecCh-hhhccccccc-cC---------------CCCCCCCCCeEEEEee--ccCCCCCccceeecC
Confidence 566669999999999977 7889998887 21 1246899999999987 999999999999876
Q ss_pred CC
Q psy4846 250 PV 251 (279)
Q Consensus 250 ~~ 251 (279)
..
T Consensus 188 ~~ 189 (715)
T COG1107 188 LD 189 (715)
T ss_pred Cc
Confidence 53
No 100
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=84.85 E-value=6.1 Score=28.98 Aligned_cols=64 Identities=19% Similarity=0.208 Sum_probs=42.8
Q ss_pred CcceEEEEEeCeEE-EEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 169 EDGYVLYVRKNALQ-ILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~-V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
+.|.|+.+..++.| |.+.+ |.+-+-|++..+ . -....+..||.|.|++. ..|..+..|.+..
T Consensus 9 ~~g~V~e~L~~~~f~v~~ed-g~~~~ahI~GKm------------r--~~~i~I~~GD~V~Ve~~--~~d~~kg~I~~Ry 71 (75)
T COG0361 9 MEGTVIEMLPNGRFRVELEN-GHERLAHISGKM------------R--KNRIRILPGDVVLVELS--PYDLTKGRIVYRY 71 (75)
T ss_pred EEEEEEEecCCCEEEEEecC-CcEEEEEccCcc------------h--heeEEeCCCCEEEEEec--ccccccccEEEEe
Confidence 34555577766664 44444 777777776410 0 00235889999999998 8888899998877
Q ss_pred ec
Q psy4846 248 VR 249 (279)
Q Consensus 248 v~ 249 (279)
..
T Consensus 72 ~~ 73 (75)
T COG0361 72 KK 73 (75)
T ss_pred cC
Confidence 54
No 101
>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=84.66 E-value=2.9 Score=40.52 Aligned_cols=78 Identities=15% Similarity=0.012 Sum_probs=48.9
Q ss_pred CCcceEEEEEeC--eEEEEecCcceeEEEEcccCCCCCceeeecCCc---eEeecCeEecCCCeEEEEEEeccccCCCCe
Q psy4846 168 DEDGYVLYVRKN--ALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQ---SQSCGSVVFHSFDPVTVQLSLDRSNVQHEK 242 (279)
Q Consensus 168 ~~~g~V~~V~~~--Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~---~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~ 242 (279)
.+.|.|.+|.++ |+||.+.. +-.|++|+++ .....+.+..... ....-...++.||.|.|+|+-+.+.....+
T Consensus 28 IY~GrV~~i~p~l~aAFVdiG~-~k~gfL~~~d-~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~Kgp~ 105 (414)
T TIGR00757 28 IYKGRVTRILPSLQAAFVDIGL-EKNGFLHASD-IGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGNKGAR 105 (414)
T ss_pred EEEEEEeeecCCCceEEEEcCC-CceEEEEHHH-cCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCCCCCe
Confidence 457778899998 99999975 7899999998 3212111111000 000012358999999999985445555555
Q ss_pred EEEEE
Q psy4846 243 LVLRL 247 (279)
Q Consensus 243 I~~~l 247 (279)
+.-.+
T Consensus 106 lT~~I 110 (414)
T TIGR00757 106 LTTDI 110 (414)
T ss_pred EEEEE
Confidence 65443
No 102
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=83.54 E-value=14 Score=35.36 Aligned_cols=61 Identities=21% Similarity=0.206 Sum_probs=43.0
Q ss_pred cceEEEEEeC-eEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCC---eEEE
Q psy4846 170 DGYVLYVRKN-ALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHE---KLVL 245 (279)
Q Consensus 170 ~g~V~~V~~~-Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~---~I~~ 245 (279)
.|+|.++..+ +++|.|. +++|.++-++-. ++..|++||+|+|-|. +|+...+ +|.+
T Consensus 143 ~g~V~r~~~~~~i~vdlg--~~ea~LP~~eqi----------------p~E~~~~Gdrik~~i~--~V~~~~k~gp~Iil 202 (374)
T PRK12328 143 FGTVVRVDNEENTFIEID--EIRAVLPMKNRI----------------KGEKFKVGDVVKAVLK--RVKIDKNNGILIEL 202 (374)
T ss_pred EEEEEEEecCCCEEEEcC--CeEEEeCHHHcC----------------CCCcCCCCCEEEEEEE--EEecCCCCCCEEEE
Confidence 3444488764 4778775 688888876511 2457999999999988 7766543 7877
Q ss_pred EEecC
Q psy4846 246 RLVRP 250 (279)
Q Consensus 246 ~lv~~ 250 (279)
|..+|
T Consensus 203 SRt~p 207 (374)
T PRK12328 203 SRTSP 207 (374)
T ss_pred EcCCH
Confidence 77665
No 103
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=81.86 E-value=21 Score=34.84 Aligned_cols=63 Identities=14% Similarity=0.177 Sum_probs=43.8
Q ss_pred cceEEEEEeCeEEEEec-Ccc---eeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCC---CCe
Q psy4846 170 DGYVLYVRKNALQILIP-KYG---LEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQ---HEK 242 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp-~~g---iEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~---~~~ 242 (279)
+|+|.++...++.|.|. .+| +++.++-++-. .+..|+.||+|+|-|. +|+.. ..+
T Consensus 157 ~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi----------------p~E~y~~Gdrika~i~--~V~~~~~kGpq 218 (449)
T PRK12329 157 TARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL----------------PNDNYRANATFKVFLK--EVSEGPRRGPQ 218 (449)
T ss_pred EEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC----------------CCCcCCCCCEEEEEEE--EeecCCCCCCE
Confidence 45555888888888773 234 78888776611 2457999999999988 77553 356
Q ss_pred EEEEEecC
Q psy4846 243 LVLRLVRP 250 (279)
Q Consensus 243 I~~~lv~~ 250 (279)
|.+|-..|
T Consensus 219 IilSRt~p 226 (449)
T PRK12329 219 LFVSRANA 226 (449)
T ss_pred EEEEcCCH
Confidence 77776554
No 104
>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=80.06 E-value=14 Score=29.58 Aligned_cols=60 Identities=10% Similarity=0.129 Sum_probs=38.3
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEee---c--CeEecCCCeEEEEEE
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSC---G--SVVFHSFDPVTVQLS 232 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~---~--~~~~~lGD~V~VkV~ 232 (279)
.|+|.+-+..|+.|.| .|.=+-+|+-.. ++.. -.||+.++.-+. . ...+.+|+.|++||.
T Consensus 8 ~g~I~~~~~~Gi~vsl-gFFddI~IP~~~-L~~p-s~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~ 72 (122)
T PF08292_consen 8 TGKIKSSTAEGIRVSL-GFFDDIFIPPSL-LPEP-SRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVE 72 (122)
T ss_dssp EEEEEEEETTEEEEEE-CCEEEEEEECCC-C-TT-EEEECCCTEEEEEESSSEEEEE-TT-EEEEEEE
T ss_pred EEEEEecCCCcEEEEe-cccccEEECHHH-CCCC-CccCccCCEEEEECCCCceeEccCCCEEEEEEe
Confidence 5777799999999988 555566666554 5532 355655554322 2 346899999999986
No 105
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=79.44 E-value=10 Score=26.28 Aligned_cols=46 Identities=20% Similarity=-0.052 Sum_probs=24.3
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEec
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLD 234 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~ 234 (279)
...|+.++++|+|+.... +-+-+++.+. . ...+++||.|+|-|+.|
T Consensus 6 ~L~V~~~~~~g~fL~~~~-~~~vlLp~~e-~-----------------~~~~~~Gd~v~VFvY~D 51 (61)
T PF13509_consen 6 TLKVVDKNEFGYFLDDGE-GKEVLLPKSE-V-----------------PEPLKVGDEVEVFVYLD 51 (61)
T ss_dssp ---EEEE-SSEEEEEETT--EEEEEEGGG------------------------TTSEEEEEEEE-
T ss_pred ceEEEEEeCCEEEEECCC-CCEEEechHH-c-----------------CCCCCCCCEEEEEEEEC
Confidence 456779999999986433 2333334333 1 23589999999999844
No 106
>CHL00010 infA translation initiation factor 1
Probab=79.13 E-value=16 Score=26.74 Aligned_cols=29 Identities=24% Similarity=0.311 Sum_probs=22.2
Q ss_pred EecCCCeEEEEEEeccccCCCCeEEEEEecC
Q psy4846 220 VFHSFDPVTVQLSLDRSNVQHEKLVLRLVRP 250 (279)
Q Consensus 220 ~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~~ 250 (279)
.+.+||.|.|.+. ..+..++.|......+
T Consensus 46 ~~~vGD~V~ve~~--~~~~~~g~Ii~r~~~~ 74 (78)
T CHL00010 46 RILPGDRVKVELS--PYDLTKGRIIYRLRNK 74 (78)
T ss_pred ccCCCCEEEEEEc--ccCCCeEEEEEEecCC
Confidence 4688999999976 5566678888877654
No 107
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=77.97 E-value=16 Score=26.21 Aligned_cols=25 Identities=28% Similarity=0.332 Sum_probs=18.1
Q ss_pred EecCCCeEEEEEEeccccCCCCeEEEE
Q psy4846 220 VFHSFDPVTVQLSLDRSNVQHEKLVLR 246 (279)
Q Consensus 220 ~~~lGD~V~VkV~~~~vd~~~~~I~~~ 246 (279)
...+||.|.|.+. ..+..++.|.+.
T Consensus 46 ~i~vGD~V~ve~~--~~~~~~g~Iv~r 70 (72)
T PRK00276 46 RILPGDKVTVELS--PYDLTKGRITYR 70 (72)
T ss_pred ccCCCCEEEEEEc--ccCCCeEEEEEE
Confidence 4789999999975 555556666654
No 108
>KOG2916|consensus
Probab=76.51 E-value=1.5 Score=39.74 Aligned_cols=66 Identities=14% Similarity=0.111 Sum_probs=46.3
Q ss_pred eEEEEEeCeEEEEecCcc-eeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEec
Q psy4846 172 YVLYVRKNALQILIPKYG-LEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVR 249 (279)
Q Consensus 172 ~V~~V~~~Gi~V~Lp~~g-iEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~ 249 (279)
.|..|.+-|++|.|-+|+ +||+|-++. +. . .++..-++.+++|-.=-|.|. .||.+++-|+|+.-.
T Consensus 23 nV~sIaemGayv~LlEYnniEGmiLlsE-LS-------r--RRIRSI~klirVGr~E~vvVl--rVDkekGYIDLSkrr 89 (304)
T KOG2916|consen 23 NVRSIAEMGAYVKLLEYNNIEGMILLSE-LS-------R--RRIRSIQKLIRVGRNEPVVVL--RVDKEKGYIDLSKRR 89 (304)
T ss_pred EeeEehhccceEeeeecCCcccchhhhH-HH-------H--HHHHHHHHHHhcCCcceEEEE--EEcCCCCceechhcc
Confidence 455899999999998776 999999987 31 0 001011445778865555555 899999999998754
No 109
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=74.81 E-value=17 Score=28.08 Aligned_cols=65 Identities=12% Similarity=-0.017 Sum_probs=45.4
Q ss_pred cCCcceEEEEEeCeEEE-EecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 167 QDEDGYVLYVRKNALQI-LIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 167 ~~~~g~V~~V~~~Gi~V-~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
..+.|.|+....++.|- .+++ |.+-+++++.. +. ...-+..||.|.|.+. .-+..+..|.+
T Consensus 21 ~e~~g~V~~~lG~~~~~V~~~d-G~~~la~i~GK--------------~R-k~IwI~~GD~VlVe~~--~~~~~kg~Iv~ 82 (100)
T PRK04012 21 GEVFGVVEQMLGANRVRVRCMD-GVERMGRIPGK--------------MK-KRMWIREGDVVIVAPW--DFQDEKADIIW 82 (100)
T ss_pred CEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEchh--------------hc-ccEEecCCCEEEEEec--ccCCCEEEEEE
Confidence 34567777888777754 5555 77777777651 11 1345899999999987 77788888888
Q ss_pred EEec
Q psy4846 246 RLVR 249 (279)
Q Consensus 246 ~lv~ 249 (279)
.+..
T Consensus 83 r~~~ 86 (100)
T PRK04012 83 RYTK 86 (100)
T ss_pred EcCH
Confidence 7753
No 110
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=73.57 E-value=28 Score=25.25 Aligned_cols=47 Identities=11% Similarity=0.044 Sum_probs=30.2
Q ss_pred ceEEEEEe-CeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeecC-eEecCCCeEEEEEE
Q psy4846 171 GYVLYVRK-NAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGS-VVFHSFDPVTVQLS 232 (279)
Q Consensus 171 g~V~~V~~-~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~-~~~~lGD~V~VkV~ 232 (279)
|+|..... .|+ ||.-++-+-+-+||++. + ...+ ..++.||+|...+.
T Consensus 4 G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~-i--------------~~~g~~~l~~G~~V~f~~~ 53 (74)
T PRK09937 4 GTVKWFNNAKGFGFICPEGGGEDIFAHYST-I--------------QMDGYRTLKAGQSVQFDVH 53 (74)
T ss_pred eEEEEEeCCCCeEEEeeCCCCccEEEEEee-c--------------cccCCCCCCCCCEEEEEEE
Confidence 44444443 454 55555656778888886 2 1122 57899999999985
No 111
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=67.61 E-value=21 Score=31.99 Aligned_cols=73 Identities=15% Similarity=0.059 Sum_probs=49.6
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
.+-|.|+.|...+..|.|-. ...+.+++++ .+.-.+.-++.++ ...|++||.|..+|. .+|. ...+.+.+
T Consensus 67 ~VIG~I~~v~~~~W~VDI~s-p~~A~L~ls~-~~~r~~~~~~~~~-----r~~l~vGD~v~AkV~--~vd~-~~~~~L~~ 136 (239)
T COG1097 67 VVIGKIIEVGPSGWKVDIGS-PYPALLSLSD-FLRRKFENAEKDL-----RPFLNVGDLVYAKVV--DVDR-DGEVELTL 136 (239)
T ss_pred EEEEEEEEEcccceEEEcCC-ccceEeehhh-hhccccccccccc-----ccccccCCEEEEEEE--EccC-CCceEEEe
Confidence 35788999999999998865 4567888876 2111111111111 457999999999987 7875 56777777
Q ss_pred ecC
Q psy4846 248 VRP 250 (279)
Q Consensus 248 v~~ 250 (279)
.++
T Consensus 137 k~~ 139 (239)
T COG1097 137 KDE 139 (239)
T ss_pred ecC
Confidence 544
No 112
>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=67.51 E-value=30 Score=25.94 Aligned_cols=67 Identities=15% Similarity=0.051 Sum_probs=46.0
Q ss_pred CcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
+-|.|+.+...+..|.|-. ...+.+++.+ .++- .++ ....+++||-|-.+|. .+|.. ....++.+
T Consensus 10 VIG~V~~~~~~~~~VdI~s-~~~a~L~~~~-f~ga-----tk~-----~rp~L~~GDlV~ArV~--~~~~~-~~~eLtc~ 74 (86)
T cd05790 10 VIGIVVAKAGDFFKVDIGG-SEPASLSYLA-FEGA-----TKR-----NRPNLNVGDLVYARVV--KANRD-MEPELSCV 74 (86)
T ss_pred EEEEEEEEcCCeEEEEcCC-CcceEechHH-cccc-----ccc-----ccccCCCCCEEEEEEE--ecCCC-CCeEEEEe
Confidence 3467779999999999865 3467777654 2110 000 1357999999999998 78764 56788888
Q ss_pred cC
Q psy4846 249 RP 250 (279)
Q Consensus 249 ~~ 250 (279)
.+
T Consensus 75 ~~ 76 (86)
T cd05790 75 DS 76 (86)
T ss_pred CC
Confidence 75
No 113
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=66.25 E-value=30 Score=25.34 Aligned_cols=61 Identities=15% Similarity=0.030 Sum_probs=41.8
Q ss_pred ceEEEEEeCeEE-EEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEec
Q psy4846 171 GYVLYVRKNALQ-ILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVR 249 (279)
Q Consensus 171 g~V~~V~~~Gi~-V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~ 249 (279)
|.|+....++.| |.+++ |.+-+.+++.. +. ...-++.||.|.|.+. .-|..+..|...+..
T Consensus 4 g~V~~~~g~~~~~V~~~~-g~~~la~i~gK--------------~r-k~iwI~~GD~V~Ve~~--~~d~~kg~Iv~r~~~ 65 (77)
T cd05793 4 GQVEKMLGNGRLEVRCFD-GKKRLCRIRGK--------------MR-KRVWINEGDIVLVAPW--DFQDDKADIIYKYTP 65 (77)
T ss_pred EEEEEEcCCCEEEEEECC-CCEEEEEEchh--------------hc-ccEEEcCCCEEEEEec--cccCCEEEEEEEcCH
Confidence 455577766664 45555 77777777651 11 1346899999999986 668888888887754
No 114
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: 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 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=61.38 E-value=21 Score=25.44 Aligned_cols=57 Identities=12% Similarity=0.095 Sum_probs=35.0
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccC
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNV 238 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~ 238 (279)
+++|-.+.+.-+.|-|.+.|-=..++.+..+ ++.|.|+. ..+++|+.+.|.+. ..++
T Consensus 5 tA~VQh~~kdfAvvSL~~t~~L~a~p~~sHL-Ndtfrf~s---------eklkvG~~l~v~lk--~~~~ 61 (69)
T cd05701 5 TAIVQHADKDFAIVSLATTGDLAAFPTRSHL-NDTFRFDS---------EKLSVGQCLDVTLK--DPNC 61 (69)
T ss_pred chhhhhhhhceEEEEeeccccEEEEEchhhc-cccccccc---------eeeeccceEEEEEe--cCcc
Confidence 4444466666666666665544555555411 24455543 46899999999986 5555
No 115
>PRK14998 cold shock-like protein CspD; Provisional
Probab=59.29 E-value=65 Score=23.25 Aligned_cols=47 Identities=11% Similarity=0.043 Sum_probs=29.9
Q ss_pred ceEEEEEe-CeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeecC-eEecCCCeEEEEEE
Q psy4846 171 GYVLYVRK-NAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGS-VVFHSFDPVTVQLS 232 (279)
Q Consensus 171 g~V~~V~~-~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~-~~~~lGD~V~VkV~ 232 (279)
|+|..-.. .|+ ||.-++-+-+-++|++. + ...+ ..++.|++|...+.
T Consensus 4 G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~-l--------------~~~g~~~l~~G~~V~f~~~ 53 (73)
T PRK14998 4 GTVKWFNNAKGFGFICPEGGGEDIFAHYST-I--------------QMDGYRTLKAGQSVRFDVH 53 (73)
T ss_pred eEEEEEeCCCceEEEecCCCCccEEEEeee-e--------------cccCCCCCCCCCEEEEEEE
Confidence 44444443 444 45555656778888876 2 1122 56899999999985
No 116
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=57.90 E-value=66 Score=24.77 Aligned_cols=73 Identities=11% Similarity=0.000 Sum_probs=46.0
Q ss_pred hcCCCcccCCcceEEEEEeCeEEE-EecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccC
Q psy4846 160 LIPKSRVQDEDGYVLYVRKNALQI-LIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNV 238 (279)
Q Consensus 160 ~~p~~~~~~~~g~V~~V~~~Gi~V-~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~ 238 (279)
-+|......+.|.|+.+..++.|- .+++ |.+-+++++.. +. ...-++.||.|.|... +..+.
T Consensus 12 ~~p~~~e~e~~g~V~~~lG~~~~~V~~~d-G~~~la~i~GK--------------~R-k~iwI~~GD~VlVsp~-d~~~~ 74 (99)
T TIGR00523 12 RLPRKEEGEILGVIEQMLGAGRVKVRCLD-GKTRLGRIPGK--------------LK-KRIWIREGDVVIVKPW-EFQGD 74 (99)
T ss_pred eCCCCCCCEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEchh--------------hc-ccEEecCCCEEEEEEc-cCCCC
Confidence 345544555677788888777754 5555 77777777651 11 1345899999999654 22224
Q ss_pred CCCeEEEEEec
Q psy4846 239 QHEKLVLRLVR 249 (279)
Q Consensus 239 ~~~~I~~~lv~ 249 (279)
.+..|...+..
T Consensus 75 ~kg~Iv~r~~~ 85 (99)
T TIGR00523 75 DKCDIVWRYTK 85 (99)
T ss_pred ccEEEEEEcCH
Confidence 47777777654
No 117
>PRK10811 rne ribonuclease E; Reviewed
Probab=56.06 E-value=30 Score=37.11 Aligned_cols=75 Identities=15% Similarity=0.051 Sum_probs=44.2
Q ss_pred CCcceEEEEEe--CeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEE
Q psy4846 168 DEDGYVLYVRK--NALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLV 244 (279)
Q Consensus 168 ~~~g~V~~V~~--~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~ 244 (279)
.+.|.|.+|-+ +++||.|.. |..|++++++ .....|...-........+..++.||.|-|+|.-+.+.-..-++.
T Consensus 41 IYkGkVenIvPGInAAFVDIG~-gknGFL~L~D-i~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KEa~gtKGp~LT 117 (1068)
T PRK10811 41 IYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKE-IAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALT 117 (1068)
T ss_pred eEEEEEecccCCcceeEEEecC-CcceEEEhhh-ccccccccccccccccccccccCCCCEEEEEEeecccCCCCCcee
Confidence 34666667765 788999997 8999999988 311222110000000001345899999999997444444444444
No 118
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=55.90 E-value=59 Score=27.23 Aligned_cols=63 Identities=16% Similarity=0.086 Sum_probs=43.3
Q ss_pred cceEEEEEeCeEEE-EecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 170 DGYVLYVRKNALQI-LIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V-~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
=|.|+.+..++.|- .+.+ |.+-+.|++.. +. ...-+..||.|.|.+. .-+..+..|.+.+.
T Consensus 35 ~g~V~~~LGn~~f~V~c~d-G~~rLa~I~GK--------------mR-K~IWI~~GD~VlVel~--~yd~~KgdIi~Ry~ 96 (155)
T PTZ00329 35 YAQVLRMLGNGRLEAYCFD-GVKRLCHIRGK--------------MR-KRVWINIGDIILVSLR--DFQDSKADVILKYT 96 (155)
T ss_pred EEEEEEEcCCCEEEEEECC-CCEEEEEeecc--------------ce-eeEEecCCCEEEEecc--CCCCCEEEEEEEcC
Confidence 35566777777654 4454 77777777651 11 1245899999999986 77888888988875
Q ss_pred cC
Q psy4846 249 RP 250 (279)
Q Consensus 249 ~~ 250 (279)
.+
T Consensus 97 ~d 98 (155)
T PTZ00329 97 PD 98 (155)
T ss_pred HH
Confidence 43
No 119
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=54.40 E-value=51 Score=23.44 Aligned_cols=48 Identities=8% Similarity=0.083 Sum_probs=30.2
Q ss_pred cceEEEEEe-CeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeecC-eEecCCCeEEEEEE
Q psy4846 170 DGYVLYVRK-NAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGS-VVFHSFDPVTVQLS 232 (279)
Q Consensus 170 ~g~V~~V~~-~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~-~~~~lGD~V~VkV~ 232 (279)
+|+|..... .|+ ||.-++-+-+-++|++. + ...+ ..++.||+|...+.
T Consensus 5 ~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~-l--------------~~~g~~~l~~G~~V~f~~~ 55 (69)
T PRK09507 5 KGNVKWFNESKGFGFITPEDGSKDVFVHFSA-I--------------QTNGFKTLAEGQRVEFEIT 55 (69)
T ss_pred ceEEEEEeCCCCcEEEecCCCCeeEEEEeec-c--------------cccCCCCCCCCCEEEEEEE
Confidence 455555553 444 45555545678888876 2 1112 46899999999875
No 120
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=52.44 E-value=36 Score=25.35 Aligned_cols=33 Identities=6% Similarity=0.188 Sum_probs=23.4
Q ss_pred CeEecCCCeEEEEEEecccc-----CCCCeEEEEEecC
Q psy4846 218 SVVFHSFDPVTVQLSLDRSN-----VQHEKLVLRLVRP 250 (279)
Q Consensus 218 ~~~~~lGD~V~VkV~~~~vd-----~~~~~I~~~lv~~ 250 (279)
...|+.||.|++++.+-..+ +....+.+.+..|
T Consensus 8 r~iYrPGetV~~~~~~~~~~~~~~~~~~~~~~v~i~dp 45 (99)
T PF01835_consen 8 RPIYRPGETVHFRAIVRDLDNDFKPPANSPVTVTIKDP 45 (99)
T ss_dssp SSEE-TTSEEEEEEEEEEECTTCSCESSEEEEEEEEET
T ss_pred ccCcCCCCEEEEEEEEeccccccccccCCceEEEEECC
Confidence 45799999999998754444 3456788888877
No 121
>PRK11712 ribonuclease G; Provisional
Probab=52.41 E-value=41 Score=33.43 Aligned_cols=78 Identities=17% Similarity=0.050 Sum_probs=46.3
Q ss_pred CcceEEEEEe--CeEEEEecCcceeEEEEcccCCCCCceeeecCCce--EeecCeEecCCCeEEEEEEeccccCCCCeEE
Q psy4846 169 EDGYVLYVRK--NALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQS--QSCGSVVFHSFDPVTVQLSLDRSNVQHEKLV 244 (279)
Q Consensus 169 ~~g~V~~V~~--~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~--l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~ 244 (279)
+.|.|..|-+ +++||.+.. +-.|++|++|..|..++..+..... ..+-+..++.||.|-|+|+-+.+.....++.
T Consensus 42 Y~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke~~~~KG~~lT 120 (489)
T PRK11712 42 YKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKDPLGTKGARLT 120 (489)
T ss_pred EEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeCCcCCCCCeEE
Confidence 3566666665 688999985 8889999998212111111111000 0001335899999999998555555555665
Q ss_pred EEE
Q psy4846 245 LRL 247 (279)
Q Consensus 245 ~~l 247 (279)
-.+
T Consensus 121 ~~I 123 (489)
T PRK11712 121 TDI 123 (489)
T ss_pred EEE
Confidence 443
No 122
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=51.89 E-value=29 Score=30.24 Aligned_cols=44 Identities=16% Similarity=0.172 Sum_probs=30.0
Q ss_pred CCcceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEE
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQ 230 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~Vk 230 (279)
.++|.|+.|.++-|+++...|+=.-.|++.. ...+++||.|+|.
T Consensus 41 tiEGrVvEV~~~~i~iesk~yn~~v~i~~d~-------------------~~nvKVGD~VKaT 84 (213)
T PRK06763 41 TIEGRVVEVDNGVIVIKSKQYEEPVSVYIDS-------------------LSNVKVGDEVKAT 84 (213)
T ss_pred eeeeEEEEEeCCEEEEEeccCCCceEEEecC-------------------CCCcccCcEEEEc
Confidence 3456666999999999888876555555433 2245788888775
No 123
>PRK15464 cold shock-like protein CspH; Provisional
Probab=51.23 E-value=41 Score=24.17 Aligned_cols=48 Identities=13% Similarity=-0.048 Sum_probs=31.2
Q ss_pred cceEEEEEe-CeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeec-CeEecCCCeEEEEEE
Q psy4846 170 DGYVLYVRK-NAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCG-SVVFHSFDPVTVQLS 232 (279)
Q Consensus 170 ~g~V~~V~~-~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~-~~~~~lGD~V~VkV~ 232 (279)
+|+|..... .|+ ||.-++-+-+-+||++. + ... -..++.||+|...+.
T Consensus 6 ~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~-l--------------~~~g~~~l~~G~~V~f~v~ 56 (70)
T PRK15464 6 TGIVKTFDRKSGKGFIIPSDGRKEVQVHISA-F--------------TPRDAEVLIPGLRVEFCRV 56 (70)
T ss_pred eEEEEEEECCCCeEEEccCCCCccEEEEehh-e--------------hhcCCCCCCCCCEEEEEEE
Confidence 455555553 455 56556656788899887 2 111 236899999999985
No 124
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=49.35 E-value=1.1e+02 Score=22.76 Aligned_cols=62 Identities=13% Similarity=0.043 Sum_probs=41.9
Q ss_pred cceEEEEEeCeEE-EEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 170 DGYVLYVRKNALQ-ILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 170 ~g~V~~V~~~Gi~-V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
.|.|+....++.| |.+++ |.+-+++++.. +. ...-++.||.|.|.+. ..+..++.|.+.+.
T Consensus 8 ~g~V~~~lG~~~~~V~~~d-G~~~la~ipgK--------------~R-k~iwI~~GD~VlVe~~--~~~~~kg~Iv~r~~ 69 (83)
T smart00652 8 IAQVVKMLGNGRLEVMCAD-GKERLARIPGK--------------MR-KKVWIRRGDIVLVDPW--DFQDVKADIIYKYT 69 (83)
T ss_pred EEEEEEEcCCCEEEEEECC-CCEEEEEEchh--------------hc-ccEEEcCCCEEEEEec--CCCCCEEEEEEEeC
Confidence 4555577766664 45555 88777777651 11 1345899999999986 66777788887765
Q ss_pred c
Q psy4846 249 R 249 (279)
Q Consensus 249 ~ 249 (279)
.
T Consensus 70 ~ 70 (83)
T smart00652 70 K 70 (83)
T ss_pred H
Confidence 4
No 125
>KOG1856|consensus
Probab=49.29 E-value=15 Score=39.87 Aligned_cols=68 Identities=9% Similarity=0.026 Sum_probs=48.1
Q ss_pred CcceEEEEEeCe---EEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEE
Q psy4846 169 EDGYVLYVRKNA---LQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVL 245 (279)
Q Consensus 169 ~~g~V~~V~~~G---i~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~ 245 (279)
+.+.|.+|+... +-|.+. .|+.|+|+.++ ..+. .+......+++|+.|.++|. ++|.++-.+.+
T Consensus 989 V~~~V~~vt~rr~~Cv~v~ld-~G~~g~i~~~~-~Sd~---------~v~~p~~~v~vgq~v~~kvi--~id~e~f~v~L 1055 (1299)
T KOG1856|consen 989 VPVTVTKVTHRRGICVRVRLD-CGVTGFILAKN-LSDR---------DVRRPENRVKVGQTVYCKVI--KIDKERFSVEL 1055 (1299)
T ss_pred EEEeeeEEEecccceeEEEec-CCCceeeeccc-cChh---------hccCHHHhhccCceEEEEee--eeeHhhhhhhh
Confidence 467777888766 455665 49999999876 2210 12223446789999999998 89888888887
Q ss_pred EEec
Q psy4846 246 RLVR 249 (279)
Q Consensus 246 ~lv~ 249 (279)
+.+.
T Consensus 1056 s~r~ 1059 (1299)
T KOG1856|consen 1056 SCRT 1059 (1299)
T ss_pred hhhh
Confidence 7764
No 126
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=48.28 E-value=98 Score=22.68 Aligned_cols=62 Identities=10% Similarity=0.042 Sum_probs=40.9
Q ss_pred ceEEEEEeCeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccc-cCCCCeEEEEEe
Q psy4846 171 GYVLYVRKNAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRS-NVQHEKLVLRLV 248 (279)
Q Consensus 171 g~V~~V~~~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~v-d~~~~~I~~~lv 248 (279)
|.|+....++. .|.+++ |.+-+++++.. +. ...-++.||.|.|.+. +. |..+..|...+.
T Consensus 4 ~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK--------------~R-k~iwI~~GD~VlV~~~--~~~~~~kg~Iv~r~~ 65 (78)
T cd04456 4 VRVLRMLGNNRHEVECAD-GQRRLVSIPGK--------------LR-KNIWIKRGDFLIVDPI--EEGEDVKADIIFVYC 65 (78)
T ss_pred EEEEEECCCCEEEEEECC-CCEEEEEEchh--------------hc-cCEEEcCCCEEEEEec--ccCCCceEEEEEEeC
Confidence 34456666665 456666 77777777651 11 1245899999999986 55 677788887775
Q ss_pred cC
Q psy4846 249 RP 250 (279)
Q Consensus 249 ~~ 250 (279)
.+
T Consensus 66 ~~ 67 (78)
T cd04456 66 KD 67 (78)
T ss_pred HH
Confidence 43
No 127
>PRK10943 cold shock-like protein CspC; Provisional
Probab=46.27 E-value=1e+02 Score=21.79 Aligned_cols=48 Identities=8% Similarity=0.067 Sum_probs=30.2
Q ss_pred cceEEEEEe-CeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeecC-eEecCCCeEEEEEE
Q psy4846 170 DGYVLYVRK-NAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGS-VVFHSFDPVTVQLS 232 (279)
Q Consensus 170 ~g~V~~V~~-~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~-~~~~lGD~V~VkV~ 232 (279)
+|+|..-.. .|+ |+.-++-+-+-++|++. + ...+ ..+..||+|...+.
T Consensus 5 ~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~-l--------------~~~g~~~l~~G~~V~f~~~ 55 (69)
T PRK10943 5 KGQVKWFNESKGFGFITPADGSKDVFVHFSA-I--------------QGNGFKTLAEGQNVEFEIQ 55 (69)
T ss_pred ceEEEEEeCCCCcEEEecCCCCeeEEEEhhH-c--------------cccCCCCCCCCCEEEEEEE
Confidence 455556554 444 45445545678888886 2 1112 46889999999875
No 128
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=46.22 E-value=57 Score=23.20 Aligned_cols=48 Identities=8% Similarity=0.052 Sum_probs=29.5
Q ss_pred cceEEEEEe-CeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeecC-eEecCCCeEEEEEE
Q psy4846 170 DGYVLYVRK-NAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGS-VVFHSFDPVTVQLS 232 (279)
Q Consensus 170 ~g~V~~V~~-~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~-~~~~lGD~V~VkV~ 232 (279)
.|+|..... .|+ ||.-++-+-+-++|++. +. ..+ ..++.||+|+..+.
T Consensus 6 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~-l~--------------~~g~~~l~~G~~V~f~~~ 56 (70)
T PRK10354 6 TGIVKWFNADKGFGFITPDDGSKDVFVHFSA-IQ--------------NDGYKSLDEGQKVSFTIE 56 (70)
T ss_pred eEEEEEEeCCCCcEEEecCCCCccEEEEEee-cc--------------ccCCCCCCCCCEEEEEEE
Confidence 355545442 444 45555545678888876 21 112 46899999999875
No 129
>PLN00208 translation initiation factor (eIF); Provisional
Probab=45.61 E-value=1.1e+02 Score=25.35 Aligned_cols=63 Identities=17% Similarity=0.120 Sum_probs=43.0
Q ss_pred cceEEEEEeCeEE-EEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEe
Q psy4846 170 DGYVLYVRKNALQ-ILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLV 248 (279)
Q Consensus 170 ~g~V~~V~~~Gi~-V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv 248 (279)
=|.|+.+..++.+ |.+.+ |.+-+++++.. +. ...-++.||.|.|.+. .-+..+..|.+.+.
T Consensus 35 ~g~V~~~lGn~~~~V~c~d-G~~rLa~IpGK--------------mR-KrIWI~~GD~VlVel~--~~d~~KgdIv~ry~ 96 (145)
T PLN00208 35 YAQVLRMLGNGRCEALCID-GTKRLCHIRGK--------------MR-KKVWIAAGDIILVGLR--DYQDDKADVILKYM 96 (145)
T ss_pred EEEEEEEcCCCEEEEEECC-CCEEEEEEecc--------------ce-eeEEecCCCEEEEEcc--CCCCCEEEEEEEcC
Confidence 3556677776664 44454 77777777651 11 1245899999999987 77888888888775
Q ss_pred cC
Q psy4846 249 RP 250 (279)
Q Consensus 249 ~~ 250 (279)
.+
T Consensus 97 ~d 98 (145)
T PLN00208 97 PD 98 (145)
T ss_pred HH
Confidence 43
No 130
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=44.46 E-value=1e+02 Score=21.08 Aligned_cols=47 Identities=15% Similarity=0.099 Sum_probs=28.8
Q ss_pred ceEEEEEe-CeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeec-CeEecCCCeEEEEEE
Q psy4846 171 GYVLYVRK-NAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCG-SVVFHSFDPVTVQLS 232 (279)
Q Consensus 171 g~V~~V~~-~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~-~~~~~lGD~V~VkV~ 232 (279)
|+|..... .|+ |+..++.+-+-++|.++ + ... ...++.||.|+..+.
T Consensus 3 G~Vk~~~~~kGfGFI~~~~~g~diffh~~~-~--------------~~~~~~~~~~G~~V~f~~~ 52 (65)
T cd04458 3 GTVKWFDDEKGFGFITPDDGGEDVFVHISA-L--------------EGDGFRSLEEGDRVEFELE 52 (65)
T ss_pred EEEEEEECCCCeEEEecCCCCcCEEEEhhH-h--------------hccCCCcCCCCCEEEEEEE
Confidence 44445554 333 45555556667777776 2 111 246899999999885
No 131
>PRK09890 cold shock protein CspG; Provisional
Probab=43.50 E-value=74 Score=22.64 Aligned_cols=48 Identities=8% Similarity=0.086 Sum_probs=29.3
Q ss_pred cceEEEEEe-CeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeecC-eEecCCCeEEEEEE
Q psy4846 170 DGYVLYVRK-NAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGS-VVFHSFDPVTVQLS 232 (279)
Q Consensus 170 ~g~V~~V~~-~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~-~~~~lGD~V~VkV~ 232 (279)
.|+|..... .|+ |+.-++-+-+-++|++. +. ..+ ..++.||+|...+.
T Consensus 6 ~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~-l~--------------~~~~~~l~~G~~V~f~~~ 56 (70)
T PRK09890 6 TGLVKWFNADKGFGFITPDDGSKDVFVHFTA-IQ--------------SNEFRTLNENQKVEFSIE 56 (70)
T ss_pred eEEEEEEECCCCcEEEecCCCCceEEEEEee-ec--------------cCCCCCCCCCCEEEEEEE
Confidence 455555553 444 45545545677888876 21 112 46789999999875
No 132
>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=43.24 E-value=28 Score=25.93 Aligned_cols=56 Identities=13% Similarity=-0.013 Sum_probs=28.9
Q ss_pred CcceEEEEEeCeEEEEecCc-----------------ceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKY-----------------GLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQL 231 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~-----------------giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV 231 (279)
+.|.|+.|+..-+.+.|-.. ...|.|+.+| .-. .. .++.. -..-|++||-|+.+|
T Consensus 8 V~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~D-VR~--te--~Dkv~---~~~~FrpGDIVrA~V 79 (82)
T PF10447_consen 8 VIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQD-VRA--TE--KDKVK---MYDCFRPGDIVRARV 79 (82)
T ss_dssp EEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEG-GGT---S--S-------GGGT--SSSEEEEEE
T ss_pred EEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeee-ecc--cc--cchhh---HHhccCCCCEEEEEE
Confidence 45777788888888876533 3456666655 100 00 00000 034689999999998
Q ss_pred E
Q psy4846 232 S 232 (279)
Q Consensus 232 ~ 232 (279)
.
T Consensus 80 i 80 (82)
T PF10447_consen 80 I 80 (82)
T ss_dssp E
T ss_pred e
Confidence 5
No 133
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=40.61 E-value=1.3e+02 Score=21.19 Aligned_cols=47 Identities=9% Similarity=-0.002 Sum_probs=29.5
Q ss_pred ceEEEEE-eCeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeecC-eEecCCCeEEEEEE
Q psy4846 171 GYVLYVR-KNAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGS-VVFHSFDPVTVQLS 232 (279)
Q Consensus 171 g~V~~V~-~~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~-~~~~lGD~V~VkV~ 232 (279)
|+|.... +.|+ ||.-++-+-+-++|.+. +. ..+ ..++.||+|+..+.
T Consensus 4 G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~-~~--------------~~g~~~l~~G~~V~f~~~ 53 (68)
T TIGR02381 4 GIVKWFNNAKGFGFICPEGVDGDIFAHYST-IQ--------------MDGYRTLKAGQKVQFEVV 53 (68)
T ss_pred eEEEEEeCCCCeEEEecCCCCccEEEEHHH-hh--------------hcCCCCCCCCCEEEEEEE
Confidence 4444444 3455 45555556778888876 21 112 46899999999875
No 134
>PRK15463 cold shock-like protein CspF; Provisional
Probab=40.23 E-value=95 Score=22.17 Aligned_cols=49 Identities=8% Similarity=-0.132 Sum_probs=30.7
Q ss_pred cceEEEEEe-CeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEE
Q psy4846 170 DGYVLYVRK-NAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLS 232 (279)
Q Consensus 170 ~g~V~~V~~-~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~ 232 (279)
.|+|..-.. .|+ |+.-++-+-+-+||++. +... +...++.||+|...+.
T Consensus 6 ~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sa-l~~~-------------g~~~l~~G~~V~f~v~ 56 (70)
T PRK15463 6 TGIVKTFDGKSGKGLITPSDGRKDVQVHISA-LNLR-------------DAEELTTGLRVEFCRI 56 (70)
T ss_pred eEEEEEEeCCCceEEEecCCCCccEEEEehh-hhhc-------------CCCCCCCCCEEEEEEE
Confidence 455555554 454 45555555678888887 3100 1246899999999875
No 135
>PRK11570 peptidyl-prolyl cis-trans isomerase; Provisional
Probab=40.20 E-value=2.5e+02 Score=24.41 Aligned_cols=22 Identities=18% Similarity=0.024 Sum_probs=16.2
Q ss_pred cCccccccchhhhccccccccc
Q psy4846 257 VSSAGEQGEEKMEEGETRSLYC 278 (279)
Q Consensus 257 ~~~~~~~~~~~~~~~~~~~~~~ 278 (279)
+..+|+++-..|.+|++.-++|
T Consensus 154 vipG~~eaL~~M~~G~k~~~~I 175 (206)
T PRK11570 154 VIPGWIEALTLMPVGSKWELTI 175 (206)
T ss_pred hhhHHHHHHcCCCCCCEEEEEE
Confidence 4557777888888888776665
No 136
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=38.81 E-value=1.3e+02 Score=23.09 Aligned_cols=59 Identities=22% Similarity=0.295 Sum_probs=39.9
Q ss_pred HHHHhhc-cceeeEEEEEeecchhhhhcCCCcccCCcceEEEEEeCeEEEEecCcceeEEEEc
Q psy4846 135 HLFFRSR-VQDEDGYVLYVRKNALQILIPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFL 196 (279)
Q Consensus 135 ~~~l~~~-~~~~~g~V~~~~~~~~~~~~p~~~~~~~~g~V~~V~~~Gi~V~Lp~~giEG~V~l 196 (279)
..||+++ +++. +.+.|++..-++ +|.-+-|..+|+|++++...+.|.+.+-+.+..|.+
T Consensus 27 sr~l~ey~~Gd~--V~I~IdpSv~kG-mPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k~K~liv 86 (98)
T COG2139 27 SRYLQEYKVGDK--VHIDIDPSVHKG-MPHPRFQGKTGTVVGVRGRAYKVEVYDGNKEKTLIV 86 (98)
T ss_pred hhHHhhccCCCE--EEEEeCcccccC-CCCccccCcceEEEeccCCEEEEEEecCCceEEEEe
Confidence 3567665 3433 333345544455 899999999999999999999888776455544433
No 137
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=37.59 E-value=1.2e+02 Score=26.14 Aligned_cols=66 Identities=17% Similarity=0.055 Sum_probs=40.4
Q ss_pred CCcceEEEEEeCeEEEEecCcce-----------eEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccc
Q psy4846 168 DEDGYVLYVRKNALQILIPKYGL-----------EGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRS 236 (279)
Q Consensus 168 ~~~g~V~~V~~~Gi~V~Lp~~gi-----------EG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~v 236 (279)
.+=|.|++++...+.|.+- ++ .|-+|+++ ..+.+.. .-...|++||-|+.+|. +.
T Consensus 67 iV~grV~~v~~~~a~V~i~--~ve~~~r~~~~~~~~~ihvs~-~~~~~~~---------~~~d~f~~GDivrA~Vi--s~ 132 (188)
T COG1096 67 IVYGRVTDVREQRALVRIV--GVEGKERELATSGAADIHVSQ-VRDGYVE---------KLSDAFRIGDIVRARVI--ST 132 (188)
T ss_pred EEEEEEeeccceEEEEEEE--EEecccccCCCCceeeEEEEe-ccccccc---------ccccccccccEEEEEEE--ec
Confidence 4567788888888877763 33 34556655 1111110 01357999999999997 43
Q ss_pred cCCCCeEEEEEecC
Q psy4846 237 NVQHEKLVLRLVRP 250 (279)
Q Consensus 237 d~~~~~I~~~lv~~ 250 (279)
- ..+.|+..++
T Consensus 133 ~---~~~~Lst~~~ 143 (188)
T COG1096 133 G---DPIQLSTKGN 143 (188)
T ss_pred C---CCeEEEecCC
Confidence 1 3367777665
No 138
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=36.46 E-value=1.5e+02 Score=20.68 Aligned_cols=56 Identities=18% Similarity=0.116 Sum_probs=32.2
Q ss_pred ceEEEEEeCeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEE
Q psy4846 171 GYVLYVRKNAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLV 244 (279)
Q Consensus 171 g~V~~V~~~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~ 244 (279)
|.|+....++. .|.+++ |.+-+++++. . + ....-++.||.|.|.+. .-|..+++|.
T Consensus 7 ~~V~~~lG~~~~~V~~~d-g~~~l~~i~g----K-~----------r~~iwI~~GD~V~V~~~--~~d~~kG~Ii 63 (65)
T PF01176_consen 7 GRVTEMLGNNLFEVECED-GEERLARIPG----K-F----------RKRIWIKRGDFVLVEPS--PYDKVKGRII 63 (65)
T ss_dssp EEEEEEESSSEEEEEETT-SEEEEEEE-H----H-H----------HTCC---TTEEEEEEES--TTCTTEEEEE
T ss_pred EEEEEECCCCEEEEEeCC-CCEEEEEecc----c-e----------eeeEecCCCCEEEEEec--ccCCCeEEEE
Confidence 44457776665 455665 7777777764 1 0 01335899999999875 5565555554
No 139
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=35.50 E-value=1.5e+02 Score=20.33 Aligned_cols=47 Identities=15% Similarity=0.082 Sum_probs=24.9
Q ss_pred ceEEEEEe-CeE-EEEecCcceeEEEEcccCCCCCceeeecCCceEeecC-eEecCCCeEEEEEE
Q psy4846 171 GYVLYVRK-NAL-QILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGS-VVFHSFDPVTVQLS 232 (279)
Q Consensus 171 g~V~~V~~-~Gi-~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~-~~~~lGD~V~VkV~ 232 (279)
|+|....+ .|+ ||.-++-+-+-++|.++ + .... ..++.||.|+..+.
T Consensus 3 G~V~~~~~~kgyGFI~~~~~~~diFfh~s~-~--------------~~~~~~~l~~G~~V~F~~~ 52 (66)
T PF00313_consen 3 GTVKWFDDEKGYGFITSDDGGEDIFFHISD-L--------------SGNGFRSLKEGDRVEFEVE 52 (66)
T ss_dssp EEEEEEETTTTEEEEEETTSSSEEEEEGGG-B--------------CSSSSTS--TTSEEEEEEE
T ss_pred EEEEEEECCCCceEEEEcccceeEEecccc-c--------------cccccccCCCCCEEEEEEE
Confidence 34445554 222 34444434456677765 2 1112 46899999999986
No 140
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=34.52 E-value=92 Score=21.26 Aligned_cols=30 Identities=10% Similarity=0.073 Sum_probs=23.8
Q ss_pred CeEecCCCeEEEEEEeccccCCCCeEEEEEecCC
Q psy4846 218 SVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVRPV 251 (279)
Q Consensus 218 ~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~~~ 251 (279)
+..+.+||.|+|+|. +++ .+++++.+.-|.
T Consensus 9 gE~I~Ig~~I~I~Vl--~i~--~~~VklgI~AP~ 38 (54)
T PF02599_consen 9 GESIVIGDDIEITVL--EIS--GGQVKLGIDAPK 38 (54)
T ss_dssp T-EEEETTTEEEEEE--EEE--TTEEEEEEEECT
T ss_pred CCEEEECCCEEEEEE--EEc--CCEEEEEEECCC
Confidence 567889999999987 666 778999887764
No 141
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=32.41 E-value=2e+02 Score=23.00 Aligned_cols=30 Identities=20% Similarity=0.258 Sum_probs=21.8
Q ss_pred CCcceEEEEEe--CeEEEEecCcceeEEEEccc
Q psy4846 168 DEDGYVLYVRK--NALQILIPKYGLEGTLFLRC 198 (279)
Q Consensus 168 ~~~g~V~~V~~--~Gi~V~Lp~~giEG~V~l~~ 198 (279)
.++|.|..+.+ ..+-+.-++ |+|-+||+--
T Consensus 41 P~~G~v~~i~~T~HA~~i~~~~-G~eiLiHiGi 72 (124)
T cd00210 41 PVDGTIVQIFPTKHAIGIESDS-GVEILIHIGI 72 (124)
T ss_pred cCCeEEEEEccCCCEEEEEeCC-CcEEEEEeee
Confidence 45888888865 555555554 9999999864
No 142
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=31.88 E-value=1.1e+02 Score=20.54 Aligned_cols=14 Identities=14% Similarity=0.126 Sum_probs=9.2
Q ss_pred eEecCCCeEEEEEE
Q psy4846 219 VVFHSFDPVTVQLS 232 (279)
Q Consensus 219 ~~~~lGD~V~VkV~ 232 (279)
..++.||+|.+.+.
T Consensus 45 L~L~~G~~V~~~ik 58 (64)
T PF03459_consen 45 LGLKPGDEVYASIK 58 (64)
T ss_dssp CT-STT-EEEEEE-
T ss_pred cCCCCCCEEEEEEe
Confidence 35789999999875
No 143
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: 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 Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=30.01 E-value=2e+02 Score=20.26 Aligned_cols=28 Identities=7% Similarity=0.027 Sum_probs=22.2
Q ss_pred CeEecCCCeEEEEEEeccccCCCCeEEEEE
Q psy4846 218 SVVFHSFDPVTVQLSLDRSNVQHEKLVLRL 247 (279)
Q Consensus 218 ~~~~~lGD~V~VkV~~~~vd~~~~~I~~~l 247 (279)
+..+..|+++++.|. .+|..+-++..+|
T Consensus 38 g~nl~pGqK~kaviL--hvD~l~~~VhVSl 65 (65)
T cd05700 38 GVNVTPGCKLKAVIL--HVDFVKSQVHVSL 65 (65)
T ss_pred ceecCCCceeEEEEE--EEeeEEeEEEEeC
Confidence 667899999999988 8888766666553
No 144
>TIGR00830 PTBA PTS system, glucose subfamily, IIA component. These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are demonstrably homologous. These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-c
Probab=29.84 E-value=2.4e+02 Score=22.47 Aligned_cols=31 Identities=19% Similarity=0.145 Sum_probs=21.4
Q ss_pred cCCcceEEEEEe--CeEEEEecCcceeEEEEccc
Q psy4846 167 QDEDGYVLYVRK--NALQILIPKYGLEGTLFLRC 198 (279)
Q Consensus 167 ~~~~g~V~~V~~--~Gi~V~Lp~~giEG~V~l~~ 198 (279)
+.++|.|..+.+ ..+-+.-. -|+|-+||+--
T Consensus 40 AP~~G~v~~v~~T~HA~gi~~~-~G~evLiHiGi 72 (121)
T TIGR00830 40 APVDGKIGKIFPTKHAFGIESD-SGVEILIHIGI 72 (121)
T ss_pred ccCCeEEEEEccCCCEEEEEeC-CCcEEEEEeee
Confidence 345888888876 44444444 49999999864
No 145
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=26.98 E-value=60 Score=20.57 Aligned_cols=32 Identities=9% Similarity=0.110 Sum_probs=24.4
Q ss_pred cCCcceEEEEE-eCeEEEEecCcceeEEEEccc
Q psy4846 167 QDEDGYVLYVR-KNALQILIPKYGLEGTLFLRC 198 (279)
Q Consensus 167 ~~~~g~V~~V~-~~Gi~V~Lp~~giEG~V~l~~ 198 (279)
+...|.|+++. +..+.|+..+||-...|..++
T Consensus 13 ~wyra~V~~~~~~~~~~V~f~DyG~~~~v~~~~ 45 (48)
T cd04508 13 KWYRAKITSILSDGKVEVFFVDYGNTEVVPLSD 45 (48)
T ss_pred eEEEEEEEEECCCCcEEEEEEcCCCcEEEeHHH
Confidence 34567777888 666889999999888877654
No 146
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=26.86 E-value=2.4e+02 Score=24.44 Aligned_cols=13 Identities=31% Similarity=0.623 Sum_probs=10.7
Q ss_pred HHHHHHHHHHcCC
Q psy4846 84 IVHRLLAACIGAD 96 (279)
Q Consensus 84 ivHR~L~a~l~~~ 96 (279)
|||.+++.+|...
T Consensus 96 IvHelfQ~~l~~~ 108 (209)
T PF08696_consen 96 IVHELFQKALRTN 108 (209)
T ss_pred eHHHHHHHHHhcc
Confidence 7999999999543
No 147
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=25.24 E-value=1.6e+02 Score=27.03 Aligned_cols=61 Identities=21% Similarity=0.176 Sum_probs=34.8
Q ss_pred cceEEEEEeCeEEEEecCcceeEEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEEeccccCCCCeEEEEEec
Q psy4846 170 DGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVR 249 (279)
Q Consensus 170 ~g~V~~V~~~Gi~V~Lp~~giEG~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~ 249 (279)
+|.|+...++|..|.+ |.+..+.++. .+..|++|+|+|. +.. ..+.....+
T Consensus 110 eG~v~~~~~~~~~v~i---G~~~~~~l~~---------------------~~~~~~RvTvri~--~~~---~p~~~~~~~ 160 (272)
T COG2106 110 EGLVIRRGKKGNLVDI---GKDKLAKLSS---------------------PAPPGARVTVRII--SRS---SPLRVEPAE 160 (272)
T ss_pred ceEEEEecCCceEEEe---cCCcceeccC---------------------CCCCCceEEEEEE--ecc---CceeeecCC
Confidence 6666677777755544 4444444432 2789999999986 331 334444444
Q ss_pred CCc-cCcccCc
Q psy4846 250 PVI-EGFSVSS 259 (279)
Q Consensus 250 ~~~-~~~~~~~ 259 (279)
|.. -|..+..
T Consensus 161 ~~~YwGY~V~~ 171 (272)
T COG2106 161 PPDYWGYKVRI 171 (272)
T ss_pred CCCcCcEEEEe
Confidence 433 4554433
No 148
>COG0141 HisD Histidinol dehydrogenase [Amino acid transport and metabolism]
Probab=24.27 E-value=1.1e+02 Score=29.81 Aligned_cols=41 Identities=17% Similarity=0.348 Sum_probs=26.7
Q ss_pred HHHHHHHHHhh-ccccccCcCCCCCccccccCCC------CccccccCcc
Q psy4846 36 GKELATSLDAA-AVYFSSGMLQQSDFHHYGLATP------IYTHFTSPIR 78 (279)
Q Consensus 36 ~~~l~~~L~~~-A~Y~~~~~~~~~~~~H~gL~~~------~YthfTSPIR 78 (279)
+.++...++.+ +.|. |.+++++.|+|..|-. -|+-|+||+-
T Consensus 329 p~~~l~~I~nAGsIFl--G~~sPe~~GDY~aG~NHVLPT~g~AR~~s~L~ 376 (425)
T COG0141 329 PRELLGKIRNAGSIFL--GHYSPESLGDYAAGPNHVLPTSGTARFSSGLS 376 (425)
T ss_pred HHHHHHHhcccceeee--cCCCCccccccccCCCccCCCCccchhcCCcc
Confidence 33444444444 4443 7788999999998865 4677777764
No 149
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=24.11 E-value=85 Score=20.60 Aligned_cols=33 Identities=12% Similarity=0.067 Sum_probs=26.0
Q ss_pred ccCCcceEEEEEe-CeEEEEecCcceeEEEEccc
Q psy4846 166 VQDEDGYVLYVRK-NALQILIPKYGLEGTLFLRC 198 (279)
Q Consensus 166 ~~~~~g~V~~V~~-~Gi~V~Lp~~giEG~V~l~~ 198 (279)
.....|.|+++.+ ..+.|...+||-...|...+
T Consensus 16 ~~wyra~I~~~~~~~~~~V~f~D~G~~~~v~~~~ 49 (57)
T smart00333 16 GEWYRARIIKVDGEQLYEVFFIDYGNEEVVPPSD 49 (57)
T ss_pred CCEEEEEEEEECCCCEEEEEEECCCccEEEeHHH
Confidence 3456778889988 78899999999888777655
No 150
>PRK01712 carbon storage regulator; Provisional
Probab=23.02 E-value=2.1e+02 Score=20.36 Aligned_cols=30 Identities=10% Similarity=0.098 Sum_probs=23.9
Q ss_pred CeEecCCCeEEEEEEeccccCCCCeEEEEEecCC
Q psy4846 218 SVVFHSFDPVTVQLSLDRSNVQHEKLVLRLVRPV 251 (279)
Q Consensus 218 ~~~~~lGD~V~VkV~~~~vd~~~~~I~~~lv~~~ 251 (279)
+..+.+||.++|+|. .++ .+++++.+--|.
T Consensus 9 gE~I~Igd~I~I~V~--~i~--~~~VrlGI~AP~ 38 (64)
T PRK01712 9 GESLMIGDDIEVTVL--GVK--GNQVRIGINAPK 38 (64)
T ss_pred CCEEEeCCCEEEEEE--EEe--CCEEEEEEECCC
Confidence 567899999999987 554 678999887764
No 151
>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]
Probab=22.70 E-value=16 Score=32.39 Aligned_cols=22 Identities=41% Similarity=0.816 Sum_probs=18.6
Q ss_pred CCccccccCccccchHHHHHHH
Q psy4846 68 PIYTHFTSPIRRYADIIVHRLL 89 (279)
Q Consensus 68 ~~YthfTSPIRRY~DlivHR~L 89 (279)
|.|-+|==|.++|||+|+++-.
T Consensus 170 p~~~~fIeptk~~ADiiip~~~ 191 (218)
T COG0572 170 PMYEQFIEPTKKYADIIIPSGG 191 (218)
T ss_pred hhhhhccCcccccceEEeecCC
Confidence 4577888899999999998854
No 152
>COG1278 CspC Cold shock proteins [Transcription]
Probab=22.04 E-value=2.8e+02 Score=19.81 Aligned_cols=47 Identities=11% Similarity=0.179 Sum_probs=28.1
Q ss_pred ceEEEEEe-CeEEEEecCcc-eeEEEEcccCCCCCceeeecCCceEeec-CeEecCCCeEEEEEE
Q psy4846 171 GYVLYVRK-NALQILIPKYG-LEGTLFLRCDSPSVSWTYNEKEQSQSCG-SVVFHSFDPVTVQLS 232 (279)
Q Consensus 171 g~V~~V~~-~Gi~V~Lp~~g-iEG~V~l~~~~~~d~~~~~~~~~~l~~~-~~~~~lGD~V~VkV~ 232 (279)
|+|..... .|+=...|+-| -+.+||++. . ... -+.+..||+|...+.
T Consensus 4 GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sa-i--------------~~~g~~~L~eGQ~V~f~~~ 53 (67)
T COG1278 4 GTVKWFNATKGFGFITPEDGGKDVFVHISA-I--------------QRAGFRTLREGQKVEFEVE 53 (67)
T ss_pred ceEEEeeCCCcceEcCCCCCCcCEEEEeee-e--------------ccCCCcccCCCCEEEEEEe
Confidence 33434433 34433335556 678899886 2 112 257899999999875
No 153
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=21.38 E-value=1.2e+02 Score=18.74 Aligned_cols=32 Identities=19% Similarity=0.300 Sum_probs=17.7
Q ss_pred CCccCHHHHHHHHHHcCCcccCCCH-HHHHHHH
Q psy4846 12 PPPANFEPLLHAARRQGFELSVGTG-KELATSL 43 (279)
Q Consensus 12 P~~~~~~~l~~~~~~~g~~~~~~~~-~~l~~~L 43 (279)
|..-++.+|+..+..+|++++.+.. .+|-+.+
T Consensus 1 p~sltV~~Lk~iL~~~~I~~ps~AkKaeLv~L~ 33 (35)
T PF12949_consen 1 PKSLTVAQLKRILDEHGIEFPSNAKKAELVALF 33 (35)
T ss_dssp STT--SHHHHHHHHHHT---SSS--SHHHHHH-
T ss_pred CCcCcHHHHHHHHHHcCCCCCCCCCHHHHHHHH
Confidence 4556788999999999999876643 3454443
No 154
>PF14444 S1-like: S1-like
Probab=20.92 E-value=1.4e+02 Score=20.75 Aligned_cols=15 Identities=27% Similarity=0.007 Sum_probs=11.5
Q ss_pred CeEecCCCeEEEEEE
Q psy4846 218 SVVFHSFDPVTVQLS 232 (279)
Q Consensus 218 ~~~~~lGD~V~VkV~ 232 (279)
+...++||+|.|.-.
T Consensus 31 G~~P~vGdrV~v~A~ 45 (58)
T PF14444_consen 31 GNVPKVGDRVLVEAI 45 (58)
T ss_pred cCCCccCCEEEEEEE
Confidence 445699999999753
No 155
>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=20.79 E-value=3.1e+02 Score=21.39 Aligned_cols=44 Identities=16% Similarity=0.062 Sum_probs=26.9
Q ss_pred CcceEEEEEeCeEEEEecCccee--EEEEcccCCCCCceeeecCCceEeecCeEecCCCeEEEEEE
Q psy4846 169 EDGYVLYVRKNALQILIPKYGLE--GTLFLRCDSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLS 232 (279)
Q Consensus 169 ~~g~V~~V~~~Gi~V~Lp~~giE--G~V~l~~~~~~d~~~~~~~~~~l~~~~~~~~lGD~V~VkV~ 232 (279)
+.|.|..|.++-++|.+ |.. +.+.-.. ..+..|..|++|+|+|.
T Consensus 27 V~G~I~hvv~ddLYIDf---G~KFhcVc~rp~-----------------~~~~~y~~G~rV~lrLk 72 (104)
T PF10246_consen 27 VIGKIFHVVDDDLYIDF---GGKFHCVCKRPA-----------------VNGEKYVRGSRVRLRLK 72 (104)
T ss_pred EEEEEEEEecCceEEEe---CCceeEEEeccc-----------------ccccccccCCEEEEEEC
Confidence 36777788888776643 322 2222111 01346899999999986
No 156
>PRK09439 PTS system glucose-specific transporter subunit; Provisional
Probab=20.47 E-value=3.5e+02 Score=22.87 Aligned_cols=31 Identities=19% Similarity=0.144 Sum_probs=21.0
Q ss_pred cCCcceEEEEEeC--eEEEEecCcceeEEEEccc
Q psy4846 167 QDEDGYVLYVRKN--ALQILIPKYGLEGTLFLRC 198 (279)
Q Consensus 167 ~~~~g~V~~V~~~--Gi~V~Lp~~giEG~V~l~~ 198 (279)
+.++|.|..+.+. .+-+.-. -|+|-+||+--
T Consensus 62 AP~dG~V~~vf~T~HAigi~t~-~G~eiLIHiGi 94 (169)
T PRK09439 62 APVDGTIGKIFETNHAFSIESD-SGVELFVHFGI 94 (169)
T ss_pred ecCCeEEEEEcCCCCEEEEEeC-CCcEEEEEEee
Confidence 3458888888753 3334434 49999999864
Done!