Query 030170
Match_columns 182
No_of_seqs 160 out of 1404
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 09:37:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030170.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030170hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00448 rpoE DNA-directed RN 100.0 1.3E-47 2.8E-52 299.7 21.9 176 1-180 1-178 (179)
2 COG1095 RPB7 DNA-directed RNA 100.0 1.9E-47 4.1E-52 293.9 19.8 176 1-180 1-178 (183)
3 KOG3297 DNA-directed RNA polym 100.0 6.1E-48 1.3E-52 293.9 16.4 175 1-179 1-200 (202)
4 PTZ00162 DNA-directed RNA poly 100.0 2.3E-46 4.9E-51 291.3 20.9 168 1-175 1-171 (176)
5 PRK08563 DNA-directed RNA poly 100.0 4.5E-46 9.8E-51 292.8 19.7 176 1-180 1-178 (187)
6 KOG3298 DNA-directed RNA polym 100.0 3.5E-37 7.5E-42 231.0 19.5 168 1-175 1-170 (170)
7 PF08292 RNA_pol_Rbc25: RNA po 99.9 8.8E-26 1.9E-30 165.7 12.3 96 83-178 1-122 (122)
8 cd04330 RNAP_III_Rpc25_N RNAP_ 99.9 7.8E-24 1.7E-28 144.8 10.5 80 2-85 1-80 (80)
9 cd04329 RNAP_II_Rpb7_N RNAP_II 99.9 1.1E-23 2.4E-28 144.1 9.9 80 2-85 1-80 (80)
10 cd00655 RNAP_Rpb7_N_like RNAP_ 99.9 1.5E-23 3.3E-28 143.4 10.6 80 2-85 1-80 (80)
11 cd04331 RNAP_E_N RNAP_E_N: Rpo 99.9 3E-23 6.5E-28 141.9 10.1 79 2-84 1-79 (80)
12 cd04462 S1_RNAPII_Rpb7 S1_RNAP 99.8 4.6E-20 1E-24 128.4 11.7 87 85-173 1-88 (88)
13 PF03876 SHS2_Rpb7-N: SHS2 dom 99.7 2.8E-16 6.1E-21 104.6 10.2 70 8-81 1-70 (70)
14 cd04460 S1_RpoE S1_RpoE: RpoE, 99.6 3.4E-15 7.4E-20 105.9 9.0 94 87-180 1-96 (99)
15 cd04328 RNAP_I_Rpa43_N RNAP_I_ 99.5 1.8E-13 3.9E-18 95.4 9.5 79 1-85 8-89 (89)
16 cd04471 S1_RNase_R S1_RNase_R: 99.3 1.6E-11 3.5E-16 83.5 9.7 71 85-155 1-74 (83)
17 COG0539 RpsA Ribosomal protein 99.3 5.7E-11 1.2E-15 105.8 12.0 131 30-174 96-267 (541)
18 PRK11642 exoribonuclease R; Pr 99.2 2.7E-11 5.9E-16 113.4 8.4 158 17-174 565-736 (813)
19 PF00575 S1: S1 RNA binding do 99.2 1.3E-10 2.8E-15 77.5 9.0 66 82-157 1-67 (74)
20 cd05686 S1_pNO40 S1_pNO40: pNO 99.2 7.5E-11 1.6E-15 79.0 7.7 63 83-155 1-65 (73)
21 COG1098 VacB Predicted RNA bin 99.1 6.6E-11 1.4E-15 85.9 4.1 63 82-154 2-65 (129)
22 cd05705 S1_Rrp5_repeat_hs14 S1 99.1 3.2E-10 7E-15 76.3 6.6 66 84-156 2-68 (74)
23 TIGR02063 RNase_R ribonuclease 99.1 2.6E-10 5.6E-15 105.8 8.1 141 17-157 553-702 (709)
24 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.1 6.6E-10 1.4E-14 74.0 7.9 61 86-156 1-64 (71)
25 TIGR00358 3_prime_RNase VacB a 99.1 2.8E-10 6E-15 104.7 7.1 141 17-157 501-647 (654)
26 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.1 9.8E-10 2.1E-14 72.5 7.5 62 86-157 1-63 (69)
27 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.1 6E-10 1.3E-14 76.6 6.8 84 81-175 2-86 (86)
28 cd05706 S1_Rrp5_repeat_sc10 S1 99.1 1.5E-09 3.3E-14 72.2 8.5 63 84-156 2-65 (73)
29 cd05708 S1_Rrp5_repeat_sc12 S1 99.0 1.4E-09 3.1E-14 72.7 8.3 72 85-170 2-75 (77)
30 PRK08582 hypothetical protein; 99.0 7.8E-10 1.7E-14 83.2 7.7 63 82-154 2-65 (139)
31 cd05698 S1_Rrp5_repeat_hs6_sc5 99.0 1E-09 2.2E-14 72.5 7.1 61 86-156 1-62 (70)
32 cd04461 S1_Rrp5_repeat_hs8_sc7 99.0 1E-09 2.3E-14 75.0 7.3 65 82-156 11-76 (83)
33 cd04452 S1_IF2_alpha S1_IF2_al 99.0 2.4E-09 5.2E-14 71.6 8.7 64 83-156 1-67 (76)
34 cd05690 S1_RPS1_repeat_ec5 S1_ 99.0 1.5E-09 3.2E-14 71.3 7.2 62 86-156 1-63 (69)
35 cd05689 S1_RPS1_repeat_ec4 S1_ 99.0 3.5E-09 7.6E-14 70.3 8.2 63 85-156 3-66 (72)
36 cd05707 S1_Rrp5_repeat_sc11 S1 99.0 1.7E-09 3.6E-14 71.2 6.4 61 86-156 1-62 (68)
37 cd05684 S1_DHX8_helicase S1_DH 99.0 3E-09 6.4E-14 72.1 7.6 59 86-153 1-63 (79)
38 cd05704 S1_Rrp5_repeat_hs13 S1 99.0 1.6E-09 3.5E-14 72.3 5.6 60 84-153 2-63 (72)
39 PRK07252 hypothetical protein; 99.0 5.5E-09 1.2E-13 76.7 8.8 64 84-157 2-66 (120)
40 cd04454 S1_Rrp4_like S1_Rrp4_l 98.9 4.2E-09 9.1E-14 71.8 7.6 80 81-175 2-82 (82)
41 cd05703 S1_Rrp5_repeat_hs12_sc 98.9 5.7E-09 1.2E-13 69.9 7.5 64 86-157 1-65 (73)
42 PRK05807 hypothetical protein; 98.9 4.6E-09 1E-13 78.7 7.3 63 82-154 2-64 (136)
43 cd05688 S1_RPS1_repeat_ec3 S1_ 98.9 8.9E-09 1.9E-13 67.0 7.3 62 85-156 1-62 (68)
44 cd05692 S1_RPS1_repeat_hs4 S1_ 98.9 7.7E-09 1.7E-13 67.2 6.8 59 86-154 1-60 (69)
45 cd05685 S1_Tex S1_Tex: The C-t 98.9 6.6E-09 1.4E-13 67.5 6.1 61 86-156 1-62 (68)
46 cd05691 S1_RPS1_repeat_ec6 S1_ 98.9 1.2E-08 2.7E-13 67.5 7.5 61 86-156 1-62 (73)
47 cd04453 S1_RNase_E S1_RNase_E: 98.8 2E-08 4.4E-13 69.7 8.0 69 82-157 4-75 (88)
48 PLN00207 polyribonucleotide nu 98.8 1.2E-09 2.5E-14 102.4 2.1 69 76-154 744-814 (891)
49 PTZ00248 eukaryotic translatio 98.8 1.3E-08 2.9E-13 85.7 7.2 64 83-156 15-81 (319)
50 COG0539 RpsA Ribosomal protein 98.8 4.6E-08 9.9E-13 87.5 10.5 64 84-157 276-340 (541)
51 TIGR03591 polynuc_phos polyrib 98.8 4.2E-09 9.1E-14 97.3 4.0 90 55-154 586-678 (684)
52 PRK08059 general stress protei 98.8 4.5E-08 9.9E-13 72.0 8.2 64 83-156 5-69 (123)
53 cd05694 S1_Rrp5_repeat_hs2_sc2 98.8 7.4E-08 1.6E-12 64.7 8.4 65 84-168 3-69 (74)
54 PRK07899 rpsA 30S ribosomal pr 98.8 5.8E-08 1.3E-12 86.5 10.1 77 84-174 207-283 (486)
55 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.8 4.4E-08 9.5E-13 64.3 7.0 59 86-156 1-60 (66)
56 cd04472 S1_PNPase S1_PNPase: P 98.7 3.5E-08 7.5E-13 64.2 6.5 59 86-154 1-60 (68)
57 smart00316 S1 Ribosomal protei 98.7 7E-08 1.5E-12 62.6 7.9 62 85-156 2-64 (72)
58 cd05687 S1_RPS1_repeat_ec1_hs1 98.7 6.1E-08 1.3E-12 63.9 7.6 59 86-154 1-60 (70)
59 PRK04163 exosome complex RNA-b 98.7 1.6E-07 3.4E-12 76.5 10.8 85 81-176 59-144 (235)
60 PRK07400 30S ribosomal protein 98.7 8.2E-08 1.8E-12 81.4 8.4 82 83-178 194-275 (318)
61 COG0557 VacB Exoribonuclease R 98.7 3E-08 6.4E-13 92.1 6.0 141 17-157 552-697 (706)
62 PRK05054 exoribonuclease II; P 98.6 5.2E-08 1.1E-12 89.6 6.7 136 17-157 495-637 (644)
63 cd05702 S1_Rrp5_repeat_hs11_sc 98.6 1.9E-07 4.1E-12 61.7 6.8 62 86-155 1-63 (70)
64 TIGR02696 pppGpp_PNP guanosine 98.6 8E-08 1.7E-12 88.5 6.6 63 82-154 644-711 (719)
65 PRK03987 translation initiatio 98.6 1.5E-07 3.2E-12 77.8 7.4 64 83-156 6-72 (262)
66 PRK09521 exosome complex RNA-b 98.6 5.1E-07 1.1E-11 71.1 9.8 84 76-176 55-149 (189)
67 cd04473 S1_RecJ_like S1_RecJ_l 98.6 2.8E-07 6E-12 62.2 7.1 55 82-155 13-68 (77)
68 PRK11824 polynucleotide phosph 98.5 2.4E-07 5.3E-12 85.9 7.8 67 79-155 615-682 (693)
69 cd04465 S1_RPS1_repeat_ec2_hs2 98.5 6.6E-07 1.4E-11 58.5 7.5 58 86-155 1-58 (67)
70 cd04455 S1_NusA S1_NusA: N-uti 98.5 9.8E-07 2.1E-11 57.9 7.8 57 84-156 2-58 (67)
71 TIGR02062 RNase_B exoribonucle 98.4 3E-07 6.6E-12 84.5 6.0 134 17-157 491-633 (639)
72 PRK13806 rpsA 30S ribosomal pr 98.4 6.8E-07 1.5E-11 79.9 8.0 64 84-157 378-442 (491)
73 PRK13806 rpsA 30S ribosomal pr 98.4 8.1E-07 1.7E-11 79.5 8.2 78 84-174 291-369 (491)
74 PHA02945 interferon resistance 98.4 1.6E-06 3.4E-11 59.6 7.7 62 82-156 8-74 (88)
75 PRK07899 rpsA 30S ribosomal pr 98.4 1.2E-06 2.5E-11 78.2 8.6 63 85-157 293-356 (486)
76 cd05693 S1_Rrp5_repeat_hs1_sc1 98.4 6.5E-07 1.4E-11 63.6 5.3 85 84-169 2-96 (100)
77 COG2183 Tex Transcriptional ac 98.4 7.5E-07 1.6E-11 82.1 6.3 63 84-156 657-720 (780)
78 COG1185 Pnp Polyribonucleotide 98.3 2.1E-07 4.6E-12 84.5 2.5 69 76-154 610-679 (692)
79 cd00164 S1_like S1_like: Ribos 98.3 1.6E-06 3.5E-11 55.0 5.9 58 89-156 1-59 (65)
80 PRK06676 rpsA 30S ribosomal pr 98.3 1.8E-06 3.9E-11 74.9 7.8 74 83-170 190-263 (390)
81 PRK12269 bifunctional cytidyla 98.3 3.2E-06 6.8E-11 80.0 8.6 72 84-169 492-563 (863)
82 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.2 5.1E-06 1.1E-10 58.1 7.1 82 81-175 2-92 (92)
83 PRK12269 bifunctional cytidyla 98.2 4.3E-06 9.2E-11 79.2 8.5 67 84-157 751-818 (863)
84 PRK06299 rpsA 30S ribosomal pr 98.2 3.9E-06 8.4E-11 76.2 8.1 63 84-156 200-262 (565)
85 PRK06676 rpsA 30S ribosomal pr 98.2 6.7E-06 1.5E-10 71.3 8.7 64 84-157 276-340 (390)
86 PRK06299 rpsA 30S ribosomal pr 98.2 6.2E-06 1.3E-10 74.9 7.7 65 84-157 372-437 (565)
87 TIGR00717 rpsA ribosomal prote 98.1 8E-06 1.7E-10 73.2 8.2 64 84-157 445-509 (516)
88 PRK09202 nusA transcription el 98.1 5.2E-06 1.1E-10 73.8 6.6 69 84-170 133-201 (470)
89 TIGR00717 rpsA ribosomal prote 98.1 8E-06 1.7E-10 73.3 7.8 73 84-169 358-431 (516)
90 PRK00087 4-hydroxy-3-methylbut 98.1 1E-05 2.2E-10 74.7 8.4 64 84-157 561-625 (647)
91 KOG4134 DNA-dependent RNA poly 98.1 5E-05 1.1E-09 60.7 10.9 93 5-102 30-124 (253)
92 COG1093 SUI2 Translation initi 98.1 2.2E-06 4.8E-11 69.9 2.9 64 83-156 9-75 (269)
93 PRK07400 30S ribosomal protein 98.1 1.4E-05 3E-10 67.9 7.5 74 82-169 28-102 (318)
94 PRK00087 4-hydroxy-3-methylbut 98.0 1.5E-05 3.3E-10 73.6 7.3 63 84-156 476-538 (647)
95 PRK12327 nusA transcription el 97.9 3.4E-05 7.3E-10 66.5 6.3 69 84-170 133-201 (362)
96 COG1097 RRP4 RNA-binding prote 97.8 0.00036 7.7E-09 56.6 11.6 85 80-176 59-145 (239)
97 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.8 0.00021 4.5E-09 49.4 7.9 82 81-175 2-86 (86)
98 TIGR01953 NusA transcription t 97.7 9.1E-05 2E-09 63.4 6.5 70 84-171 130-200 (341)
99 PF03293 Pox_RNA_pol: Poxvirus 97.4 0.02 4.2E-07 42.7 14.7 148 9-169 10-160 (160)
100 PRK12328 nusA transcription el 97.4 0.00056 1.2E-08 59.1 6.7 75 81-172 134-209 (374)
101 TIGR00757 RNaseEG ribonuclease 97.3 0.0014 2.9E-08 57.7 9.1 76 82-157 22-102 (414)
102 COG1096 Predicted RNA-binding 96.9 0.0094 2E-07 46.7 8.8 80 79-175 58-148 (188)
103 PF10447 EXOSC1: Exosome compo 96.8 0.0051 1.1E-07 42.1 6.1 60 83-152 2-82 (82)
104 KOG1067 Predicted RNA-binding 96.8 0.0016 3.4E-08 58.7 4.3 63 84-156 667-730 (760)
105 PRK12329 nusA transcription el 96.8 0.004 8.6E-08 54.9 6.5 75 81-172 148-228 (449)
106 COG1107 Archaea-specific RecJ- 95.7 0.0088 1.9E-07 54.2 3.3 58 84-157 121-179 (715)
107 PRK11712 ribonuclease G; Provi 95.6 0.073 1.6E-06 47.9 8.6 75 82-157 35-115 (489)
108 PHA02858 EIF2a-like PKR inhibi 95.3 0.032 6.9E-07 38.2 4.1 64 80-155 11-77 (86)
109 KOG1070 rRNA processing protei 95.2 0.023 5E-07 56.1 4.4 64 84-157 598-662 (1710)
110 PRK10811 rne ribonuclease E; R 94.9 0.18 4E-06 48.5 9.1 75 82-157 35-112 (1068)
111 PF13509 S1_2: S1 domain; PDB: 94.7 0.094 2E-06 33.6 4.8 61 85-168 1-61 (61)
112 KOG3409 Exosomal 3'-5' exoribo 94.5 0.24 5.2E-06 38.5 7.5 63 82-154 65-138 (193)
113 cd05699 S1_Rrp5_repeat_hs7 S1_ 92.5 0.37 8.1E-06 32.1 4.9 55 86-150 1-60 (72)
114 COG1530 CafA Ribonucleases G a 92.2 1 2.2E-05 40.6 8.8 93 59-157 11-106 (487)
115 PF10246 MRP-S35: Mitochondria 91.9 0.85 1.8E-05 32.4 6.3 58 81-155 19-77 (104)
116 KOG1004 Exosomal 3'-5' exoribo 91.8 2.4 5.2E-05 34.0 9.5 95 70-176 50-146 (230)
117 KOG1070 rRNA processing protei 91.6 0.89 1.9E-05 45.5 8.2 63 84-156 1161-1224(1710)
118 COG2996 Predicted RNA-bindinin 88.1 1.6 3.5E-05 36.4 6.0 52 85-154 155-207 (287)
119 KOG2916 Translation initiation 83.8 0.56 1.2E-05 38.9 1.3 63 83-155 14-79 (304)
120 PF00313 CSD: 'Cold-shock' DNA 82.0 9.7 0.00021 24.1 6.5 49 89-151 1-53 (66)
121 COG4776 Rnb Exoribonuclease II 79.4 0.98 2.1E-05 40.4 1.3 76 82-157 558-637 (645)
122 PRK12442 translation initiatio 79.2 13 0.00028 25.6 6.5 54 88-155 8-63 (87)
123 KOG4078 Putative mitochondrial 78.2 6 0.00013 29.8 5.0 63 77-156 74-137 (173)
124 TIGR00008 infA translation ini 73.1 23 0.00051 23.2 6.7 53 88-154 6-60 (68)
125 KOG1856 Transcription elongati 72.2 10 0.00022 37.6 6.1 62 84-155 984-1049(1299)
126 PRK15464 cold shock-like prote 67.5 24 0.00052 23.1 5.5 50 89-152 5-58 (70)
127 PRK15463 cold shock-like prote 64.5 28 0.00061 22.7 5.4 49 89-151 5-57 (70)
128 COG0361 InfA Translation initi 64.5 40 0.00087 22.6 6.7 54 87-154 7-62 (75)
129 PRK09750 hypothetical protein; 61.0 7.3 0.00016 24.9 1.9 20 160-179 3-22 (64)
130 PRK09937 stationary phase/star 55.6 56 0.0012 21.6 5.7 50 90-153 3-56 (74)
131 COG2996 Predicted RNA-bindinin 53.5 1.2E+02 0.0027 25.4 8.4 71 82-153 2-85 (287)
132 PRK09507 cspE cold shock prote 50.0 68 0.0015 20.7 5.6 51 89-153 4-58 (69)
133 PRK10943 cold shock-like prote 49.8 66 0.0014 20.8 5.2 51 89-153 4-58 (69)
134 COG2106 Uncharacterized conser 48.8 39 0.00085 28.2 4.8 27 82-108 102-128 (272)
135 PRK09890 cold shock protein Cs 48.0 75 0.0016 20.6 5.7 49 89-151 5-57 (70)
136 TIGR02381 cspD cold shock doma 42.2 86 0.0019 20.1 4.9 50 90-153 3-56 (68)
137 PF08206 OB_RNB: Ribonuclease 42.0 51 0.0011 20.4 3.6 14 138-151 31-44 (58)
138 cd04458 CSP_CDS Cold-Shock Pro 41.9 85 0.0019 19.5 5.2 16 137-152 39-54 (65)
139 PRK10354 RNA chaperone/anti-te 41.0 98 0.0021 20.0 5.6 49 89-152 5-58 (70)
140 KOG3013 Exosomal 3'-5' exoribo 39.0 54 0.0012 27.3 4.2 42 79-120 79-122 (301)
141 PF01938 TRAM: TRAM domain; I 38.8 51 0.0011 20.4 3.3 24 82-105 37-60 (61)
142 PF11604 CusF_Ec: Copper bindi 38.7 37 0.00081 22.0 2.7 52 91-153 1-57 (70)
143 PF07238 PilZ: PilZ domain; I 38.5 1.1E+02 0.0024 19.9 5.6 33 74-106 10-42 (102)
144 PF06688 DUF1187: Protein of u 38.2 19 0.00042 22.9 1.2 18 161-178 1-18 (61)
145 COG3323 Uncharacterized protei 35.0 59 0.0013 23.4 3.4 67 10-104 9-75 (109)
146 PF02237 BPL_C: Biotin protein 34.9 71 0.0015 18.9 3.3 19 85-103 11-29 (48)
147 PRK04012 translation initiatio 30.6 1.9E+02 0.0042 20.3 7.2 58 80-153 15-74 (100)
148 cd04486 YhcR_OBF_like YhcR_OBF 29.8 1.7E+02 0.0036 19.3 5.8 17 89-105 2-22 (78)
149 PRK09838 periplasmic copper-bi 27.6 2E+02 0.0043 20.8 5.2 55 89-151 45-101 (115)
150 PRK14998 cold shock-like prote 26.0 2E+02 0.0043 18.8 5.5 50 90-153 3-56 (73)
151 KOG0459 Polypeptide release fa 25.6 1.4E+02 0.0029 26.9 4.7 33 137-170 360-392 (501)
152 PF14326 DUF4384: Domain of un 24.7 1.7E+02 0.0036 19.3 4.2 14 138-151 2-15 (83)
153 cd05701 S1_Rrp5_repeat_hs10 S1 23.9 1.5E+02 0.0032 19.4 3.4 55 90-155 5-62 (69)
154 PF01629 DUF22: Domain of unkn 23.7 2.1E+02 0.0047 20.6 4.7 26 132-157 42-67 (112)
155 PF01835 A2M_N: MG2 domain; I 22.4 1.9E+02 0.004 19.4 4.2 19 137-155 9-27 (99)
156 KOG3342 Signal peptidase I [In 20.8 1.9E+02 0.0042 22.3 4.1 42 111-153 51-92 (180)
157 PF00394 Cu-oxidase: Multicopp 20.2 1.9E+02 0.0042 21.4 4.2 18 138-155 63-80 (159)
No 1
>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=100.00 E-value=1.3e-47 Score=299.71 Aligned_cols=176 Identities=22% Similarity=0.436 Sum_probs=161.1
Q ss_pred CeEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEE
Q 030170 1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGIT 80 (182)
Q Consensus 1 MF~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~ 80 (182)
||++++++|+|+|||++|++ ++++++.++|+++| +||+++++|+||+++++.++++|+|.||||+++++|+|+|++
T Consensus 1 Mf~~~~l~d~v~i~P~~~~~---~~~~~i~~~l~~~~-~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~ 76 (179)
T TIGR00448 1 MYILSKIADTVRIPPDQFGE---DLEEVITHQLNEKF-EGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALV 76 (179)
T ss_pred CeEEEEEeeEEEECHHHhCc---cHHHHHHHHHHHHh-cCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEE
Confidence 99999999999999999998 89999999998887 799999999999999999999999999999999999999999
Q ss_pred eeecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecC-CCcEEEcCCCceEcCCCeEEEEEEEEEeccc-c
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQA-ENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA-E 158 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~-~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~-~ 158 (182)
|+|++||+++|+|++++++|+|+++||++|++|+++++++++.+++ +..|.|.+...+|+.||.|||||.++++.++ .
T Consensus 77 f~p~~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~ 156 (179)
T TIGR00448 77 FKPELGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP 156 (179)
T ss_pred EeccCCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC
Confidence 9999999999999999999999999999999999999999876665 4556665444799999999999999998654 2
Q ss_pred cceEEEEeccCCCccccCCCCC
Q 030170 159 REFQALVSLEGDFLGPVSCENP 180 (182)
Q Consensus 159 ~~~~i~gs~~~~gLG~i~w~~~ 180 (182)
....+.+||+++|||++.|+++
T Consensus 157 ~~~~I~lt~k~~~LG~~~w~~~ 178 (179)
T TIGR00448 157 EGSKIGLTMRQPLLGKLEWIEE 178 (179)
T ss_pred CcceEEEEeccCcCCccccccc
Confidence 3446899999999999999975
No 2
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=100.00 E-value=1.9e-47 Score=293.92 Aligned_cols=176 Identities=26% Similarity=0.437 Sum_probs=163.8
Q ss_pred CeEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEE
Q 030170 1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGIT 80 (182)
Q Consensus 1 MF~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~ 80 (182)
||++++++|+|+|||++|+. ++++++.+.|.++| +|||+.+.|+||+++++.++++|+|.+|||+++++|.|++++
T Consensus 1 My~l~~~~d~VripP~~fg~---~~~~~v~~~L~~k~-eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~ 76 (183)
T COG1095 1 MYKLVELEDTVRIPPSYFGE---DLEEAVKEELKEKY-EGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALV 76 (183)
T ss_pred CcEEEEEeeEEEeCHHHcCc---cHHHHHHHHHHHHh-cceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEE
Confidence 99999999999999999988 89999999998887 899999999999999999999999999999999999999999
Q ss_pred eeecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCC-ceEcCCCeEEEEEEEEEeccc-c
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKN-PKIEKDVVVRVIVIGTKWLEA-E 158 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~-~~~~~Gd~VrvrV~~v~~~~~-~ 158 (182)
|+|+.||+++|.|+++++||+||.+||+++++|.+++++|+..+++++..+.++++ +.++.||.||+||+++++..+ .
T Consensus 77 fkP~~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~ 156 (183)
T COG1095 77 FKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRP 156 (183)
T ss_pred EEeccccEEEEEEEEEeecceEEEeccccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcc
Confidence 99999999999999999999999999999999999999997767776666777777 599999999999999999654 2
Q ss_pred cceEEEEeccCCCccccCCCCC
Q 030170 159 REFQALVSLEGDFLGPVSCENP 180 (182)
Q Consensus 159 ~~~~i~gs~~~~gLG~i~w~~~ 180 (182)
....|.+||+++|||.+.||.+
T Consensus 157 ~~~~I~lTmrq~~LGklew~~~ 178 (183)
T COG1095 157 RESKIGLTMRQPGLGKLEWIEE 178 (183)
T ss_pred ccceEEEEeccccCCcchhhhh
Confidence 3568999999999999999965
No 3
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=6.1e-48 Score=293.89 Aligned_cols=175 Identities=22% Similarity=0.345 Sum_probs=162.0
Q ss_pred CeEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEE
Q 030170 1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGIT 80 (182)
Q Consensus 1 MF~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~ 80 (182)
||++++++|+|+|||++|.+ +++++|.++|.+++ +||+++|+|+|||++||..+++|.|.||||..+.+|.||+++
T Consensus 1 MF~Lsel~D~VrI~P~qf~~---~~~~ai~~eL~~k~-anKvl~nvGLCI~vyDi~~v~e~~v~pGDGas~~~V~FR~vV 76 (202)
T KOG3297|consen 1 MFYLSELEDTVRIPPSQFEK---PLEDAIKEELNRKL-ANKVLPNVGLCICVYDILEVEEGIVLPGDGASYARVWFRVVV 76 (202)
T ss_pred CeeehhcccceecChHHhCc---hHHHHHHHHHHHHH-HhhhcccccEEEEEeEeeeecceEEecCCCceEEEEEEEEEE
Confidence 99999999999999999999 79999998888776 899999999999999999999999999999999999999999
Q ss_pred eeecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeec-CCCcEEEcCC------Cc-eEcCCCeEEEEEEEE
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQ-AENPVFLSEK------NP-KIEKDVVVRVIVIGT 152 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~-~~~~~~~~~~------~~-~~~~Gd~VrvrV~~v 152 (182)
||||+||++.|+|+++++.|+.+.++|||++++|.++++++..++ ++..|+|.++ ++ ++..|..|||||.+.
T Consensus 77 FrPF~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e 156 (202)
T KOG3297|consen 77 FRPFVGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDE 156 (202)
T ss_pred EecccceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeee
Confidence 999999999999999999999999999999999999999885544 5667999876 23 899999999999999
Q ss_pred Eeccc-----------------ccceEEEEeccCCCccccCCCC
Q 030170 153 KWLEA-----------------EREFQALVSLEGDFLGPVSCEN 179 (182)
Q Consensus 153 ~~~~~-----------------~~~~~i~gs~~~~gLG~i~w~~ 179 (182)
+|.+. .++|.++|+|+++|||+++||.
T Consensus 157 ~f~d~~p~~~~~~~t~~e~~e~~~py~l~gs~~~~GLG~lsWW~ 200 (202)
T KOG3297|consen 157 SFVDVSPEGNSTAITGAEDPEKESPYTLLGSMNEDGLGPLSWWD 200 (202)
T ss_pred cccccCccccccccccccccccCCCeEEEEEecCCCCccchhhh
Confidence 77542 3689999999999999999995
No 4
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=100.00 E-value=2.3e-46 Score=291.32 Aligned_cols=168 Identities=27% Similarity=0.456 Sum_probs=150.1
Q ss_pred CeEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEE
Q 030170 1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGIT 80 (182)
Q Consensus 1 MF~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~ 80 (182)
||++++++|+|+|||++|++ ++++++.+.|.+++ +||+++++|+||+++|+.++++|+|.+|||.++|+|+|+|++
T Consensus 1 MF~~~~l~d~v~i~P~~f~~---~~~~~i~~~L~~~~-egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~Fraiv 76 (176)
T PTZ00162 1 MFFVVELWKNVSLKPSQLGP---RYQQIIEDMLRSQV-EGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIV 76 (176)
T ss_pred CcEEEEEEEEEEECHHHcCc---cHHHHHHHHHHHHH-CCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEE
Confidence 99999999999999999988 79998888887776 899999999999999999999999999999999999999999
Q ss_pred eeecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeec-CCCcEEEc-CCC-ceEcCCCeEEEEEEEEEeccc
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQ-AENPVFLS-EKN-PKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~-~~~~~~~~-~~~-~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
|||++||+++|+|++++++|+|+++||++ ++++.++++++..++ +++.|.|. +++ .+++.|+.||+||.++.++.+
T Consensus 77 FrPf~gEVv~g~V~~v~~~G~~v~~Gp~~-ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~ 155 (176)
T PTZ00162 77 FKPFKDEVLDAIVTDVNKLGFFAQAGPLK-AFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDAS 155 (176)
T ss_pred EecCCCCEEEEEEEEEecceEEEEeeCeE-EEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCC
Confidence 99999999999999999999999999998 555555556555555 45667774 444 599999999999999999765
Q ss_pred ccceEEEEeccCCCcccc
Q 030170 158 EREFQALVSLEGDFLGPV 175 (182)
Q Consensus 158 ~~~~~i~gs~~~~gLG~i 175 (182)
.+.++|||++|+||++
T Consensus 156 --~~~~i~T~~~~~LG~~ 171 (176)
T PTZ00162 156 --NLFAIATINSDYLGPI 171 (176)
T ss_pred --CcEEEEEecCCCcCcc
Confidence 4789999999999998
No 5
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=100.00 E-value=4.5e-46 Score=292.76 Aligned_cols=176 Identities=25% Similarity=0.378 Sum_probs=158.5
Q ss_pred CeEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEE
Q 030170 1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGIT 80 (182)
Q Consensus 1 MF~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~ 80 (182)
||++++|+|+|+|||++|++ ++++++.+.|.++| +||+++++||||+++|+.++++|+|.||||.++++|+|++++
T Consensus 1 MF~~~~l~d~v~i~P~~~~~---~~~~~i~~~l~~~~-~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lv 76 (187)
T PRK08563 1 MYKLVKLEDVVRIPPEMFGE---DLEEAALEVLREKY-EGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALV 76 (187)
T ss_pred CeEEEEEeEEEEECHHHcCc---cHHHHHHHHHHHHh-hCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEE
Confidence 99999999999999999998 89998887777766 899999999999999999999999999999999999999999
Q ss_pred eeecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCc-EEEcCCCceEcCCCeEEEEEEEEEeccccc
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENP-VFLSEKNPKIEKDVVVRVIVIGTKWLEAER 159 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~-~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~ 159 (182)
|+|++||+++|+|++++++|+|+++||+++++|++++++++..++++++ |.+.+...+++.||.|||||.++++.+...
T Consensus 77 f~P~~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~ 156 (187)
T PRK08563 77 FKPELQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156 (187)
T ss_pred EeccCCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCC
Confidence 9999999999999999999999999999999999999998776665554 555444479999999999999999965421
Q ss_pred -ceEEEEeccCCCccccCCCCC
Q 030170 160 -EFQALVSLEGDFLGPVSCENP 180 (182)
Q Consensus 160 -~~~i~gs~~~~gLG~i~w~~~ 180 (182)
...+.+||+++|||+++||.+
T Consensus 157 ~~~~I~ls~~~~~LG~~~w~~~ 178 (187)
T PRK08563 157 RGSKIGLTMRQPGLGKLEWIEE 178 (187)
T ss_pred CCCEEEEEecCCCCCcHHHHHH
Confidence 247888999999999999954
No 6
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=3.5e-37 Score=231.03 Aligned_cols=168 Identities=45% Similarity=0.748 Sum_probs=150.4
Q ss_pred CeEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEE
Q 030170 1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGIT 80 (182)
Q Consensus 1 MF~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~ 80 (182)
||+...++..+.++|+++++ ++++.+.+.|.+.. +|||+.++||++++.+++++++|+|.+++|.+.|.|+|+|++
T Consensus 1 mff~~~l~~~i~l~p~~~gp---~~~~~l~~~L~~~v-eg~ctg~~Gyvi~vt~ld~Ig~g~I~~~~G~v~FpVky~av~ 76 (170)
T KOG3298|consen 1 MFFHKDLDLNICLHPSYFGP---NLQAILKRKLLAEV-EGKCTGKYGYVIAVTTLDNIGEGRIRPGTGFVTFPVKYKAVT 76 (170)
T ss_pred CcceeeeeeeeeecccccCc---hHHHHHHHHHHHHh-hccccccccEEEEEEEhhhccCCccccCCceEEEEEEEEEEE
Confidence 99999999999999999988 78876666666665 899999999999999999999999999999999999999999
Q ss_pred eeecCCCEEEEEEEEEecceEEEEecCcceEEEcCCc-CCCceeecCCC-cEEEcCCCceEcCCCeEEEEEEEEEecccc
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSK-MPDYRYVQAEN-PVFLSEKNPKIEKDVVVRVIVIGTKWLEAE 158 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~-~~d~~~~~~~~-~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~ 158 (182)
|+||+||+++|+|+++++.|+|+++||++ .+..|++ +||+.|.+.++ +.+...+...++.|+.||++|++.++..+
T Consensus 77 FkpfKGEVvdgvV~~Vnk~G~F~~~GPl~-~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~- 154 (170)
T KOG3298|consen 77 FKPFKGEVVDGVVTKVNKMGVFARSGPLE-VFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDET- 154 (170)
T ss_pred EeecCCcEEEEEEEEEeeeeEEEeccceE-eeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeee-
Confidence 99999999999999999999999999995 5555555 56787777766 56766666799999999999999999764
Q ss_pred cceEEEEeccCCCcccc
Q 030170 159 REFQALVSLEGDFLGPV 175 (182)
Q Consensus 159 ~~~~i~gs~~~~gLG~i 175 (182)
.+.++|||++|+||++
T Consensus 155 -~i~algtl~~D~LG~i 170 (170)
T KOG3298|consen 155 -EIFALGTLKGDYLGPI 170 (170)
T ss_pred -eEEEEEEecCcccccC
Confidence 6899999999999986
No 7
>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=99.93 E-value=8.8e-26 Score=165.67 Aligned_cols=96 Identities=22% Similarity=0.287 Sum_probs=77.3
Q ss_pred ecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeec-CCCcEEEcC-CC--ceEcCCCeEEEEEEEEEeccc-
Q 030170 83 IFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQ-AENPVFLSE-KN--PKIEKDVVVRVIVIGTKWLEA- 157 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~-~~~~~~~~~-~~--~~~~~Gd~VrvrV~~v~~~~~- 157 (182)
||+||++.|+|+++++.|+.|++|||+++++|.++|+++..++ +++.|+|.+ ++ -++..|+.|||||.++.|.+.
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f~d~~ 80 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIFPDVP 80 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE----
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEEecCC
Confidence 8999999999999999999999999999999999999886666 466799998 55 389999999999999999431
Q ss_pred ---------------------ccceEEEEeccCCCccccCCC
Q 030170 158 ---------------------EREFQALVSLEGDFLGPVSCE 178 (182)
Q Consensus 158 ---------------------~~~~~i~gs~~~~gLG~i~w~ 178 (182)
.++|.|+|||+++|||+++||
T Consensus 81 p~~~~~~~~~~~~~~~~~~~~~~Py~I~gs~~~~GLG~~sWW 122 (122)
T PF08292_consen 81 PTPPPSAEASGEEEEEEEDEPKPPYQIIGSINEDGLGLVSWW 122 (122)
T ss_dssp -----------------------SEEEEEEB-STT-EEGGGC
T ss_pred CCCcccccccccccccccccCCCCeEEEEEecCCCCcccccC
Confidence 369999999999999999999
No 8
>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.
Probab=99.91 E-value=7.8e-24 Score=144.83 Aligned_cols=80 Identities=18% Similarity=0.372 Sum_probs=76.1
Q ss_pred eEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEEe
Q 030170 2 FLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITF 81 (182)
Q Consensus 2 F~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~f 81 (182)
|++++++|+|+|||++|++ ++++++.++|.++| +||++++.|+||+++|+.++++|+|.+|||+++++|+|++++|
T Consensus 1 F~~~~l~d~v~i~P~~fg~---~~~~~i~~~L~~ky-~gkv~~~~Gl~v~v~di~~i~eG~I~~gdG~~~~~V~Fr~lvF 76 (80)
T cd04330 1 FILSEIEDTVRIPPSQFSR---PLNDAIEDELNKKY-ANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVF 76 (80)
T ss_pred CEEEEEEEEEEECHHHcCc---CHHHHHHHHHHHHh-CCcEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEE
Confidence 7899999999999999988 89998888887776 8999999999999999999999999999999999999999999
Q ss_pred eecC
Q 030170 82 KIFR 85 (182)
Q Consensus 82 ~p~~ 85 (182)
+|++
T Consensus 77 rPf~ 80 (80)
T cd04330 77 RPFV 80 (80)
T ss_pred ECCC
Confidence 9985
No 9
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter.
Probab=99.90 E-value=1.1e-23 Score=144.05 Aligned_cols=80 Identities=35% Similarity=0.689 Sum_probs=76.7
Q ss_pred eEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEEe
Q 030170 2 FLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITF 81 (182)
Q Consensus 2 F~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~f 81 (182)
|++++++|+|+|||++|++ ++++++.++|++++ +||+.+++|+||+++++.++++|+|.+|||.++++|+|+|++|
T Consensus 1 F~~~~l~d~v~i~P~~fg~---~l~~~i~~~L~~~~-egk~~~~~G~iv~v~di~~i~~G~I~~gdG~~~~~V~F~aivf 76 (80)
T cd04329 1 FFKIELEHNILLHPSYFGP---NLKEYLEQKLLEEV-EGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVF 76 (80)
T ss_pred CEEEEEEEEEEECHHHhCc---cHHHHHHHHHHHHh-CCcCcCceeEEEEEEEeeEecCcEEEcCCCCEEEEEEEEEEEE
Confidence 8899999999999999988 89999999998887 8999999999999999999999999999999999999999999
Q ss_pred eecC
Q 030170 82 KIFR 85 (182)
Q Consensus 82 ~p~~ 85 (182)
+|++
T Consensus 77 rPf~ 80 (80)
T cd04329 77 KPFK 80 (80)
T ss_pred EccC
Confidence 9985
No 10
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.
Probab=99.90 E-value=1.5e-23 Score=143.44 Aligned_cols=80 Identities=24% Similarity=0.325 Sum_probs=76.2
Q ss_pred eEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEEe
Q 030170 2 FLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITF 81 (182)
Q Consensus 2 F~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~f 81 (182)
|++++++|+|+|||++|++ ++++++.++|++++ +||+++++|+||+++++.++++|+|.+|||.++++|+|++++|
T Consensus 1 f~l~~l~d~v~i~P~~f~~---~~~~~i~~~L~~k~-~gkv~~~~G~~v~v~di~~i~~G~I~~gdG~~~~~V~F~~ivF 76 (80)
T cd00655 1 FQILEIADLVSVPPKYFGD---DCKGVKKCLLQEKG-EGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVF 76 (80)
T ss_pred CEEEEEEEEEEECHHHhCc---cHHHHHHHHHHHHh-CCeEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEE
Confidence 7899999999999999998 89998888888777 8999999999999999999999999999999999999999999
Q ss_pred eecC
Q 030170 82 KIFR 85 (182)
Q Consensus 82 ~p~~ 85 (182)
+|+.
T Consensus 77 rPf~ 80 (80)
T cd00655 77 KPFS 80 (80)
T ss_pred EcCC
Confidence 9984
No 11
>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.
Probab=99.90 E-value=3e-23 Score=141.85 Aligned_cols=79 Identities=28% Similarity=0.466 Sum_probs=75.8
Q ss_pred eEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEEe
Q 030170 2 FLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITF 81 (182)
Q Consensus 2 F~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~f 81 (182)
|++++++|+|+|||++|++ ++++++.++|++++ +||+++++|+||+++|+.++++|+|.+|||.++++|+|+|++|
T Consensus 1 f~~~~l~d~vri~P~~fg~---~~~~~i~~~L~~~~-egk~~~~~G~iv~v~di~~i~eG~I~~gdG~~~~~V~F~~ivF 76 (80)
T cd04331 1 YKLVELEDVVRVPPELFGE---DLEEAVLEILKEKY-EGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVF 76 (80)
T ss_pred CEEEEEEEeEEECHHHcCc---CHHHHHHHHHHHHh-cCcCcCCCCEEEEEEEEEEecCCEEEcCCCCEEEEEEEEEEEE
Confidence 7899999999999999988 89999998888887 7999999999999999999999999999999999999999999
Q ss_pred eec
Q 030170 82 KIF 84 (182)
Q Consensus 82 ~p~ 84 (182)
||.
T Consensus 77 rP~ 79 (80)
T cd04331 77 KPE 79 (80)
T ss_pred ecC
Confidence 996
No 12
>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=99.84 E-value=4.6e-20 Score=128.40 Aligned_cols=87 Identities=29% Similarity=0.463 Sum_probs=76.6
Q ss_pred CCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCC-ceEcCCCeEEEEEEEEEecccccceEE
Q 030170 85 RGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKN-PKIEKDVVVRVIVIGTKWLEAEREFQA 163 (182)
Q Consensus 85 ~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~-~~~~~Gd~VrvrV~~v~~~~~~~~~~i 163 (182)
+||+++|+|++++++|+|+++||++++++.+++++++.++++++.|.|..++ .+++.|+.||+||.++.++. +.+.+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~--~~~~~ 78 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVDA--TDIFA 78 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEcc--CceEE
Confidence 5999999999999999999999999999999988786665556777776444 69999999999999999964 46899
Q ss_pred EEeccCCCcc
Q 030170 164 LVSLEGDFLG 173 (182)
Q Consensus 164 ~gs~~~~gLG 173 (182)
+|||++|+||
T Consensus 79 igt~~~~~LG 88 (88)
T cd04462 79 IGTIKDDYLG 88 (88)
T ss_pred EEEccCCCCC
Confidence 9999999998
No 13
>PF03876 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; InterPro: IPR005576 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable []. This entry represents the N-terminal, heterodimerisation domain of RPB7.; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2C35_F 3HKZ_E 2PMZ_T 2CKZ_D 2Y0S_E 2RF4_A 2JA7_G 1Y1V_G 2JA5_G 4A3D_G ....
Probab=99.69 E-value=2.8e-16 Score=104.62 Aligned_cols=70 Identities=33% Similarity=0.526 Sum_probs=64.4
Q ss_pred ceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEEe
Q 030170 8 PWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITF 81 (182)
Q Consensus 8 ~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~f 81 (182)
+|+|+|||++|++ ++++++.++|++++ +||++++.|+|+++.++..+++|+|.+++|.++++|+|++++|
T Consensus 1 e~~v~l~P~~l~~---~~~~~i~~~L~~~~-~~k~~~~~G~~i~v~~i~~~~~g~I~~~~g~~~~~V~f~~lvF 70 (70)
T PF03876_consen 1 EDTVRLPPSYLGP---DLKDGIKEQLLDKY-EGKYIPELGVVIAVTDIKEISEGKIIPGDGFVYFKVTFRALVF 70 (70)
T ss_dssp EEEEEE-GGGTTS---THHHHHHHHHHHHH-TTEEETTTEEEEEEEEEEEESCEEE-TTTSSEEEEEEEEEEEE
T ss_pred CcEEEECHHHhCc---CHHHHHHHHHHHHH-hCcCcCCceEEEEEeeeeEecCcEEECCCCCEEEEEEEEEEEC
Confidence 5899999999987 69999989998887 7999999999999999999999999999999999999999998
No 14
>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=99.61 E-value=3.4e-15 Score=105.86 Aligned_cols=94 Identities=23% Similarity=0.375 Sum_probs=80.4
Q ss_pred CEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCC-ceEcCCCeEEEEEEEEEeccccc-ceEEE
Q 030170 87 EVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKN-PKIEKDVVVRVIVIGTKWLEAER-EFQAL 164 (182)
Q Consensus 87 Ev~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~-~~~~~Gd~VrvrV~~v~~~~~~~-~~~i~ 164 (182)
+++.|+|++++++|+||++++.+|++|.+++.++++.+++.+.++.+++. ..|++||.|+|+|.+++...+.+ .-.+.
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ 80 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIG 80 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEE
Confidence 68999999999999999999899999999999888877777788888775 69999999999999999854321 12456
Q ss_pred EeccCCCccccCCCCC
Q 030170 165 VSLEGDFLGPVSCENP 180 (182)
Q Consensus 165 gs~~~~gLG~i~w~~~ 180 (182)
.|+++++||++.|-.+
T Consensus 81 ls~k~~~~g~~~~~~~ 96 (99)
T cd04460 81 LTMRQPGLGKLEWIEE 96 (99)
T ss_pred EEEecCCCCcHHHhhh
Confidence 6999999999999754
No 15
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo
Probab=99.50 E-value=1.8e-13 Score=95.38 Aligned_cols=79 Identities=16% Similarity=0.235 Sum_probs=70.3
Q ss_pred CeEEEEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCc-cEEEEEEeeeeeCc--eEEecCCCceEEEEEEE
Q 030170 1 MFLKVKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDL-GYFLAVTTLENIGE--GRVRENTGEVLFPVVFS 77 (182)
Q Consensus 1 MF~~~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~-G~~v~i~~i~~~~~--g~i~~~~g~~~~~v~fk 77 (182)
||.+.++++.|+|+|++|++ ..+ ++.++|.+.+ . |+.++. |+|++.+++...++ +.+.+++|..+++|+|+
T Consensus 8 ~f~~~~~~~~v~l~P~~~~~---~~~-~i~~~l~~~l-~-ky~~~l~Gv~l~~~di~~~~~~~~~i~~~~~~~~~~V~~~ 81 (89)
T cd04328 8 CFETLTVSLYVSLAPKYLGN---PLT-GIKAQLLNPL-L-KYSPKLKGVVLAYSNIKLLEGELAKIVDDSPFIFVWISAD 81 (89)
T ss_pred cEEEEEEEEEEEECchhhcC---HhH-HHHHHHhhhH-h-hhcccCCeEEEEecceEeccccceeeeCCCcEEEEEEEEE
Confidence 89999999999999999988 444 6777776665 5 999997 99999999988756 99999999999999999
Q ss_pred EEEeeecC
Q 030170 78 GITFKIFR 85 (182)
Q Consensus 78 ~~~f~p~~ 85 (182)
+++|+|++
T Consensus 82 ~lVFrP~~ 89 (89)
T cd04328 82 FLVFRPKI 89 (89)
T ss_pred EEEEecCC
Confidence 99999985
No 16
>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=99.33 E-value=1.6e-11 Score=83.52 Aligned_cols=71 Identities=24% Similarity=0.327 Sum_probs=62.1
Q ss_pred CCCEEEEEEEEEecceEEEEecC--cceEEEcCCcCCCceeecCCCcEEEcCCC-ceEcCCCeEEEEEEEEEec
Q 030170 85 RGEVLDGTVHKVLKHGVFLKCGP--VENIYLTCSKMPDYRYVQAENPVFLSEKN-PKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 85 ~gEv~~g~V~~v~~~Gifv~lg~--~~gl~~~s~~~~d~~~~~~~~~~~~~~~~-~~~~~Gd~VrvrV~~v~~~ 155 (182)
+|++++|+|++++++|+||++++ .+|++|.+++.++++.+++.+..+.++.. +.|++||.|+|+|.+++..
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~ 74 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLD 74 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccc
Confidence 48999999999999999999995 89999999998887777777666666544 7999999999999999974
No 17
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.26 E-value=5.7e-11 Score=105.84 Aligned_cols=131 Identities=18% Similarity=0.152 Sum_probs=97.3
Q ss_pred HHHHHHhHhcCe-----eeC--CccEEEEEEee------eeeCceEEecCCCceEEEEEEEEEEeee-------------
Q 030170 30 VVRLLDDFARRK-----ATK--DLGYFLAVTTL------ENIGEGRVRENTGEVLFPVVFSGITFKI------------- 83 (182)
Q Consensus 30 ~~~l~~~~~~~k-----~~~--~~G~~v~i~~i------~~~~~g~i~~~~g~~~~~v~fk~~~f~p------------- 83 (182)
-.+|.+.+..|. ++. ..|+.+.+-.+ ++++...+...+........|+.+-+.+
T Consensus 96 w~~l~~~~e~~~~V~~~v~~~vKGG~~Vdi~gvr~FlP~S~v~~r~v~d~~~~~Gk~~~~kiie~d~~~n~vv~SrR~~~ 175 (541)
T COG0539 96 WEKLEEAFENGEIVEGKITGKVKGGLTVDIEGVRAFLPGSLVDVRPVRDLDPLIGKELEFKILELDKKRNNVVLSRRAVL 175 (541)
T ss_pred HHHHHHHHhcCCeEEEEEEEEecCcEEEEECCEEEeccHHHhcccccccccccCCceEEEEEEEEccccCcEEEEhHHHh
Confidence 345555554442 222 47788877443 4555666655555555556677776654
Q ss_pred ---------------cCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEE
Q 030170 84 ---------------FRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVI 148 (182)
Q Consensus 84 ---------------~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~Vrvr 148 (182)
.+|++++|+|+++++||+||++|.++|++|++++.+.+..+ +++.+++||+|+|+
T Consensus 176 e~~~~~~r~e~~~~l~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv~~----------P~~vvkvGd~Vkvk 245 (541)
T COG0539 176 EEERSEQREELLNKLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDH----------PSEVVKVGDEVKVK 245 (541)
T ss_pred hHHHHHHHHHHHhcCCCCceEEEEEEEeecCcEEEEecCeeeEEehhhccccccCC----------HHHhcccCCEEEEE
Confidence 69999999999999999999999999999999998877643 33799999999999
Q ss_pred EEEEEecccccceEEEEeccCCCccc
Q 030170 149 VIGTKWLEAEREFQALVSLEGDFLGP 174 (182)
Q Consensus 149 V~~v~~~~~~~~~~i~gs~~~~gLG~ 174 (182)
|+++|.... .+.-||+.-.-+|
T Consensus 246 Vi~~D~e~~----RVsLSlK~l~~dP 267 (541)
T COG0539 246 VISLDEERG----RVSLSLKQLEEDP 267 (541)
T ss_pred EEEEccCCC----eEEEEehhcccCc
Confidence 999998543 4677777766666
No 18
>PRK11642 exoribonuclease R; Provisional
Probab=99.22 E-value=2.7e-11 Score=113.36 Aligned_cols=158 Identities=13% Similarity=0.111 Sum_probs=106.4
Q ss_pred CCCCCCCChHHHHHHHHHHhHhcCeeeCC------ccEEEEEE---e-eeeeCceEEecCCCceEEEEEEEEEEeeecCC
Q 030170 17 NLDAKGPMLQRSIVVRLLDDFARRKATKD------LGYFLAVT---T-LENIGEGRVRENTGEVLFPVVFSGITFKIFRG 86 (182)
Q Consensus 17 ~l~~~~~~~~~~i~~~l~~~~~~~k~~~~------~G~~v~i~---~-i~~~~~g~i~~~~g~~~~~v~fk~~~f~p~~g 86 (182)
||-+|-.+|.+.+.|+++..++.+..... .+.-...- . ..+++.......+.+....-.+++.+++.++|
T Consensus 565 HFTSPIRRY~DLivHR~Lk~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~s~~er~A~~aeR~~~~~~~~~~m~~~iG 644 (813)
T PRK11642 565 HFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEATRDVADWLKCDFMLDQVG 644 (813)
T ss_pred ccCchhhhhHHHHHHHHHHHHHhCCCCcccccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCC
Confidence 44444558999999999988865432110 11000000 0 11122222221111111111267777888999
Q ss_pred CEEEEEEEEEecceEEEEec--CcceEEEcCCcCCCceeecCCCcEEEcCCC-ceEcCCCeEEEEEEEEEecccccceEE
Q 030170 87 EVLDGTVHKVLKHGVFLKCG--PVENIYLTCSKMPDYRYVQAENPVFLSEKN-PKIEKDVVVRVIVIGTKWLEAEREFQA 163 (182)
Q Consensus 87 Ev~~g~V~~v~~~Gifv~lg--~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~-~~~~~Gd~VrvrV~~v~~~~~~~~~~i 163 (182)
++|+|+|+++++||+||+|. +++|++|.+++.+|++.+++.++.+.+.++ +.|++||+|+|+|.+++...+.-.+.+
T Consensus 645 e~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~f~l 724 (813)
T PRK11642 645 NVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKIDFSL 724 (813)
T ss_pred cEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEEEEE
Confidence 99999999999999999997 389999999999899888888888988876 799999999999999999765434433
Q ss_pred EEe-ccCCCccc
Q 030170 164 LVS-LEGDFLGP 174 (182)
Q Consensus 164 ~gs-~~~~gLG~ 174 (182)
+.+ +...|+|.
T Consensus 725 ~~~~~~~~~~~~ 736 (813)
T PRK11642 725 ISSERAPRNVGK 736 (813)
T ss_pred ecccccCCCCCc
Confidence 322 44566774
No 19
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=99.21 E-value=1.3e-10 Score=77.53 Aligned_cols=66 Identities=24% Similarity=0.312 Sum_probs=56.5
Q ss_pred eecCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
++.+|++++|+|++++++|+||+++ ..++++|.+++.+++.. .....+++||+|+|+|.+++...+
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~----------~~~~~~~~G~~v~v~v~~vd~~~~ 67 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRID----------DPSEVYKIGQTVRVKVIKVDKEKG 67 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEES----------SSHGTCETTCEEEEEEEEEETTTT
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCcccc----------ccccccCCCCEEEEEEEEEECCCC
Confidence 5789999999999999999999999 79999999999776331 223699999999999999998643
No 20
>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=99.21 E-value=7.5e-11 Score=78.96 Aligned_cols=63 Identities=17% Similarity=0.136 Sum_probs=53.3
Q ss_pred ecCCCEEEEEEEEEecceEEEEecC--cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 83 IFRGEVLDGTVHKVLKHGVFLKCGP--VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gifv~lg~--~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
|.+|++++|+|+++++||+|+++.. .+|++|.+++.++.+. +..+.|+.||+|+|+|.+++..
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~----------~~~~~~~~Gd~v~vkv~~vd~~ 65 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVD----------DPSEVVDVGEKVWVKVIGREMK 65 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCccc----------CHhhEECCCCEEEEEEEEECCC
Confidence 4689999999999999999999964 6999999998765331 2236899999999999999974
No 21
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.11 E-value=6.6e-11 Score=85.90 Aligned_cols=63 Identities=13% Similarity=0.147 Sum_probs=55.6
Q ss_pred eecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
.+.+|++++|+|+++++||+||++.. -.||+|+|+..++|+.+- ...+++||+|.|+|++++-
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI----------~d~L~vG~eV~vKVl~ide 65 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDI----------HDHLKVGQEVKVKVLDIDE 65 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhH----------HHHhcCCCEEEEEEEeecc
Confidence 46789999999999999999999974 779999999998887432 2689999999999999996
No 22
>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=99.09 E-value=3.2e-10 Score=76.26 Aligned_cols=66 Identities=18% Similarity=0.205 Sum_probs=54.7
Q ss_pred cCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
.+|+++.|+|++++++|+||++++ ++|++|.+++.+++..... ...+.|++||.|+++|++++.+.
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~-------~~~~~~~~G~~v~~kVl~id~~~ 68 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPS-------LYNKYLPEGKLLTAKVLSVNSEK 68 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChh-------hHhcccCCCCEEEEEEEEEECCC
Confidence 479999999999999999999985 8999999999877542110 01268999999999999999853
No 23
>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=99.09 E-value=2.6e-10 Score=105.81 Aligned_cols=141 Identities=15% Similarity=0.142 Sum_probs=97.0
Q ss_pred CCCCCCCChHHHHHHHHHHhHhcCeee-C-CccE--EEE-EEee-eeeCceEEecCCCceEEEEEEEEEEeeecCCCEEE
Q 030170 17 NLDAKGPMLQRSIVVRLLDDFARRKAT-K-DLGY--FLA-VTTL-ENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLD 90 (182)
Q Consensus 17 ~l~~~~~~~~~~i~~~l~~~~~~~k~~-~-~~G~--~v~-i~~i-~~~~~g~i~~~~g~~~~~v~fk~~~f~p~~gEv~~ 90 (182)
||-+|-.+|.+.+.|+++..+..++-. . ...+ .-. +..+ .+++.........+....-.++|.++++++|++++
T Consensus 553 hfTSPIRRY~DLivHr~L~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~ 632 (709)
T TIGR02063 553 HFTSPIRRYPDLIVHRLIKKALFGGENTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFE 632 (709)
T ss_pred ccCCccccchHHHHHHHHHHHHcCCCCCCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCcEEE
Confidence 344445588899999999888755421 1 0000 000 0011 11222222111111111123677888999999999
Q ss_pred EEEEEEecceEEEEecC--cceEEEcCCcCCCceeecCCCcEEEcCCC-ceEcCCCeEEEEEEEEEeccc
Q 030170 91 GTVHKVLKHGVFLKCGP--VENIYLTCSKMPDYRYVQAENPVFLSEKN-PKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 91 g~V~~v~~~Gifv~lg~--~~gl~~~s~~~~d~~~~~~~~~~~~~~~~-~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
|+|+++++||+||++.+ ++|++|.+++.++++.+++....+.++++ +.|++||+|+|+|.++|...+
T Consensus 633 g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~ 702 (709)
T TIGR02063 633 GVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTG 702 (709)
T ss_pred EEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccC
Confidence 99999999999999984 89999999999888888888888888765 699999999999999998544
No 24
>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=99.09 E-value=6.6e-10 Score=74.05 Aligned_cols=61 Identities=16% Similarity=0.153 Sum_probs=51.5
Q ss_pred CCEEE-EEEEEE-ecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 86 GEVLD-GTVHKV-LKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 86 gEv~~-g~V~~v-~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
|++++ |+|+++ .++|+||++.+ ++|++|.|++.++... +..+.++.||++++||.+++...
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~----------~~~~~~~vG~~v~~kV~~id~~~ 64 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVP----------SDTGPFKAGTTHKARIIGYSPMD 64 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhc----------CcccccCCCCEEEEEEEEEeCCC
Confidence 79999 999999 69999999974 9999999998765432 22368999999999999999754
No 25
>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=99.06 E-value=2.8e-10 Score=104.71 Aligned_cols=141 Identities=12% Similarity=0.116 Sum_probs=97.5
Q ss_pred CCCCCCCChHHHHHHHHHHhHhcCeeeCCccE-EE-EEEee-eeeCceEEecCCCceEEEEEEEEEEeeecCCCEEEEEE
Q 030170 17 NLDAKGPMLQRSIVVRLLDDFARRKATKDLGY-FL-AVTTL-ENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTV 93 (182)
Q Consensus 17 ~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~-~v-~i~~i-~~~~~g~i~~~~g~~~~~v~fk~~~f~p~~gEv~~g~V 93 (182)
||-+|-.+|.+.+.|++++.++.|+....... .. .+..+ .+++.......+.+....-.+++.+++.++|++++|+|
T Consensus 501 hfTSPIRRY~DLivHr~L~a~l~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g~I 580 (654)
T TIGR00358 501 HFTSPIRRYPDLTNHRLIKAVLAKEQTDTERYQPQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVGTEFSGEI 580 (654)
T ss_pred ccCCccccchHHHHHHHHHHHHcCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCcEEEEEE
Confidence 34344457888999999988876542111111 00 00011 11121111111111111112667888999999999999
Q ss_pred EEEecceEEEEec-C-cceEEEcCCcCCCceeecCCCcEEEcCCC-ceEcCCCeEEEEEEEEEeccc
Q 030170 94 HKVLKHGVFLKCG-P-VENIYLTCSKMPDYRYVQAENPVFLSEKN-PKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 94 ~~v~~~Gifv~lg-~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~-~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
++++++|+||++. + ++|++|.+++.++++.+++.+..+.++++ +.|++||+|+|+|.++|...+
T Consensus 581 ~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~ 647 (654)
T TIGR00358 581 SSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETR 647 (654)
T ss_pred EeEEcCcEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccC
Confidence 9999999999997 4 89999999999888888888888888776 799999999999999998654
No 26
>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=99.05 E-value=9.8e-10 Score=72.47 Aligned_cols=62 Identities=18% Similarity=0.258 Sum_probs=52.8
Q ss_pred CCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 86 GEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
|++++|+|++++++|+||+++ .++|++|.+++.+++.. +..+.|++||.++++|.+++...+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~----------~~~~~~~~Gd~i~~~V~~id~~~~ 63 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLK----------HPEKKFKPGLKVKCRVLSVEPERK 63 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCcccc----------CHHHcCCCCCEEEEEEEEEECCCC
Confidence 789999999999999999997 58999999998776542 123589999999999999998543
No 27
>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=99.05 E-value=6e-10 Score=76.62 Aligned_cols=84 Identities=10% Similarity=-0.009 Sum_probs=66.1
Q ss_pred eeecCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccccc
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAER 159 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~ 159 (182)
|.|.+|++++|+|++++++|++|+++ +++|++|.+++..+...... .+....+++||.++++|.+++.. .
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~------~~~~~~l~vGd~i~~~V~~~~~~---~ 72 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDE------LNMRSYLDEGDLIVAEVQSVDSD---G 72 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccch------HHHHhhCCCCCEEEEEEEEECCC---C
Confidence 56899999999999999999999998 58999999998653221000 01125799999999999999753 2
Q ss_pred ceEEEEeccCCCcccc
Q 030170 160 EFQALVSLEGDFLGPV 175 (182)
Q Consensus 160 ~~~i~gs~~~~gLG~i 175 (182)
.+.-|++.++||.+
T Consensus 73 --~i~LS~~~~~~g~~ 86 (86)
T cd05789 73 --SVSLHTRSLKYGKL 86 (86)
T ss_pred --CEEEEeCcccccCC
Confidence 47889999999964
No 28
>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=99.05 E-value=1.5e-09 Score=72.23 Aligned_cols=63 Identities=25% Similarity=0.323 Sum_probs=54.0
Q ss_pred cCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
.+|+++.|+|++++++|+||+++ .++|++|.+++.+++.. +....|++||.|+++|.+++...
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~----------~~~~~~~~Gd~v~~~V~~~d~~~ 65 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSE----------ALPYKFKKNDIVRACVLSVDVPN 65 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCcccc----------ccccccCCCCEEEEEEEEEeCCC
Confidence 47999999999999999999998 58999999998876532 12368999999999999999753
No 29
>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=99.05 E-value=1.4e-09 Score=72.71 Aligned_cols=72 Identities=19% Similarity=0.234 Sum_probs=57.9
Q ss_pred CCCEEEEEEEEEecceEEEEec--CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceE
Q 030170 85 RGEVLDGTVHKVLKHGVFLKCG--PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQ 162 (182)
Q Consensus 85 ~gEv~~g~V~~v~~~Gifv~lg--~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~ 162 (182)
+|+++.|+|++++++|+||++. ..+|++|.+++.+++.. +....|++||.|+++|.+++.+.. .
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~----------~~~~~~~~Gd~v~v~i~~vd~~~~----~ 67 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVA----------DASKLFRVGDKVRAKVLKIDAEKK----R 67 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccC----------CHhHeecCCCEEEEEEEEEeCCCC----E
Confidence 6999999999999999999997 48999999998776532 123689999999999999997543 3
Q ss_pred EEEeccCC
Q 030170 163 ALVSLEGD 170 (182)
Q Consensus 163 i~gs~~~~ 170 (182)
+..+++..
T Consensus 68 i~ls~k~~ 75 (77)
T cd05708 68 ISLGLKAS 75 (77)
T ss_pred EEEEEEee
Confidence 45555543
No 30
>PRK08582 hypothetical protein; Provisional
Probab=99.05 E-value=7.8e-10 Score=83.15 Aligned_cols=63 Identities=19% Similarity=0.200 Sum_probs=54.6
Q ss_pred eecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
...+|++++|+|++++++|+||+|++ .+|++|++++.++++.+ ....|++||.|+|+|.+++.
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~----------~~~~l~vGD~VkvkV~~id~ 65 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKD----------INDHLKVGDEVEVKVLNVED 65 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccc----------cccccCCCCEEEEEEEEECC
Confidence 45689999999999999999999985 89999999998766431 23689999999999999986
No 31
>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=99.04 E-value=1e-09 Score=72.47 Aligned_cols=61 Identities=18% Similarity=0.154 Sum_probs=52.0
Q ss_pred CCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 86 GEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
|+++.|+|++++++|+||+++ .++|++|.+++.+++... ....+++||.++|+|.+++...
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~----------~~~~~~~G~~i~v~v~~~d~~~ 62 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKD----------PEEHFRVGQVVKVKVLSCDPEQ 62 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCC----------HHHcccCCCEEEEEEEEEcCCC
Confidence 789999999999999999997 489999999987665321 2258999999999999999754
No 32
>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=99.03 E-value=1e-09 Score=75.02 Aligned_cols=65 Identities=15% Similarity=0.153 Sum_probs=55.6
Q ss_pred eecCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
...+|+++.|+|++++++|+||+++ ..++++|.+++.+++.. +....|++||.|+|+|.+++...
T Consensus 11 ~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~----------~~~~~~~~Gd~v~vkV~~id~~~ 76 (83)
T cd04461 11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVT----------DPSFGFKKGQSVTAKVTSVDEEK 76 (83)
T ss_pred hCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCccccc----------CHHHhcCCCCEEEEEEEEEcCCC
Confidence 3679999999999999999999997 68999999998776542 12368999999999999999854
No 33
>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=99.02 E-value=2.4e-09 Score=71.60 Aligned_cols=64 Identities=16% Similarity=0.061 Sum_probs=54.3
Q ss_pred ecCCCEEEEEEEEEecceEEEEec---CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 83 IFRGEVLDGTVHKVLKHGVFLKCG---PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gifv~lg---~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
|..|+++.|+|+++.++|+|+++. ..+|++|.+++.+++.. +.++.|+.||.|+++|.+++...
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~----------~~~~~~~~Gd~v~vkv~~~d~~~ 67 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIR----------SIRKLVKVGRKEVVKVIRVDKEK 67 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccC----------CHHHeeCCCCEEEEEEEEEECCC
Confidence 568999999999999999999996 27999999998766542 12368999999999999999853
No 34
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.02 E-value=1.5e-09 Score=71.29 Aligned_cols=62 Identities=15% Similarity=0.262 Sum_probs=50.4
Q ss_pred CCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 86 GEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
|+++.|+|++++++|+||+++ ..+|++|.+++.+... ..+..+.|++||.|+|+|.+++.+.
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~---------~~~~~~~~~~G~~v~v~v~~id~~~ 63 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQR---------VRHPSEIYKKGQEVEAVVLNIDVER 63 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccc---------cCChhhEECCCCEEEEEEEEEECCc
Confidence 789999999999999999997 4899999998852111 0122368999999999999999754
No 35
>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=98.99 E-value=3.5e-09 Score=70.27 Aligned_cols=63 Identities=19% Similarity=0.177 Sum_probs=51.3
Q ss_pred CCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 85 RGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 85 ~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
+|+++.|+|++++++|+|+++.+ .+|++|.+++.++.. . .+....|++||.|+|+|.+++...
T Consensus 3 ~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~-----~----~~~~~~~~~Gd~v~v~v~~id~~~ 66 (72)
T cd05689 3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNK-----N----IHPSKVVSLGDEVEVMVLDIDEER 66 (72)
T ss_pred CCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCccc-----c----cCcccEeCCCCEEEEEEEEeeCCc
Confidence 69999999999999999999974 899999998843211 0 012368999999999999999754
No 36
>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=98.98 E-value=1.7e-09 Score=71.15 Aligned_cols=61 Identities=18% Similarity=0.290 Sum_probs=52.1
Q ss_pred CCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 86 GEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
|+++.|+|+++.++|+||++++ ++|++|.+++.+++.. +....|++||.|+++|.+++...
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~----------~~~~~~~~Gd~v~~~v~~~d~~~ 62 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLK----------DWKKRFKVGQLVKGKIVSIDPDN 62 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhc----------CHhhccCCCCEEEEEEEEEeCCC
Confidence 7899999999999999999984 8999999998766542 22368999999999999999743
No 37
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=98.98 E-value=3e-09 Score=72.05 Aligned_cols=59 Identities=19% Similarity=0.345 Sum_probs=50.7
Q ss_pred CCEEEEEEEEEecceEEEEec----CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEE
Q 030170 86 GEVLDGTVHKVLKHGVFLKCG----PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg----~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 153 (182)
|+++.|+|++++++|+||+++ +.+|++|.+++.+++. +++..+.|+.||.|+|+|.+++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~---------~~~~~~~~~~Gd~v~v~v~~vd 63 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGR---------VANPSDVVKRGQKVKVKVISIQ 63 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCC---------cCChhheeCCCCEEEEEEEEEe
Confidence 789999999999999999998 4799999999876643 1223468999999999999999
No 38
>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=98.95 E-value=1.6e-09 Score=72.32 Aligned_cols=60 Identities=18% Similarity=0.195 Sum_probs=51.1
Q ss_pred cCCCEEEEEEEEEec-ceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEE
Q 030170 84 FRGEVLDGTVHKVLK-HGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~-~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 153 (182)
.+|+++.|+|+++.+ +|+|+++++ .+|++|++++.+++.. +....|++||.||++|.+++
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~----------~~~~~~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTE----------NPLEGFKPGKIVRCCILSKK 63 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccC----------CHHHhCCCCCEEEEEEEEec
Confidence 379999999999986 899999985 8999999998876542 12258999999999999997
No 39
>PRK07252 hypothetical protein; Provisional
Probab=98.95 E-value=5.5e-09 Score=76.66 Aligned_cols=64 Identities=14% Similarity=0.124 Sum_probs=54.2
Q ss_pred cCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
.+|+++.|+|++++++|+||+++ ..+|++|.+++.++++. +.+..|++||.|+|+|.+++...+
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~----------~~~~~~~vGD~V~VkI~~iD~~~~ 66 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFID----------NIHQLLKVGEEVLVQVVDFDEYTG 66 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCcccc----------ChhhccCCCCEEEEEEEEEeCCCC
Confidence 47999999999999999999997 58999999998766542 223689999999999999998543
No 40
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.94 E-value=4.2e-09 Score=71.84 Aligned_cols=80 Identities=14% Similarity=0.029 Sum_probs=66.4
Q ss_pred eeecCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccccc
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAER 159 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~ 159 (182)
|.|.+|+++.|+|+++++.|++|+++ ..+++++.+++..++.. +....+++||.++++|.+++-. .
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~----------~~~~~~~~GD~i~~~V~~~~~~-~-- 68 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKK----------EIRKSLQPGDLILAKVISLGDD-M-- 68 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchH----------HHHhcCCCCCEEEEEEEEeCCC-C--
Confidence 56999999999999999999999998 58999999998654221 1125799999999999999863 2
Q ss_pred ceEEEEeccCCCcccc
Q 030170 160 EFQALVSLEGDFLGPV 175 (182)
Q Consensus 160 ~~~i~gs~~~~gLG~i 175 (182)
.+.-|++++.||.+
T Consensus 69 --~i~LS~~~~~~Gvi 82 (82)
T cd04454 69 --NVLLTTADNELGVI 82 (82)
T ss_pred --CEEEEECCCCCccC
Confidence 47899999999975
No 41
>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=98.93 E-value=5.7e-09 Score=69.92 Aligned_cols=64 Identities=20% Similarity=0.227 Sum_probs=52.3
Q ss_pred CCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 86 GEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
|.++.|+|++++++|+||++++ ++|++|.+++.++.... .+..+.|++||.|+++|+++|.+.+
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~--------~~~~~~~~vG~~v~~kV~~id~~~~ 65 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVL--------EHPEKKFPIGQALKAKVVGVDKEHK 65 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccc--------cCHHHhCCCCCEEEEEEEEEeCCCC
Confidence 7899999999999999999985 99999999987653110 1122689999999999999998643
No 42
>PRK05807 hypothetical protein; Provisional
Probab=98.91 E-value=4.6e-09 Score=78.68 Aligned_cols=63 Identities=19% Similarity=0.262 Sum_probs=54.2
Q ss_pred eecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
...+|++++|+|++++++|+||++...+|++|++++.+++... ....|++||.|+|+|.+++.
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~----------~~~~~kvGd~V~VkV~~id~ 64 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKD----------IREHLKEQDKVKVKVISIDD 64 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccC----------ccccCCCCCEEEEEEEEECC
Confidence 3458999999999999999999997789999999998766431 22579999999999999986
No 43
>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=98.89 E-value=8.9e-09 Score=67.00 Aligned_cols=62 Identities=19% Similarity=0.264 Sum_probs=51.8
Q ss_pred CCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 85 RGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 85 ~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
+|+++.|+|++++++|+||+++..+|++|.+++.+.+. ....+.|++||.|+|+|.+++...
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e~~~~~~----------~~~~~~~~~Gd~v~v~i~~vd~~~ 62 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRV----------KHPSEVVNVGDEVEVKVLKIDKER 62 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccc----------cCHhHEECCCCEEEEEEEEEECCC
Confidence 48999999999999999999998999999998764222 112368999999999999999753
No 44
>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=98.88 E-value=7.7e-09 Score=67.24 Aligned_cols=59 Identities=19% Similarity=0.302 Sum_probs=50.8
Q ss_pred CCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 86 GEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
|+++.|+|++++++|+||+++ +.++++|.+++.+++.. +..+.+++||.|+++|.+++.
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~----------~~~~~~~~Gd~v~v~v~~~~~ 60 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVK----------DVKDVLKEGDKVKVKVLSIDA 60 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccC----------CHHHccCCCCEEEEEEEEECC
Confidence 789999999999999999998 68999999998766532 122589999999999999986
No 45
>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=98.87 E-value=6.6e-09 Score=67.46 Aligned_cols=61 Identities=21% Similarity=0.292 Sum_probs=51.3
Q ss_pred CCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 86 GEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
|+++.|+|++++++|+||+++. .+|++|.+++.++++. +....+++||.++++|.+++..+
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~----------~~~~~~~~Gd~v~v~i~~vd~~~ 62 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVS----------HPSDVVSVGDIVEVKVISIDEER 62 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCcccc----------CHHHhcCCCCEEEEEEEEEECCC
Confidence 7899999999999999999984 7999999988665432 12357999999999999999754
No 46
>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=98.87 E-value=1.2e-08 Score=67.46 Aligned_cols=61 Identities=18% Similarity=0.219 Sum_probs=52.4
Q ss_pred CCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 86 GEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
|+++.|+|++++++|+||+++ +++|++|.+++.+++.. +....|++||.++++|.+++...
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~----------~~~~~~~~Gd~v~~~v~~~d~~~ 62 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVE----------DATERFKVGDEVEAKITNVDRKN 62 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCcccc----------CHHHccCCCCEEEEEEEEEeCCC
Confidence 789999999999999999996 68999999998876541 12358999999999999999854
No 47
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=98.84 E-value=2e-08 Score=69.73 Aligned_cols=69 Identities=14% Similarity=0.187 Sum_probs=54.5
Q ss_pred eecCCCEEEEEEEEEecc--eEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 82 KIFRGEVLDGTVHKVLKH--GVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~--Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
++.+|+++.|+|+++.++ |+||++++ .+|++|.+++.+..+.. . .+....++.||.|.|+|........
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~-v------~~~~~~~~~Gd~v~VqV~~~~~~~K 75 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKK-H------KKIAKLLKEGQEILVQVVKEPIGTK 75 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccc-c------CCHHHcCCCCCEEEEEEEEecCCCC
Confidence 357999999999999997 99999995 89999999986532210 0 1112589999999999999888654
No 48
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.83 E-value=1.2e-09 Score=102.38 Aligned_cols=69 Identities=13% Similarity=0.185 Sum_probs=58.8
Q ss_pred EEEEEeeecCCCEEE-EEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEE
Q 030170 76 FSGITFKIFRGEVLD-GTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 76 fk~~~f~p~~gEv~~-g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 153 (182)
++.+++.|.+|++|+ |+|++|++||+||++.+ .+|++|+|++.++++.+. .+.|++||.|+|+|.++|
T Consensus 744 I~~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~----------~dv~kvGD~V~VkVi~ID 813 (891)
T PLN00207 744 ISSLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKP----------EDAFKVGDRIDVKLIEVN 813 (891)
T ss_pred HHHHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCH----------HHhcCCCCEEEEEEEEEC
Confidence 455666899999996 69999999999999985 899999999987765322 268999999999999999
Q ss_pred e
Q 030170 154 W 154 (182)
Q Consensus 154 ~ 154 (182)
.
T Consensus 814 ~ 814 (891)
T PLN00207 814 D 814 (891)
T ss_pred C
Confidence 5
No 49
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.80 E-value=1.3e-08 Score=85.72 Aligned_cols=64 Identities=13% Similarity=0.057 Sum_probs=55.2
Q ss_pred ecCCCEEEEEEEEEecceEEEEec---CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 83 IFRGEVLDGTVHKVLKHGVFLKCG---PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gifv~lg---~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
|.+|+++.|+|+++++||+||+|+ .++|++|.|++.+.+.. +..+.+++||+|.|+|+++|...
T Consensus 15 P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~----------~i~d~vkvGd~v~vkVl~VD~ek 81 (319)
T PTZ00248 15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIR----------SINKLIRVGRHEVVVVLRVDKEK 81 (319)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccC----------CHHHhcCCCCEEEEEEEEEeCCC
Confidence 678999999999999999999994 69999999998775542 22368999999999999998754
No 50
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.79 E-value=4.6e-08 Score=87.47 Aligned_cols=64 Identities=16% Similarity=0.143 Sum_probs=56.5
Q ss_pred cCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
.+|..+.|+|+++++||+|+++.+ ++|++|+|++.+.+.. .+.+.++.||+|.|+|+++|.+.+
T Consensus 276 ~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~----------~P~evv~~Gq~V~V~Vl~id~e~r 340 (541)
T COG0539 276 PVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKN----------VPSEVVKVGQEVEVKVLDIDPERR 340 (541)
T ss_pred CCCCEEEEEEEEeecCcEEEEecCCccceeechhhcccccC----------CHHHhcccCCEEEEEEEeeCchhc
Confidence 699999999999999999999995 9999999999876552 233699999999999999999765
No 51
>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=98.78 E-value=4.2e-09 Score=97.32 Aligned_cols=90 Identities=18% Similarity=0.285 Sum_probs=69.4
Q ss_pred eeeeCceEEecCCCceEEEE--EEEEEEeeecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEE
Q 030170 55 LENIGEGRVRENTGEVLFPV--VFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVF 131 (182)
Q Consensus 55 i~~~~~g~i~~~~g~~~~~v--~fk~~~f~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~ 131 (182)
|.+-+..++...++..+.++ .++.+...|.+|+++.|+|+++.+||+||++.+ .+|++|+|++.++++.
T Consensus 586 i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~-------- 657 (684)
T TIGR03591 586 IEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVE-------- 657 (684)
T ss_pred EecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCccc--------
Confidence 34444555555565554444 355567789999999999999999999999975 8999999998765442
Q ss_pred EcCCCceEcCCCeEEEEEEEEEe
Q 030170 132 LSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 132 ~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
+..+.|++||.|+|||.+++.
T Consensus 658 --~~~~~~kvGD~V~VkVi~id~ 678 (684)
T TIGR03591 658 --KVEDVLKEGDEVKVKVLEIDK 678 (684)
T ss_pred --ChhhccCCCCEEEEEEEEECC
Confidence 223689999999999999986
No 52
>PRK08059 general stress protein 13; Validated
Probab=98.76 E-value=4.5e-08 Score=72.03 Aligned_cols=64 Identities=14% Similarity=0.147 Sum_probs=54.2
Q ss_pred ecCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 83 IFRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
..+|+++.|+|++++++|+||+++ ..+|++|.+++.+++.. +....|++||.|+|+|.+++...
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~----------~~~~~~~vGD~I~vkI~~id~~~ 69 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVK----------DIHDFLSVGDEVKVKVLSVDEEK 69 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCccccc----------CHHHcCCCCCEEEEEEEEEECCC
Confidence 568999999999999999999998 48999999998766431 12358999999999999999744
No 53
>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=98.75 E-value=7.4e-08 Score=64.73 Aligned_cols=65 Identities=22% Similarity=0.182 Sum_probs=53.6
Q ss_pred cCCCEEEEEEEEEecceEEEEec--CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccce
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG--PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREF 161 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg--~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~ 161 (182)
..|+++.|+|++++++|+|+++| .++|++|.+++.++ ..+++||.+.++|.+++.+.+
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~----------------~~~~~Gq~v~~~V~~vd~~~~---- 62 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF----------------SKLKVGQLLLCVVEKVKDDGR---- 62 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc----------------cccCCCCEEEEEEEEEECCCC----
Confidence 47999999999999999999998 58999999887543 478899999999999997432
Q ss_pred EEEEecc
Q 030170 162 QALVSLE 168 (182)
Q Consensus 162 ~i~gs~~ 168 (182)
.+..|++
T Consensus 63 ~v~ls~k 69 (74)
T cd05694 63 VVSLSAD 69 (74)
T ss_pred EEEEEEe
Confidence 3455554
No 54
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.75 E-value=5.8e-08 Score=86.48 Aligned_cols=77 Identities=19% Similarity=0.236 Sum_probs=60.9
Q ss_pred cCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceEE
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQA 163 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~i 163 (182)
.+|+++.|+|++++++|+||+++.++|++|.+++.+.+.. +..+.|++||.|+|+|++++...+ .+
T Consensus 207 k~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~----------~~~~~~kvGd~V~vkVl~iD~e~~----rI 272 (486)
T PRK07899 207 QKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHID----------HPSEVVEVGQEVTVEVLDVDMDRE----RV 272 (486)
T ss_pred cCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccC----------CHHHhcCCCCEEEEEEEEEECCCC----EE
Confidence 3799999999999999999999999999999998764432 122589999999999999998543 35
Q ss_pred EEeccCCCccc
Q 030170 164 LVSLEGDFLGP 174 (182)
Q Consensus 164 ~gs~~~~gLG~ 174 (182)
..|++...-.|
T Consensus 273 ~LSlK~~~~dP 283 (486)
T PRK07899 273 SLSLKATQEDP 283 (486)
T ss_pred EEEEeeccccc
Confidence 56665544344
No 55
>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=98.75 E-value=4.4e-08 Score=64.29 Aligned_cols=59 Identities=17% Similarity=0.162 Sum_probs=49.8
Q ss_pred CCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 86 GEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
|++++|+|++++++|+||++. .++|+++.+++.++... .+.|++|++|++||++++...
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~~------------~~~~~~G~~i~~kVi~id~~~ 60 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSS------------KSTYKEGQKVRARILYVDPST 60 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccCc------------ccCcCCCCEEEEEEEEEeCCC
Confidence 789999999999999999995 59999999987543221 357999999999999999854
No 56
>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=98.75 E-value=3.5e-08 Score=64.25 Aligned_cols=59 Identities=17% Similarity=0.192 Sum_probs=50.3
Q ss_pred CCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 86 GEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
|+++.|+|++++++|+|++++ ..+|++|.+++.+++.. ...+.|+.||.|+|+|.+++.
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~----------~~~~~~~~Gd~v~v~v~~~d~ 60 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVE----------KVEDVLKVGDEVKVKVIEVDD 60 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCcccc----------CHHHccCCCCEEEEEEEEECC
Confidence 789999999999999999998 48999999988766432 122589999999999999986
No 57
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.75 E-value=7e-08 Score=62.62 Aligned_cols=62 Identities=21% Similarity=0.301 Sum_probs=52.4
Q ss_pred CCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 85 RGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 85 ~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
+|+++.|+|++++++|+|++++ .+++++|.+++.+++. .+....|++||.++++|.+++...
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~----------~~~~~~~~~G~~v~~~V~~~~~~~ 64 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRV----------KDPEEVLKVGDEVKVKVLSVDEEK 64 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCcccc----------CCHHHeecCCCEEEEEEEEEeCCC
Confidence 6999999999999999999999 6899999998876541 111258999999999999999743
No 58
>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=98.74 E-value=6.1e-08 Score=63.87 Aligned_cols=59 Identities=22% Similarity=0.222 Sum_probs=50.5
Q ss_pred CCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 86 GEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
|+++.|+|++++++|+||+++ ..++++|.+++.+++.. +....+++||.++++|.+++.
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~----------~~~~~~~~Gd~i~~~i~~~~~ 60 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIE----------NGEDEVKVGDEVEVYVLRVED 60 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccC----------CHhHcCCCCCEEEEEEEEEEC
Confidence 789999999999999999998 58999999998765432 122579999999999999985
No 59
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.72 E-value=1.6e-07 Score=76.51 Aligned_cols=85 Identities=15% Similarity=0.183 Sum_probs=68.2
Q ss_pred eeecCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccccc
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAER 159 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~ 159 (182)
+.|.+|+++.|+|++++++|+|++++ ++++++|.++..+.+...+.. +....|++||.|++||++++.+ .
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~------~~~~~~~~GDlV~akV~~i~~~---~ 129 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGT------DLRKYLDIGDYIIAKVKDVDRT---R 129 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchh------hhHhhCCCCCEEEEEEEEECCC---C
Confidence 88999999999999999999999999 689999999886544322211 1114799999999999999853 2
Q ss_pred ceEEEEeccCCCccccC
Q 030170 160 EFQALVSLEGDFLGPVS 176 (182)
Q Consensus 160 ~~~i~gs~~~~gLG~i~ 176 (182)
. +.-|+++++||.+.
T Consensus 130 ~--~~LS~k~~~lG~L~ 144 (235)
T PRK04163 130 D--VVLTLKGKGLGKIE 144 (235)
T ss_pred c--EEEEEcCCCCCccC
Confidence 2 67788999999874
No 60
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.68 E-value=8.2e-08 Score=81.42 Aligned_cols=82 Identities=17% Similarity=0.146 Sum_probs=64.5
Q ss_pred ecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceE
Q 030170 83 IFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQ 162 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~ 162 (182)
..+|+++.|+|++++++|+||+++.++|++|.+++.+++.. +....|++||.|+++|.+++.... .
T Consensus 194 ~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~~~~----------~~~~~~~vGd~VkvkVl~iD~e~~----r 259 (318)
T PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIE----------TPHSVFNVNDEMKVMIIDLDAERG----R 259 (318)
T ss_pred CCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHccccccc----------ChhhccCCCCEEEEEEEEEeCCCC----E
Confidence 36899999999999999999999999999999999876532 123689999999999999998543 3
Q ss_pred EEEeccCCCccccCCC
Q 030170 163 ALVSLEGDFLGPVSCE 178 (182)
Q Consensus 163 i~gs~~~~gLG~i~w~ 178 (182)
+.-|++.----|-.+|
T Consensus 260 I~LS~K~l~~~P~~~~ 275 (318)
T PRK07400 260 ISLSTKQLEPEPGDML 275 (318)
T ss_pred EEEEEeccccChhhhh
Confidence 5666665555553333
No 61
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=98.67 E-value=3e-08 Score=92.15 Aligned_cols=141 Identities=19% Similarity=0.159 Sum_probs=98.5
Q ss_pred CCCCCCCChHHHHHHHHHHhHhcCeeeCCccE-EEEEEee-eeeCceEEecCCCceEEEEEEEEEEeeecCCCEEEEEEE
Q 030170 17 NLDAKGPMLQRSIVVRLLDDFARRKATKDLGY-FLAVTTL-ENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVH 94 (182)
Q Consensus 17 ~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~-~v~i~~i-~~~~~g~i~~~~g~~~~~v~fk~~~f~p~~gEv~~g~V~ 94 (182)
||-+|-.+|.|.+.|+++..+..+.-....-- .-.+..+ .+++.......+.+....-.++|.+++-++|++++|+|+
T Consensus 552 HFTSPIRRY~DLivHR~L~~~l~~~~~~~~~~~~~~l~~i~~~~s~~er~a~~aer~~~~~~~~~~m~~~vg~~f~g~V~ 631 (706)
T COG0557 552 HFTSPIRRYPDLIVHRQLKALLSGEPIPEKKTSEEELDELAAHISSAERRAQEAERDVIDLLKAEYMKKRVGEEFDGVVT 631 (706)
T ss_pred ccCCchhhchHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEE
Confidence 44444457888899999988865532211100 0000001 122222222222222122236777888999999999999
Q ss_pred EEecceEEEEecC--cceEEEcCCcCCCceeecCCCcEEEcCCC-ceEcCCCeEEEEEEEEEeccc
Q 030170 95 KVLKHGVFLKCGP--VENIYLTCSKMPDYRYVQAENPVFLSEKN-PKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 95 ~v~~~Gifv~lg~--~~gl~~~s~~~~d~~~~~~~~~~~~~~~~-~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
+++.+|+||++.. ++|++|++.+.++++.+++....+.+.++ +.++.||.|+|++.+++..++
T Consensus 632 ~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~ 697 (706)
T COG0557 632 GVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDER 697 (706)
T ss_pred EEEeccEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEccccc
Confidence 9999999999973 79999999999999988888778888776 699999999999999998654
No 62
>PRK05054 exoribonuclease II; Provisional
Probab=98.64 E-value=5.2e-08 Score=89.62 Aligned_cols=136 Identities=10% Similarity=-0.003 Sum_probs=86.9
Q ss_pred CCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEee-eeeCceEEecCCCceEEEEEEEEEEeeecCCC--EEEEEE
Q 030170 17 NLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTL-ENIGEGRVRENTGEVLFPVVFSGITFKIFRGE--VLDGTV 93 (182)
Q Consensus 17 ~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i-~~~~~g~i~~~~g~~~~~v~fk~~~f~p~~gE--v~~g~V 93 (182)
||-+|-.+|.+.+.|+++..+..++..... .-++ .++++........+....-.+++.+++.++|+ .++|.|
T Consensus 495 hfTSPIRRY~DLivHR~L~a~l~~~~~~~~-----~~~~~~~~s~~er~a~~aer~~~~~~~~~y~~~~~G~~~~f~g~I 569 (644)
T PRK05054 495 TWTSPIRKYGDMINHRLLKAVIKGETAERP-----QDEITVQLAERRRLNRMAERDVGDWLYARYLKDKAGTDTRFAAEI 569 (644)
T ss_pred ccCChhhhhHHHHHHHHHHHHHcCCCCCcc-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEEEE
Confidence 344444588999999999998766432110 0011 12222222111111111112566778899975 999999
Q ss_pred EEEecceEEEEec--CcceEEEcCCcCCCc--eeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 94 HKVLKHGVFLKCG--PVENIYLTCSKMPDY--RYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 94 ~~v~~~Gifv~lg--~~~gl~~~s~~~~d~--~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
++++++|+||++. .++|++|.+.+.+++ +.++.....+.-...+.|++||+|+|+|.++|...+
T Consensus 570 ~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~ 637 (644)
T PRK05054 570 IDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETR 637 (644)
T ss_pred EeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccC
Confidence 9999999999997 489999999987753 223322222211222799999999999999998654
No 63
>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=98.60 E-value=1.9e-07 Score=61.75 Aligned_cols=62 Identities=13% Similarity=0.135 Sum_probs=51.0
Q ss_pred CCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 86 GEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
|+++.|+|+++.++|++|+++ .++|++|.+++.+++... .+....|++||.|+++|++++-.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~--------~~~~~~~~~Gd~i~~kVl~~d~~ 63 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDG--------KNPLSKFKIGQKIKARVIGGHDA 63 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccc--------cChhHhCCCCCEEEEEEEEEeCc
Confidence 789999999999999999998 599999999987654110 11225799999999999999864
No 64
>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=98.60 E-value=8e-08 Score=88.50 Aligned_cols=63 Identities=16% Similarity=0.099 Sum_probs=52.7
Q ss_pred eecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCC----CceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMP----DYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~----d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
.|.+|++++|+|+++++||+||++.+ .+||+|+|++.+ .+. .+..+.+++||+|+|||.++|.
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv----------~~~~dv~kvGd~V~VKVl~ID~ 711 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRV----------ENVEDVLSVGQKIQVEIADIDD 711 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCc----------CCHHHcCCCCCEEEEEEEEECC
Confidence 58999999999999999999999974 899999998752 111 1123689999999999999994
No 65
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.59 E-value=1.5e-07 Score=77.78 Aligned_cols=64 Identities=19% Similarity=0.160 Sum_probs=55.2
Q ss_pred ecCCCEEEEEEEEEecceEEEEec---CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 83 IFRGEVLDGTVHKVLKHGVFLKCG---PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gifv~lg---~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
|.+|+++.|+|+++.++|+||++. .++|++|.+++.+++..+ ..+.+++||.|+|+|.+++...
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~----------i~~~~kvGd~V~vkVi~VD~~k 72 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKN----------IRDHVKEGQKVVCKVIRVDPRK 72 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccC----------HHHhCCCCCEEEEEEEEEeccc
Confidence 889999999999999999999996 479999999987665421 2258999999999999999854
No 66
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.58 E-value=5.1e-07 Score=71.11 Aligned_cols=84 Identities=17% Similarity=0.150 Sum_probs=65.1
Q ss_pred EEEEEeeecCCCEEEEEEEEEecceEEEEec-----------CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCe
Q 030170 76 FSGITFKIFRGEVLDGTVHKVLKHGVFLKCG-----------PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVV 144 (182)
Q Consensus 76 fk~~~f~p~~gEv~~g~V~~v~~~Gifv~lg-----------~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~ 144 (182)
++.....|.+|+++.|+|++++++|+||+++ ++++++|.+++.+++.. +-...|++||.
T Consensus 55 ~~~~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~----------~~~~~~~~GD~ 124 (189)
T PRK09521 55 FKKTPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVE----------SLTDAFKIGDI 124 (189)
T ss_pred CcCCCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhh----------hHHhccCCCCE
Confidence 3444567889999999999999999999995 46799999987654321 11257999999
Q ss_pred EEEEEEEEEecccccceEEEEeccCCCccccC
Q 030170 145 VRVIVIGTKWLEAEREFQALVSLEGDFLGPVS 176 (182)
Q Consensus 145 VrvrV~~v~~~~~~~~~~i~gs~~~~gLG~i~ 176 (182)
|++||.+++ . .+.-|++++.||.+.
T Consensus 125 V~akV~~i~-~------~i~LS~k~~~lGvv~ 149 (189)
T PRK09521 125 VRAKVISYT-D------PLQLSTKGKDLGVIY 149 (189)
T ss_pred EEEEEEecC-C------cEEEEEecCCceEEE
Confidence 999999998 2 256777788888764
No 67
>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=98.58 E-value=2.8e-07 Score=62.21 Aligned_cols=55 Identities=24% Similarity=0.228 Sum_probs=48.2
Q ss_pred eecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
...+|+.++|+|++++++|+|+++.+ .+|++|.+++. +.++.||.++++|.++ .+
T Consensus 13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~------------------~~~~iGd~v~v~I~~i-~e 68 (77)
T cd04473 13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL------------------RDYEVGDEVIVQVTDI-PE 68 (77)
T ss_pred hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc------------------CcCCCCCEEEEEEEEE-CC
Confidence 46789999999999999999999985 89999998741 4689999999999998 53
No 68
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=98.53 E-value=2.4e-07 Score=85.89 Aligned_cols=67 Identities=18% Similarity=0.235 Sum_probs=56.8
Q ss_pred EEeeecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 79 ITFKIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 79 ~~f~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
+...+.+|+++.|+|+++.+||+||++.+ .+|++|+|++.++++. +..+.|++||.|+|+|.+++..
T Consensus 615 ~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~----------~~~~v~kvGD~V~VkV~~iD~~ 682 (693)
T PRK11824 615 ITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVE----------KVEDVLKEGDEVKVKVLEIDKR 682 (693)
T ss_pred hcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCcccc----------CccceeCCCCEEEEEEEEECCC
Confidence 33468899999999999999999999984 8999999998766542 2236899999999999999863
No 69
>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=98.52 E-value=6.6e-07 Score=58.50 Aligned_cols=58 Identities=14% Similarity=0.120 Sum_probs=47.3
Q ss_pred CCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 86 GEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
|++++|+|+++.++|++|+++.+++++|.+++.+.+.... .. .+|+.+.|+|.+++..
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~g~~gfip~s~~~~~~~~~~----------~~--~vG~~i~~~i~~vd~~ 58 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDL----------DE--YVGKELKFKIIEIDRE 58 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCh----------HH--hCCCEEEEEEEEEeCC
Confidence 7899999999999999999977999999998865433110 11 3799999999999974
No 70
>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=98.49 E-value=9.8e-07 Score=57.93 Aligned_cols=57 Identities=21% Similarity=0.338 Sum_probs=49.2
Q ss_pred cCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
..|++++|+|.++++.|+||++|..+++++.+++.+. ..+++||.|+|.|.+++-..
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~~----------------~~~~~Gd~v~v~v~~v~~~~ 58 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPG----------------ESYRPGDRIKAYVLEVRKTS 58 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCCC----------------CcCCCCCEEEEEEEEEecCC
Confidence 5799999999999999999999989999998887531 35789999999999998643
No 71
>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=98.44 E-value=3e-07 Score=84.54 Aligned_cols=134 Identities=10% Similarity=0.013 Sum_probs=87.6
Q ss_pred CCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEee-eeeCceEEecCCCceEEEEEEEEEEeeecCCC--EEEEEE
Q 030170 17 NLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTL-ENIGEGRVRENTGEVLFPVVFSGITFKIFRGE--VLDGTV 93 (182)
Q Consensus 17 ~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i-~~~~~g~i~~~~g~~~~~v~fk~~~f~p~~gE--v~~g~V 93 (182)
||-+|-.+|.+.+.|+++..+..|+.... ..-++ .++++........+....--+++.+++.++|+ .++|+|
T Consensus 491 hfTSPIRRY~DLivHR~L~~~l~~~~~~~-----~~~~~~~~~s~~er~a~~aeR~~~~~~~~~yl~~~~g~~~~f~g~I 565 (639)
T TIGR02062 491 TWTSPIRKYGDMINHRLLKAVIKGETATR-----PQEDITVQLAERRRLNRIAERDVADWLYARFLADKAAKNTRFAAEI 565 (639)
T ss_pred ccCChhhhhHHHHHHHHHHHHHcCCCCCC-----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEEEE
Confidence 34444558899999999999876642111 01111 12222221111111111112556678888865 899999
Q ss_pred EEEecceEEEEec--CcceEEEcCCcCC--CceeecCCC--cEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 94 HKVLKHGVFLKCG--PVENIYLTCSKMP--DYRYVQAEN--PVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 94 ~~v~~~Gifv~lg--~~~gl~~~s~~~~--d~~~~~~~~--~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
++++++|+||++. .++|++|.+.+.+ +++.++... ..+.+. +.|++||+|+|+|.++|...+
T Consensus 566 ~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~--~~~~lgd~v~V~v~~vd~~~~ 633 (639)
T TIGR02062 566 VDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGE--TVYKIGDVIDVVLTEVRMETR 633 (639)
T ss_pred EeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEecc--EEEecCCEEEEEEEEeccccC
Confidence 9999999999995 4899999999876 555445433 355444 499999999999999998654
No 72
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.44 E-value=6.8e-07 Score=79.94 Aligned_cols=64 Identities=17% Similarity=0.181 Sum_probs=54.3
Q ss_pred cCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
.+|++++|+|+++++||+||++. .++|++|.+++.+++.. +....++.||+|+++|++++...+
T Consensus 378 ~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~~~~----------~~~~~~~~Gd~v~~~V~~id~e~~ 442 (491)
T PRK13806 378 APGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKP----------ATYEKLKPGDSVTLVVEEIDTAKR 442 (491)
T ss_pred CCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCccccc----------chhhcCCCCCEEEEEEEEEeCCCC
Confidence 38999999999999999999997 59999999998765441 122578999999999999998543
No 73
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.43 E-value=8.1e-07 Score=79.49 Aligned_cols=78 Identities=15% Similarity=0.141 Sum_probs=59.4
Q ss_pred cCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceE
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQ 162 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~ 162 (182)
.+|+++.|+|++++++|+||+++ .++|++|.+++.+.... .+....+++||.|+|+|.++|...+ .
T Consensus 291 ~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~---------~~~~~~~~~Gd~v~vkVl~iD~e~~----r 357 (491)
T PRK13806 291 KAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRV---------NKPEDVVAPGDAVAVKIKDIDPAKR----R 357 (491)
T ss_pred CCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCccccc---------CCHHHcCCCCCEEEEEEEEEEccCC----E
Confidence 47999999999999999999997 59999999988641110 1123589999999999999998643 3
Q ss_pred EEEeccCCCccc
Q 030170 163 ALVSLEGDFLGP 174 (182)
Q Consensus 163 i~gs~~~~gLG~ 174 (182)
+..|++..-.-|
T Consensus 358 i~Ls~K~~~~~p 369 (491)
T PRK13806 358 ISLSLRDAEGDP 369 (491)
T ss_pred EEEEEeecccCh
Confidence 555665544433
No 74
>PHA02945 interferon resistance protein; Provisional
Probab=98.43 E-value=1.6e-06 Score=59.59 Aligned_cols=62 Identities=23% Similarity=0.233 Sum_probs=51.3
Q ss_pred eecCCCEEEEEEEEEecceEEEEec---CcceEEEcCCc--CCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCG---PVENIYLTCSK--MPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg---~~~gl~~~s~~--~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
-|.+||++.|+|.. .++|+|+.|. ..++++|.|.. ++.+.. + .+++ .|++|.+||+.+|...
T Consensus 8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK---------~--rd~l-~GqkvV~KVirVd~~k 74 (88)
T PHA02945 8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFK---------Y--RDKL-VGKTVKVKVIRVDYTK 74 (88)
T ss_pred CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEe---------e--eeEe-cCCEEEEEEEEECCCC
Confidence 49999999999999 9999999996 47999999954 544332 2 3566 9999999999999854
No 75
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.40 E-value=1.2e-06 Score=78.22 Aligned_cols=63 Identities=17% Similarity=0.203 Sum_probs=54.0
Q ss_pred CCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 85 RGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 85 ~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
+|+++.|+|++++++|+||++. .++|++|.+++.+++.. .....|++||+|+|+|.++|.+.+
T Consensus 293 vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~----------~~~~~~kvGd~V~VkIi~ID~e~r 356 (486)
T PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVE----------VPEQVVQVGDEVFVKVIDIDLERR 356 (486)
T ss_pred CCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCccccc----------CccceeCCCCEEEEEEEEEECCCC
Confidence 7999999999999999999997 59999999998765442 123689999999999999998654
No 76
>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=98.39 E-value=6.5e-07 Score=63.60 Aligned_cols=85 Identities=14% Similarity=0.073 Sum_probs=58.7
Q ss_pred cCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCC--------CcEEEc-CCCceEcCCCeEEEEEEEEE
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAE--------NPVFLS-EKNPKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~--------~~~~~~-~~~~~~~~Gd~VrvrV~~v~ 153 (182)
.+|+++.|+|++++++|+|++++ .++|++|.+++.+++.....+ ...... +....|++||.|+++|++++
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d 81 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLD 81 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEcc
Confidence 47999999999999999999998 589999999998765211000 000000 01157999999999999999
Q ss_pred ecccccceEEEEeccC
Q 030170 154 WLEAEREFQALVSLEG 169 (182)
Q Consensus 154 ~~~~~~~~~i~gs~~~ 169 (182)
.... ..-.+..|++.
T Consensus 82 ~~~~-~~~~i~LSlr~ 96 (100)
T cd05693 82 KSKS-GKKRIELSLEP 96 (100)
T ss_pred CCcC-CCcEEEEEecH
Confidence 7410 01145666553
No 77
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.36 E-value=7.5e-07 Score=82.13 Aligned_cols=63 Identities=22% Similarity=0.316 Sum_probs=56.9
Q ss_pred cCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
+.|.+++|+|+++++||+||.+|- -||++|+|++.+.++.++ ..+++.||.|.|+|.++|...
T Consensus 657 k~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P----------~~vv~vGdiV~v~V~~vD~~r 720 (780)
T COG2183 657 KPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDP----------NEVVKVGDIVKVKVIEVDTAR 720 (780)
T ss_pred cCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCCh----------HHhcccCCEEEEEEEEEeccc
Confidence 799999999999999999999995 799999999998887643 369999999999999999854
No 78
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=98.35 E-value=2.1e-07 Score=84.50 Aligned_cols=69 Identities=22% Similarity=0.302 Sum_probs=59.0
Q ss_pred EEEEEeeecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 76 FSGITFKIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 76 fk~~~f~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
.+.++-.+.+|++|.|+|+++.+||+||++.| -+|++|+|++..++. .+-++++++||.|+||+..+|-
T Consensus 610 I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv----------~kv~dvlk~Gd~v~Vkv~~iD~ 679 (692)
T COG1185 610 IEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERV----------EKVEDVLKEGDEVKVKVIEIDK 679 (692)
T ss_pred HHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhh----------hcccceeecCceEEEEEeeecc
Confidence 34455678999999999999999999999986 799999999987644 2334799999999999999996
No 79
>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=98.34 E-value=1.6e-06 Score=55.02 Aligned_cols=58 Identities=19% Similarity=0.210 Sum_probs=47.7
Q ss_pred EEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 89 LDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 89 ~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
+.|+|++++++|+|++++ ..+++++.+++.+++.. +....|++||.|+++|.+++..+
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~~----------~~~~~~~~G~~v~~~v~~~d~~~ 59 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVK----------DPSEVFKVGDEVEVKVLEVDPEK 59 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCcccc----------CHhhEeCCCCEEEEEEEEEcCCc
Confidence 479999999999999998 68999999988765431 12268999999999999998743
No 80
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.33 E-value=1.8e-06 Score=74.92 Aligned_cols=74 Identities=20% Similarity=0.354 Sum_probs=58.8
Q ss_pred ecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceE
Q 030170 83 IFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQ 162 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~ 162 (182)
...|++++|+|++++++|+||+++.++|++|.+++.+++.. +....+++||.|+++|.+++.... .
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~----------~~~~~~~vGd~i~~~Vl~vd~~~~----~ 255 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVE----------KPSEVVSVGQEVEVKVLSIDWETE----R 255 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccC----------CHHHhcCCCCEEEEEEEEEeCCCC----E
Confidence 36899999999999999999999999999999998764331 112579999999999999997533 3
Q ss_pred EEEeccCC
Q 030170 163 ALVSLEGD 170 (182)
Q Consensus 163 i~gs~~~~ 170 (182)
+..|++..
T Consensus 256 i~lS~k~~ 263 (390)
T PRK06676 256 ISLSLKDT 263 (390)
T ss_pred EEEEEeec
Confidence 45565543
No 81
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.27 E-value=3.2e-06 Score=80.02 Aligned_cols=72 Identities=15% Similarity=0.166 Sum_probs=57.6
Q ss_pred cCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceEE
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQA 163 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~i 163 (182)
.+|++++|+|++++++|+||+++.++|++|.|++.+++.. +....+++|++|+|+|++++.+.+ .+
T Consensus 492 ~~G~~V~G~Vk~i~~~G~fVdl~Gv~Gfvp~SeiS~~~v~----------~~~~~~kvGq~v~vkVi~iD~e~~----rI 557 (863)
T PRK12269 492 HIEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVA----------RPREFVKKGQTIELKVIRLDQAEK----RI 557 (863)
T ss_pred CCCCEEEEEEEEEeCCcEEEEECCEEEEEEchhccccccC----------CHHHhccCCCEEEEEEEEEecCCC----eE
Confidence 4789999999999999999999999999999998766542 122567999999999999997543 35
Q ss_pred EEeccC
Q 030170 164 LVSLEG 169 (182)
Q Consensus 164 ~gs~~~ 169 (182)
..|++.
T Consensus 558 ~LSlK~ 563 (863)
T PRK12269 558 NLSLKH 563 (863)
T ss_pred EEEEec
Confidence 555554
No 82
>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=98.24 E-value=5.1e-06 Score=58.11 Aligned_cols=82 Identities=13% Similarity=0.003 Sum_probs=62.9
Q ss_pred eeecCCCEEEEEEEEEecceEEEEe--------c-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEE
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKC--------G-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIG 151 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~l--------g-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 151 (182)
+.|.+|.++.|+|++++..-+.|++ . ++.|++|.++..+.+.. .- +-.+.|++||.|+.||.+
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d--~~------~~~~~f~~GDiV~AkVis 73 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKD--KV------EMYKCFRPGDIVRAKVIS 73 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccccc--hH------HHHhhcCCCCEEEEEEEE
Confidence 4689999999999999999999999 5 57899998886543321 00 011589999999999999
Q ss_pred EEecccccceEEEEeccCCCcccc
Q 030170 152 TKWLEAEREFQALVSLEGDFLGPV 175 (182)
Q Consensus 152 v~~~~~~~~~~i~gs~~~~gLG~i 175 (182)
..-. .+ ..-|++++.||.+
T Consensus 74 ~~~~---~~--~~Lst~~~~lGVv 92 (92)
T cd05791 74 LGDA---SS--YYLSTAENELGVV 92 (92)
T ss_pred cCCC---CC--cEEEecCCCCccC
Confidence 8742 12 4678899999964
No 83
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.23 E-value=4.3e-06 Score=79.16 Aligned_cols=67 Identities=16% Similarity=0.200 Sum_probs=55.4
Q ss_pred cCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
.+|++++|+|++++++|+||+++ .++|++|.+++.+++..... +..+.|++||.|+|+|++++...+
T Consensus 751 ~vG~iV~GkV~~v~~~GvFVeL~~gVeGlI~~s~lsdd~~~~~~-------~~~~~f~vGD~V~v~Vl~iD~~~r 818 (863)
T PRK12269 751 GVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPG-------EALRKYAVGDRVKAVIVDMNVKDR 818 (863)
T ss_pred CCCCEEEEEEEEEecCeEEEEcCCCeEEEEEHHHcCCcccccch-------hhccccCCCCEEEEEEEEEEcCCC
Confidence 37999999999999999999997 59999999999887532111 113579999999999999998654
No 84
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.23 E-value=3.9e-06 Score=76.17 Aligned_cols=63 Identities=17% Similarity=0.209 Sum_probs=53.7
Q ss_pred cCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
..|++++|+|++++++|+||+++.++|++|.+++.+++.. +....|++||+|+|+|.+++.+.
T Consensus 200 ~~G~iv~g~V~~v~~~G~~V~i~g~~glv~~se~s~~~~~----------~~~~~~kvG~~v~v~V~~~d~~~ 262 (565)
T PRK06299 200 EEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVN----------HPSEVVNVGDEVKVKVLKFDKEK 262 (565)
T ss_pred CCCCEEEEEEEEEeCCeEEEEECCEEEEEEHHHhcccccC----------CHhhcCCCCCEEEEEEEEEeCCC
Confidence 5899999999999999999999999999999998665332 12257999999999999999754
No 85
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.21 E-value=6.7e-06 Score=71.34 Aligned_cols=64 Identities=22% Similarity=0.280 Sum_probs=53.4
Q ss_pred cCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
.+|+++.|+|++++++|+||++. .++|++|.+++.+++. .+....|+.||.|+++|.+++.+.+
T Consensus 276 ~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~----------~~~~~~~~~Gd~v~v~V~~id~e~~ 340 (390)
T PRK06676 276 PEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHI----------ATPSEVLEEGQEVKVKVLEVNEEEK 340 (390)
T ss_pred cCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCcccc----------CChhhccCCCCEEEEEEEEEECCCC
Confidence 47999999999999999999997 5899999998865432 1223579999999999999997543
No 86
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.16 E-value=6.2e-06 Score=74.87 Aligned_cols=65 Identities=17% Similarity=0.205 Sum_probs=53.8
Q ss_pred cCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
.+|+++.|+|++++++|+||+++ .++|++|.+++.+++.. .+....|++||.|+++|.+++...+
T Consensus 372 ~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~---------~~~~~~~~~Gd~v~v~Il~vd~~~~ 437 (565)
T PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKG---------EEAVELYKKGDEVEAVVLKVDVEKE 437 (565)
T ss_pred CCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccc---------cChHhhCCCCCEEEEEEEEEeCCCC
Confidence 47999999999999999999998 69999999998754321 1122689999999999999997543
No 87
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=98.15 E-value=8e-06 Score=73.25 Aligned_cols=64 Identities=19% Similarity=0.220 Sum_probs=54.7
Q ss_pred cCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
.+|+++.|+|++++++|+||+++. ++|++|.+++.+++.. +..+.|+.||.|+++|.+++..++
T Consensus 445 ~~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~~~~----------~~~~~~~~Gd~v~~~V~~id~~~~ 509 (516)
T TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDE----------DKTDEIKVGDEVEAKVVDIDKKNR 509 (516)
T ss_pred CcceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCccccc----------cccccCCCCCEEEEEEEEEeCCCC
Confidence 479999999999999999999985 8999999999876542 223689999999999999997543
No 88
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.13 E-value=5.2e-06 Score=73.77 Aligned_cols=69 Identities=20% Similarity=0.267 Sum_probs=56.4
Q ss_pred cCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceEE
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQA 163 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~i 163 (182)
.+|+++.|+|.+++++|+||++|..++++|.+++.|+ ..|++||.|+|.|.+++...+ ++ ++
T Consensus 133 ~~GeIV~G~V~ri~~~giiVDLggvea~LP~sE~ip~----------------E~~~~GdrIka~I~~Vd~~~k-g~-qI 194 (470)
T PRK09202 133 RVGEIITGVVKRVERGNIIVDLGRAEAILPRKEQIPR----------------ENFRPGDRVRAYVYEVRKEAR-GP-QI 194 (470)
T ss_pred hcCCEEEEEEEEEecCCEEEEECCeEEEecHHHcCCC----------------ccCCCCCEEEEEEEEEecCCC-CC-eE
Confidence 4899999999999999999999999999998887532 567899999999999988544 22 45
Q ss_pred EEeccCC
Q 030170 164 LVSLEGD 170 (182)
Q Consensus 164 ~gs~~~~ 170 (182)
+-|-..+
T Consensus 195 ilSRt~p 201 (470)
T PRK09202 195 ILSRTHP 201 (470)
T ss_pred EEEeCcH
Confidence 5555443
No 89
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=98.13 E-value=8e-06 Score=73.26 Aligned_cols=73 Identities=12% Similarity=0.183 Sum_probs=57.7
Q ss_pred cCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceE
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQ 162 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~ 162 (182)
.+|+++.|+|++++++|+||+++ .++|++|.+++.+++.. ......|++||.|.++|++++...+ .
T Consensus 358 ~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~---------~~~~~~~~~G~~V~~~Vl~vd~~~~----~ 424 (516)
T TIGR00717 358 PVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDG---------READHLYKKGDEIEAVVLAVDKEKK----R 424 (516)
T ss_pred CCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccC---------CCHhHccCCCCEEEEEEEEEeCcCC----E
Confidence 37999999999999999999999 69999999998754331 0122689999999999999997543 3
Q ss_pred EEEeccC
Q 030170 163 ALVSLEG 169 (182)
Q Consensus 163 i~gs~~~ 169 (182)
+..|++.
T Consensus 425 i~ls~K~ 431 (516)
T TIGR00717 425 ISLGVKQ 431 (516)
T ss_pred EEEeecc
Confidence 5555554
No 90
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.12 E-value=1e-05 Score=74.71 Aligned_cols=64 Identities=13% Similarity=0.119 Sum_probs=54.0
Q ss_pred cCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
.+|+++.|+|++++++|+||+++ .++|++|.+++.+++.. +....|++||.|+++|.+++.+++
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~----------~~~~~~kvGd~V~vkV~~id~e~~ 625 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRID----------KPEDVLSEGEEVKAKILEVDPEEK 625 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccC----------CHhhcCCCCCEEEEEEEEEeCCCC
Confidence 48999999999999999999997 58999999998765431 223579999999999999997544
No 91
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=98.11 E-value=5e-05 Score=60.67 Aligned_cols=93 Identities=15% Similarity=0.175 Sum_probs=73.4
Q ss_pred EEeceeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCC-ccEEEEEEeeeeeC-ceEEecCCCceEEEEEEEEEEee
Q 030170 5 VKLPWNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKD-LGYFLAVTTLENIG-EGRVRENTGEVLFPVVFSGITFK 82 (182)
Q Consensus 5 ~~l~d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~-~G~~v~i~~i~~~~-~g~i~~~~g~~~~~v~fk~~~f~ 82 (182)
.+..-.+.+.|.+|.+ .++..+.+.|..++ .+..+. .|++++..+|.-.+ .+.|.+.++..+..++-...+|+
T Consensus 30 ~t~dlhlalaP~yl~n---pl~~~i~ehld~~v--l~y~~~l~GivLgydnIKvLg~~aki~~D~pf~hlwi~adfyVf~ 104 (253)
T KOG4134|consen 30 ITTDLHLALAPYYLAN---PLHALIEEHLDTKV--LFYDSGLDGIVLGYDNIKVLGQTAKIRADDPFMHLWINADFYVFR 104 (253)
T ss_pred eeeheeeeecchhhcc---hhHHHHHHHhhHHH--hhhccCCCceEEeecceEeeccccceecCCCceEEEEeeeEEEEC
Confidence 3566678999999988 56654444444443 455555 78888888886554 58999999999999999999999
Q ss_pred ecCCCEEEEEEEEEecceEE
Q 030170 83 IFRGEVLDGTVHKVLKHGVF 102 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gif 102 (182)
|..|++++|.|-.+++..|=
T Consensus 105 Pk~Gd~LeG~Vn~vS~sHIg 124 (253)
T KOG4134|consen 105 PKAGDILEGVVNHVSRSHIG 124 (253)
T ss_pred CCCCCeeeeeeeecchhhhc
Confidence 99999999999999998653
No 92
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.08 E-value=2.2e-06 Score=69.87 Aligned_cols=64 Identities=16% Similarity=0.135 Sum_probs=54.7
Q ss_pred ecCCCEEEEEEEEEecceEEEEec---CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 83 IFRGEVLDGTVHKVLKHGVFLKCG---PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gifv~lg---~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
|.+||++.|+|.+|.+||+|+.|. ..+|++|.|+....++.+ -.++++.|+++-++|+++|...
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVkn----------Ird~vkegqkvV~kVlrVd~~r 75 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKN----------IRDYVKEGQKVVAKVLRVDPKR 75 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHH----------HHHHhhcCCeEEEEEEEEcCCC
Confidence 899999999999999999999996 489999999987654421 1158999999999999999854
No 93
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.06 E-value=1.4e-05 Score=67.89 Aligned_cols=74 Identities=11% Similarity=0.173 Sum_probs=58.6
Q ss_pred eecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccc
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAERE 160 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~ 160 (182)
+...|+++.|+|+++++.|+||++|. .+|+++.+++.+++... ....+++||+|+|+|++++....
T Consensus 28 ~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~----------~~~~~~~G~~v~~~Vi~~~~~~~--- 94 (318)
T PRK07400 28 HFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEG----------PEEVLQPNETREFFILSDENEDG--- 94 (318)
T ss_pred hcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccC----------HHHccCCCCEEEEEEEEEeCCCC---
Confidence 35789999999999999999999996 79999999987765421 22579999999999999886432
Q ss_pred eEEEEeccC
Q 030170 161 FQALVSLEG 169 (182)
Q Consensus 161 ~~i~gs~~~ 169 (182)
.++.|++.
T Consensus 95 -~i~lS~k~ 102 (318)
T PRK07400 95 -QLTLSIRR 102 (318)
T ss_pred -eEEEehhh
Confidence 34555543
No 94
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.01 E-value=1.5e-05 Score=73.58 Aligned_cols=63 Identities=14% Similarity=0.246 Sum_probs=53.1
Q ss_pred cCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
.+|+++.|+|++++++|+||+++.++|++|.+++.+.+.. +....|++||.|+++|.+++...
T Consensus 476 ~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~~~~----------~~~~~~~vGd~V~vkV~~id~~~ 538 (647)
T PRK00087 476 EEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVE----------KPSDVLKVGDEIKVYILDIDKEN 538 (647)
T ss_pred CCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCccccC----------CHHHhcCCCCEEEEEEEEEECCC
Confidence 4799999999999999999999889999999998754331 12257999999999999999754
No 95
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.86 E-value=3.4e-05 Score=66.52 Aligned_cols=69 Identities=17% Similarity=0.293 Sum_probs=56.3
Q ss_pred cCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceEE
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQA 163 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~i 163 (182)
..|+++.|+|.++++.|+||++|.++++++.+++.+ +..|++||.+++.|.+++...+ ++ ++
T Consensus 133 k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~E~ip----------------~e~~~~Gd~Ika~V~~V~~~~k-gp-~I 194 (362)
T PRK12327 133 REGDIVTGVVQRRDNRFVYVNLGKIEAVLPPAEQIP----------------GETYKHGDRIKVYVVKVEKTTK-GP-QI 194 (362)
T ss_pred hcCCEEEEEEEEEeCCcEEEEeCCeEEEecHHHcCC----------------CCCCCCCCEEEEEEEEEecCCC-CC-eE
Confidence 799999999999999999999999999888777644 2468899999999999998554 23 45
Q ss_pred EEeccCC
Q 030170 164 LVSLEGD 170 (182)
Q Consensus 164 ~gs~~~~ 170 (182)
+-|-..+
T Consensus 195 ivSRt~p 201 (362)
T PRK12327 195 FVSRTHP 201 (362)
T ss_pred EEEeCCH
Confidence 6555444
No 96
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.85 E-value=0.00036 Score=56.59 Aligned_cols=85 Identities=15% Similarity=0.141 Sum_probs=67.6
Q ss_pred EeeecCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCC-ceEcCCCeEEEEEEEEEeccc
Q 030170 80 TFKIFRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKN-PKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 80 ~f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~-~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
-|.|.+|+++-|+|..+...+-.|+++ |..++++.++.+......++ .+. .++++||-|-.||.+++-..
T Consensus 59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~-------~~~r~~l~vGD~v~AkV~~vd~~~- 130 (239)
T COG1097 59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAE-------KDLRPFLNVGDLVYAKVVDVDRDG- 130 (239)
T ss_pred cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccc-------cccccccccCCEEEEEEEEccCCC-
Confidence 578999999999999999999999998 78899999987443222111 122 59999999999999999642
Q ss_pred ccceEEEEeccCCCccccC
Q 030170 158 EREFQALVSLEGDFLGPVS 176 (182)
Q Consensus 158 ~~~~~i~gs~~~~gLG~i~ 176 (182)
.+.-++++.|+|.+.
T Consensus 131 ----~~~L~~k~~~~GkL~ 145 (239)
T COG1097 131 ----EVELTLKDEGLGKLK 145 (239)
T ss_pred ----ceEEEeecCCCcccc
Confidence 356667999999863
No 97
>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=97.77 E-value=0.00021 Score=49.37 Aligned_cols=82 Identities=17% Similarity=0.152 Sum_probs=60.5
Q ss_pred eeecCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCC-ceEcCCCeEEEEEEEEEecccc
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKN-PKIEKDVVVRVIVIGTKWLEAE 158 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~-~~~~~Gd~VrvrV~~v~~~~~~ 158 (182)
|.|.+|+.+-|+|++++..+.+|+++ +..++++..++... .++. ..++.||-|-.||.+++.. .+
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~ga------------tk~~rp~L~~GDlV~ArV~~~~~~-~~ 68 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGA------------TKRNRPNLNVGDLVYARVVKANRD-ME 68 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc------------cccccccCCCCCEEEEEEEecCCC-CC
Confidence 67999999999999999999999998 56778776543211 1223 4899999999999999874 22
Q ss_pred cceEEEEe-ccCCCcccc
Q 030170 159 REFQALVS-LEGDFLGPV 175 (182)
Q Consensus 159 ~~~~i~gs-~~~~gLG~i 175 (182)
....++.+ -+++|+|++
T Consensus 69 ~eLtc~~~~~k~~g~G~L 86 (86)
T cd05790 69 PELSCVDSSGKADGFGPL 86 (86)
T ss_pred eEEEEeCCCCcccccccC
Confidence 34344432 366799874
No 98
>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=97.70 E-value=9.1e-05 Score=63.45 Aligned_cols=70 Identities=21% Similarity=0.334 Sum_probs=55.9
Q ss_pred cCCCEEEEEEEEEecce-EEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceE
Q 030170 84 FRGEVLDGTVHKVLKHG-VFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQ 162 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~G-ifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~ 162 (182)
.+|+++.|+|.++++.| ++|++|..+++++.+++.+. ..|++||.+++.|.+++...+ ++ +
T Consensus 130 k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP~~E~ip~----------------E~~~~Gd~ik~~V~~V~~~~k-g~-q 191 (341)
T TIGR01953 130 KEGEIISGTVKRVNRRGNLYVELGKTEGILPKKEQIPG----------------EKFRIGDRIKAYVYEVRKTAK-GP-Q 191 (341)
T ss_pred hcCCEEEEEEEEEecCCcEEEEECCeEEEecHHHcCCC----------------cCCCCCCEEEEEEEEEEcCCC-CC-e
Confidence 59999999999999998 69999999999998877532 358899999999999997543 22 4
Q ss_pred EEEeccCCC
Q 030170 163 ALVSLEGDF 171 (182)
Q Consensus 163 i~gs~~~~g 171 (182)
++-|-..+.
T Consensus 192 IivSRt~~~ 200 (341)
T TIGR01953 192 IILSRTHPE 200 (341)
T ss_pred EEEEeCcHH
Confidence 666655443
No 99
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The Poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=97.44 E-value=0.02 Score=42.72 Aligned_cols=148 Identities=14% Similarity=0.182 Sum_probs=100.0
Q ss_pred eeEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeee---eeCceEEecCCCceEEEEEEEEEEeeecC
Q 030170 9 WNVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLE---NIGEGRVRENTGEVLFPVVFSGITFKIFR 85 (182)
Q Consensus 9 d~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~---~~~~g~i~~~~g~~~~~v~fk~~~f~p~~ 85 (182)
=.|.+.|++|.- ++++.|.+...++|+. | +.-|+.-.-++|- ...-|+|.. ..+...|-....+-.-.+
T Consensus 10 LpV~l~PhELtL---d~~~Ni~~aV~~eYLh-k--E~~G~MakkIei~~d~~lPLGeivN--N~ivv~VPC~vtykyYk~ 81 (160)
T PF03293_consen 10 LPVTLQPHELTL---DIRKNIKDAVYREYLH-K--ESGGIMAKKIEICEDKELPLGEIVN--NHIVVKVPCNVTYKYYKV 81 (160)
T ss_pred EEEecCcceeee---hHHHhHHHHHHHHHhh-h--cccCceeeeEEEEeccccchHhhcc--cEEEEEeeeEEEEEEEee
Confidence 357788999966 8888888888888853 2 3466655544442 334466653 334444444333334679
Q ss_pred CCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceEEEE
Q 030170 86 GEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQALV 165 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~i~g 165 (182)
|+++.|+..=-.+.-++|.+|.+ +-..+.-. .-..|++.++|++. ++..|..|++|.|...+..-.. ++.+.-+|
T Consensus 82 GDvV~GtLnIedESni~V~CgDL--iCkl~rds-GtVSf~dsKYCfir-Ng~vY~ngs~Vsv~LkEaq~g~-~S~FvFla 156 (160)
T PF03293_consen 82 GDVVRGTLNIEDESNITVQCGDL--ICKLSRDS-GTVSFNDSKYCFIR-NGVVYDNGSEVSVVLKEAQQGM-ESNFVFLA 156 (160)
T ss_pred CCEEEEEEEecccCceEEEcCcE--EEEeeccC-CeEEecCceEEEEE-CCEEecCCCEEEEEehhhhcCC-cceEEEEE
Confidence 99999999888888999999864 23332211 23566677777754 4579999999999998887643 46778888
Q ss_pred eccC
Q 030170 166 SLEG 169 (182)
Q Consensus 166 s~~~ 169 (182)
++.+
T Consensus 157 ~I~d 160 (160)
T PF03293_consen 157 SIID 160 (160)
T ss_pred EecC
Confidence 8753
No 100
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.35 E-value=0.00056 Score=59.06 Aligned_cols=75 Identities=16% Similarity=0.185 Sum_probs=58.4
Q ss_pred eeecCCCEEEEEEEEEecc-eEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccccc
Q 030170 81 FKIFRGEVLDGTVHKVLKH-GVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAER 159 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~-Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~ 159 (182)
|++.+||++.|+|.++... ++++++|..++++..+++.|. ..|++||.+++-|.+|+...+.+
T Consensus 134 y~~~~Geiv~g~V~r~~~~~~i~vdlg~~ea~LP~~eqip~----------------E~~~~Gdrik~~i~~V~~~~k~g 197 (374)
T PRK12328 134 YKKKVGKIVFGTVVRVDNEENTFIEIDEIRAVLPMKNRIKG----------------EKFKVGDVVKAVLKRVKIDKNNG 197 (374)
T ss_pred HHHhcCcEEEEEEEEEecCCCEEEEcCCeEEEeCHHHcCCC----------------CcCCCCCEEEEEEEEEecCCCCC
Confidence 3447999999999999975 599999988888887766542 57889999999999999865412
Q ss_pred ceEEEEeccCCCc
Q 030170 160 EFQALVSLEGDFL 172 (182)
Q Consensus 160 ~~~i~gs~~~~gL 172 (182)
+ +++-|-..+.|
T Consensus 198 p-~IilSRt~p~~ 209 (374)
T PRK12328 198 I-LIELSRTSPKF 209 (374)
T ss_pred C-EEEEEcCCHHH
Confidence 3 57777666543
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=97.34 E-value=0.0014 Score=57.71 Aligned_cols=76 Identities=14% Similarity=0.231 Sum_probs=54.4
Q ss_pred eecCCCEEEEEEEEEecc--eEEEEecC-cceEEEcCCcCCCceeecCCC--cEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 82 KIFRGEVLDGTVHKVLKH--GVFLKCGP-VENIYLTCSKMPDYRYVQAEN--PVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~--Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~--~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
.+.+|.+|.|+|.++.+. |+||++|. -.|++|.++..+++....... ..-..+-.+.++.||.|.|+|..--...
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke~~~~ 101 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKEPRGN 101 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeCCcCC
Confidence 457999999999999999 99999995 789999999876543221110 0000011246999999999999955543
Q ss_pred c
Q 030170 157 A 157 (182)
Q Consensus 157 ~ 157 (182)
+
T Consensus 102 K 102 (414)
T TIGR00757 102 K 102 (414)
T ss_pred C
Confidence 3
No 102
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=96.88 E-value=0.0094 Score=46.68 Aligned_cols=80 Identities=18% Similarity=0.111 Sum_probs=58.4
Q ss_pred EEeeecCCCEEEEEEEEEecceEEEEecC-----------cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEE
Q 030170 79 ITFKIFRGEVLDGTVHKVLKHGVFLKCGP-----------VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRV 147 (182)
Q Consensus 79 ~~f~p~~gEv~~g~V~~v~~~Gifv~lg~-----------~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~Vrv 147 (182)
.-..|..|.++-|.|+++....+-|++-. ..+-+|+|+....+.. +-+..|++||.||.
T Consensus 58 ~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~----------~~~d~f~~GDivrA 127 (188)
T COG1096 58 TPPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVE----------KLSDAFRIGDIVRA 127 (188)
T ss_pred CCCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEeccccccc----------ccccccccccEEEE
Confidence 34457899999999999999999998743 3456777776555543 22369999999999
Q ss_pred EEEEEEecccccceEEEEeccCCCcccc
Q 030170 148 IVIGTKWLEAEREFQALVSLEGDFLGPV 175 (182)
Q Consensus 148 rV~~v~~~~~~~~~~i~gs~~~~gLG~i 175 (182)
||++.-. + +.-|.+++-||.|
T Consensus 128 ~Vis~~~-----~--~~Lst~~~dlGVI 148 (188)
T COG1096 128 RVISTGD-----P--IQLSTKGNDLGVI 148 (188)
T ss_pred EEEecCC-----C--eEEEecCCcceEE
Confidence 9999751 2 3456666666655
No 103
>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=96.81 E-value=0.0051 Score=42.07 Aligned_cols=60 Identities=15% Similarity=0.055 Sum_probs=34.5
Q ss_pred ecCCCEEEEEEEEEecceEEEEecCc-------------------ceEEEcCCcCCCceeecCCCcEEEcCC--CceEcC
Q 030170 83 IFRGEVLDGTVHKVLKHGVFLKCGPV-------------------ENIYLTCSKMPDYRYVQAENPVFLSEK--NPKIEK 141 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gifv~lg~~-------------------~gl~~~s~~~~d~~~~~~~~~~~~~~~--~~~~~~ 141 (182)
|.+|.++.|+|+++++.-+++++--+ .|+++.++.-.... .+- .+.|++
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~----------Dkv~~~~~Frp 71 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEK----------DKVKMYDCFRP 71 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS--------------GGGT--S
T ss_pred CCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeeccccc----------chhhHHhccCC
Confidence 88999999999999999999876433 33444333211100 000 147999
Q ss_pred CCeEEEEEEEE
Q 030170 142 DVVVRVIVIGT 152 (182)
Q Consensus 142 Gd~VrvrV~~v 152 (182)
||.||.||++.
T Consensus 72 GDIVrA~ViSl 82 (82)
T PF10447_consen 72 GDIVRARVISL 82 (82)
T ss_dssp SSEEEEEEEEE
T ss_pred CCEEEEEEeeC
Confidence 99999999874
No 104
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=96.80 E-value=0.0016 Score=58.71 Aligned_cols=63 Identities=14% Similarity=0.110 Sum_probs=52.9
Q ss_pred cCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
..|-++.|+|+++.++|+||++-| -.++.|.+++..+... ..+..+++||.|.|+..+.|...
T Consensus 667 ~~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e~ia----------kpsd~levGq~I~vk~ie~d~~g 730 (760)
T KOG1067|consen 667 EFGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQEKIA----------KPSDLLEVGQEIQVKYIERDPRG 730 (760)
T ss_pred EeeeEEEEEEeeecccceEEEecCCchhhccchhccccccc----------ChHHHHhhcceeEEEEEeecCcc
Confidence 457778999999999999999987 5899999998766553 34457999999999999999743
No 105
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.76 E-value=0.004 Score=54.88 Aligned_cols=75 Identities=19% Similarity=0.226 Sum_probs=56.4
Q ss_pred eeecCCCEEEEEEEEEecceEEEEe----cC--cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKC----GP--VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~l----g~--~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
|++.+|+++.|+|.++...++++.+ |- .++++..+++.|. ..|+.||.||+-|.+|+.
T Consensus 148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~----------------E~y~~Gdrika~i~~V~~ 211 (449)
T PRK12329 148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPN----------------DNYRANATFKVFLKEVSE 211 (449)
T ss_pred HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCC----------------CcCCCCCEEEEEEEEeec
Confidence 4457999999999999999999998 42 6777776665442 578899999999999988
Q ss_pred cccccceEEEEeccCCCc
Q 030170 155 LEAEREFQALVSLEGDFL 172 (182)
Q Consensus 155 ~~~~~~~~i~gs~~~~gL 172 (182)
....++ +++-|-..++|
T Consensus 212 ~~~kGp-qIilSRt~p~l 228 (449)
T PRK12329 212 GPRRGP-QLFVSRANAGL 228 (449)
T ss_pred CCCCCC-EEEEEcCCHHH
Confidence 632234 56666555443
No 106
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=95.75 E-value=0.0088 Score=54.21 Aligned_cols=58 Identities=22% Similarity=0.214 Sum_probs=48.2
Q ss_pred cCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
..|+.+.|+|+++.++|+|+++.. +-|+.|.+++..+ ..+..|+++-|++.++..+..
T Consensus 121 e~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~----------------~~~~vgdeiiV~v~~vr~~~g 179 (715)
T COG1107 121 EAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD----------------PDYAVGDEIIVQVSDVRPEKG 179 (715)
T ss_pred ccceeeeccccchhhhcceeecChhhhccccccccCCC----------------CCCCCCCeEEEEeeccCCCCC
Confidence 689999999999999999999996 7899999987642 245668888888888887644
No 107
>PRK11712 ribonuclease G; Provisional
Probab=95.60 E-value=0.073 Score=47.86 Aligned_cols=75 Identities=17% Similarity=0.251 Sum_probs=53.3
Q ss_pred eecCCCEEEEEEEEEecc--eEEEEecC-cceEEEcCCcCCCceeec-CCCcEEEcCC--CceEcCCCeEEEEEEEEEec
Q 030170 82 KIFRGEVLDGTVHKVLKH--GVFLKCGP-VENIYLTCSKMPDYRYVQ-AENPVFLSEK--NPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~--Gifv~lg~-~~gl~~~s~~~~d~~~~~-~~~~~~~~~~--~~~~~~Gd~VrvrV~~v~~~ 155 (182)
...+|.+|.|+|.++.+- ++||++|. -.|++|.++..+...+.. +.+... ... +..++.||.|-|+|..--..
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~-~~~~i~~~l~~Gq~iLVQV~Ke~~~ 113 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQF-VVRDISELVRQGQDIMVQVVKDPLG 113 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhccccccccc-ccccHHHhccCCCEEEEEEEeCCcC
Confidence 457999999999999995 99999995 789999999866432111 110000 001 13599999999999987765
Q ss_pred cc
Q 030170 156 EA 157 (182)
Q Consensus 156 ~~ 157 (182)
.+
T Consensus 114 ~K 115 (489)
T PRK11712 114 TK 115 (489)
T ss_pred CC
Confidence 54
No 108
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=95.32 E-value=0.032 Score=38.16 Aligned_cols=64 Identities=19% Similarity=0.065 Sum_probs=49.3
Q ss_pred EeeecCCCEEEEEEEEEecceEEEEec--CcceEEE-cCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 80 TFKIFRGEVLDGTVHKVLKHGVFLKCG--PVENIYL-TCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 80 ~f~p~~gEv~~g~V~~v~~~Gifv~lg--~~~gl~~-~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
+--|.+|++.. .|..+.+.|+||+|- .++|++. .+++..+... +-.+.+ +|-.+.|+|+.+|..
T Consensus 11 y~~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~rir----------si~kll-VGk~e~v~ViRVDk~ 77 (86)
T PHA02858 11 YVFPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNADRAE----------KLKKKL-VGKTINVQVIRTDKL 77 (86)
T ss_pred EecCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHHHHH----------hhhhhh-cCCeeEEEEEEECCC
Confidence 33599999999 888999999999995 3889888 5665444331 112456 999999999999975
No 109
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=95.24 E-value=0.023 Score=56.07 Aligned_cols=64 Identities=13% Similarity=0.223 Sum_probs=55.4
Q ss_pred cCCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
..|+++.|+|..+.++|+||+.- .+.|+...+.+.+++...+ ...|.+||+||++|.+++-+.+
T Consensus 598 ~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~----------~ehf~vGqTv~~~i~nvd~ek~ 662 (1710)
T KOG1070|consen 598 IPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSD----------SEHFPVGQTVRAKIVNVDDEKR 662 (1710)
T ss_pred CCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcCh----------hhhcccccEEEEEEEecCchhc
Confidence 46999999999999999999985 6899999999988887532 3689999999999999998644
No 110
>PRK10811 rne ribonuclease E; Reviewed
Probab=94.85 E-value=0.18 Score=48.50 Aligned_cols=75 Identities=8% Similarity=0.046 Sum_probs=51.9
Q ss_pred eecCCCEEEEEEEEEecc--eEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 82 KIFRGEVLDGTVHKVLKH--GVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~--Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
.+.+|.||.|+|.+|-+. ++||++|. -.|+++.++....++...-.. .-....+..++.||.|-|+|..--...+
T Consensus 35 e~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~-~~~~~i~~~Lk~GqeILVQV~KEa~gtK 112 (1068)
T PRK10811 35 EQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSA-HGRPNIKDVLREGQEVIVQIDKEERGNK 112 (1068)
T ss_pred ccCccceEEEEEecccCCcceeEEEecCCcceEEEhhhcccccccccccc-ccccccccccCCCCEEEEEEeecccCCC
Confidence 356899999999999995 99999995 689999888754432111000 0000112368999999999998766544
No 111
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=94.68 E-value=0.094 Score=33.57 Aligned_cols=61 Identities=23% Similarity=0.331 Sum_probs=29.1
Q ss_pred CCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecccccceEEE
Q 030170 85 RGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEAEREFQAL 164 (182)
Q Consensus 85 ~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~~i~ 164 (182)
+|++-..+|++.+++|+|++.+.-..++.|....+ ..+++||.|.|-| +.+++. +++
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~-----------------~~~~~Gd~v~VFv----Y~D~~~--rl~ 57 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVP-----------------EPLKVGDEVEVFV----YLDKEG--RLV 57 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG-----------------------TTSEEEEEE----EE-TTS---EE
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcC-----------------CCCCCCCEEEEEE----EECCCC--CEE
Confidence 58889999999999999999887445555543221 3577899988866 333322 456
Q ss_pred Eecc
Q 030170 165 VSLE 168 (182)
Q Consensus 165 gs~~ 168 (182)
||++
T Consensus 58 AT~k 61 (61)
T PF13509_consen 58 ATTK 61 (61)
T ss_dssp EE--
T ss_pred EecC
Confidence 6653
No 112
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=94.52 E-value=0.24 Score=38.46 Aligned_cols=63 Identities=10% Similarity=0.016 Sum_probs=43.4
Q ss_pred eecCCCEEEEEEEEEecceEEEEecC---------cceEEEcCCcCCCceeecCCCcEEEcCCC--ceEcCCCeEEEEEE
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCGP---------VENIYLTCSKMPDYRYVQAENPVFLSEKN--PKIEKDVVVRVIVI 150 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg~---------~~gl~~~s~~~~d~~~~~~~~~~~~~~~~--~~~~~Gd~VrvrV~ 150 (182)
-|++|.++.++|+.++..=+-|++-- |.|+++..+.-+. ++ ++-. +.|++||.|+.+|+
T Consensus 65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~t-----Ek-----drv~v~ksFrPgDiVlAkVi 134 (193)
T KOG3409|consen 65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRAT-----EK-----DRVKVYKSFRPGDIVLAKVI 134 (193)
T ss_pred CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhcccc-----cc-----chhhhhhccCCCcEEEEEEe
Confidence 49999999999999999888777632 4455555443210 00 0011 57999999999999
Q ss_pred EEEe
Q 030170 151 GTKW 154 (182)
Q Consensus 151 ~v~~ 154 (182)
+..-
T Consensus 135 s~~~ 138 (193)
T KOG3409|consen 135 SLGD 138 (193)
T ss_pred ecCC
Confidence 9543
No 113
>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=92.50 E-value=0.37 Score=32.08 Aligned_cols=55 Identities=13% Similarity=0.135 Sum_probs=43.9
Q ss_pred CCEEEEEEEEEecceEEEEecC--cceEEEcCCcCCCceeecCCCcEEEcCCC--ceEcCCCeE-EEEEE
Q 030170 86 GEVLDGTVHKVLKHGVFLKCGP--VENIYLTCSKMPDYRYVQAENPVFLSEKN--PKIEKDVVV-RVIVI 150 (182)
Q Consensus 86 gEv~~g~V~~v~~~Gifv~lg~--~~gl~~~s~~~~d~~~~~~~~~~~~~~~~--~~~~~Gd~V-rvrV~ 150 (182)
|.+++|+|..=++.++.|++++ +-+++...++.+ ... +... +.+++||++ ++-|.
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD-~~~---------k~~~~~~klrvG~~L~~~lvL 60 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSD-HVS---------NCPLLWHCLQEGDTIPNLMCL 60 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC-chh---------hCHHHHhhhhcCCCccceEEE
Confidence 6789999999999999999985 678888888776 331 1122 689999999 88888
No 114
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=92.18 E-value=1 Score=40.61 Aligned_cols=93 Identities=18% Similarity=0.193 Sum_probs=67.6
Q ss_pred CceEEecCCCceEEEEEEEEEEeeecCCCEEEEEEEEEecc--eEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCC
Q 030170 59 GEGRVRENTGEVLFPVVFSGITFKIFRGEVLDGTVHKVLKH--GVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEK 135 (182)
Q Consensus 59 ~~g~i~~~~g~~~~~v~fk~~~f~p~~gEv~~g~V~~v~~~--Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~ 135 (182)
++-++.--++...+++.++.-.-+..+|.+|-|+|+++.+. .+||++|. -.|+.|.++..+ ++....+. +-
T Consensus 11 ~e~rva~v~~~~l~el~ie~~~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~-~~~~~~~~-----~i 84 (487)
T COG1530 11 EETRVAVVDGGALQELDIERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVP-YFRAVLEE-----KI 84 (487)
T ss_pred ceeEEEEEeCCEEEEEEEecCCcEeeecCceEEEecccCccchhheeeccCCccceEEecccch-hhhhcccc-----cc
Confidence 44455444566766666666666778999999999999995 89999994 679999999887 32211110 11
Q ss_pred CceEcCCCeEEEEEEEEEeccc
Q 030170 136 NPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 136 ~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
...++.|+.+-|+|.......+
T Consensus 85 ~~~lr~~~~~~Vqv~ke~~G~K 106 (487)
T COG1530 85 KVRLRGGQATLVQVVKEPRGTK 106 (487)
T ss_pred eeeecCCceEEEEEEeecCccc
Confidence 2489999999999988877543
No 115
>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=91.92 E-value=0.85 Score=32.40 Aligned_cols=58 Identities=12% Similarity=0.198 Sum_probs=43.2
Q ss_pred eeecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 81 FKIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 81 f~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
+-+..|-++.|+|..+...-+|++.|. |..+.--+. .+...|..|+.||+|+.+....
T Consensus 19 lG~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~-----------------~~~~~y~~G~rV~lrLkdlELs 77 (104)
T PF10246_consen 19 LGDPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPA-----------------VNGEKYVRGSRVRLRLKDLELS 77 (104)
T ss_pred cCCccCCEEEEEEEEEecCceEEEeCCceeEEEeccc-----------------ccccccccCCEEEEEECCHhhh
Confidence 446789999999999999999999995 543333111 1124688899999999877653
No 116
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=91.78 E-value=2.4 Score=34.02 Aligned_cols=95 Identities=14% Similarity=0.092 Sum_probs=67.6
Q ss_pred eEEEEEEEEEEeeecCCCEEEEEEEEEecceEEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCC-ceEcCCCeEEEE
Q 030170 70 VLFPVVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKN-PKIEKDVVVRVI 148 (182)
Q Consensus 70 ~~~~v~fk~~~f~p~~gEv~~g~V~~v~~~Gifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~-~~~~~Gd~Vrvr 148 (182)
-.+.+..+-.-|-|.+|+.+-|+|++-+..+..|++|.-+ ..-.+.+ .|+..+ +++ -.++.||-|-.|
T Consensus 50 ~v~~vds~~kRYiP~~~D~VIGiV~~~~gd~ykVDigg~~-~a~L~~l-----aFe~At-----krNrPnl~vGdliyak 118 (230)
T KOG1004|consen 50 GVYWVDSQQKRYIPVKGDHVIGIVTSKSGDIYKVDIGGSE-PASLSYL-----AFEGAT-----KRNRPNLQVGDLIYAK 118 (230)
T ss_pred eeEEEecccceecCCCCCEEEEEEEeccCceEEEecCCCC-eeeeeec-----cccCcc-----ccCCCccccccEEEEE
Confidence 3556778888899999999999999999999999999631 2222222 222211 233 389999999999
Q ss_pred EEEEEecccccceEEEEec-cCCCccccC
Q 030170 149 VIGTKWLEAEREFQALVSL-EGDFLGPVS 176 (182)
Q Consensus 149 V~~v~~~~~~~~~~i~gs~-~~~gLG~i~ 176 (182)
|...+.+ -++.+.++.+. ++.|.|++.
T Consensus 119 v~~a~~~-~Epel~Cids~graaGfG~Lk 146 (230)
T KOG1004|consen 119 VVDANKD-MEPELTCIDSTGRAAGFGVLK 146 (230)
T ss_pred EEecCCC-cCcceEEEcccCcccCccccc
Confidence 9999863 34566777773 556888763
No 117
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=91.64 E-value=0.89 Score=45.52 Aligned_cols=63 Identities=16% Similarity=0.171 Sum_probs=52.8
Q ss_pred cCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEecc
Q 030170 84 FRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLE 156 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 156 (182)
..|+++.|.|.++.+.|+|+.++. +++++.++++.+.+... -.+.|..|+.|..||.+++...
T Consensus 1161 k~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~k~----------w~k~~~~gklv~~rv~~ve~~s 1224 (1710)
T KOG1070|consen 1161 KIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFEKE----------WEKHLPVGKLVTGRVLSVEEDS 1224 (1710)
T ss_pred ccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchhhh----------hhccCCccceeeeEEEEeeccC
Confidence 589999999999999999999995 89999988886654321 1268999999999999999754
No 118
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=88.12 E-value=1.6 Score=36.37 Aligned_cols=52 Identities=17% Similarity=0.247 Sum_probs=45.0
Q ss_pred CCCEEEEEEEEEecceEEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 85 RGEVLDGTVHKVLKHGVFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 85 ~gEv~~g~V~~v~~~Gifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
.++.++|+|-+..+.|.|+-+. ..-|++|+|+.- ...+.|+.+.+||++++.
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~------------------~~prlG~~l~~rVi~~re 207 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSERF------------------AEPRLGERLTARVIGVRE 207 (287)
T ss_pred hcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhc------------------ccccCCceEEEEEEEEcc
Confidence 5999999999999999999986 456999988642 356789999999999998
No 119
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=83.81 E-value=0.56 Score=38.86 Aligned_cols=63 Identities=14% Similarity=0.040 Sum_probs=49.7
Q ss_pred ecCCCEEEEEEEEEecceEEEEec---CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 83 IFRGEVLDGTVHKVLKHGVFLKCG---PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 83 p~~gEv~~g~V~~v~~~Gifv~lg---~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
|.++|++-+.|.+|.+.|+||.|- .++|++..|+|+.-+... -.+.+++|-.=-|-|+.+|-+
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRS----------I~klirVGr~E~vvVlrVDke 79 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRS----------IQKLIRVGRNEPVVVLRVDKE 79 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHH----------HHHHHhcCCcceEEEEEEcCC
Confidence 899999999999999999999884 689999999986543310 014677777777778888864
No 120
>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=81.97 E-value=9.7 Score=24.11 Aligned_cols=49 Identities=12% Similarity=0.012 Sum_probs=31.4
Q ss_pred EEEEEEEEec---ceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEE
Q 030170 89 LDGTVHKVLK---HGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIG 151 (182)
Q Consensus 89 ~~g~V~~v~~---~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 151 (182)
+.|+|+..++ ||.-..-+. -+-++|.+++..... ..++.|+.|+|.+..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~--------------~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGF--------------RSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSS--------------TS--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEecccccccccc--------------ccCCCCCEEEEEEEE
Confidence 4688988886 455443333 355677776644321 578899999999988
No 121
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=79.39 E-value=0.98 Score=40.40 Aligned_cols=76 Identities=8% Similarity=0.039 Sum_probs=52.5
Q ss_pred eecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCC---ceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPD---YRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d---~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
++.....|.+.|..|+.-|+.|.+-- =--.|+|..++.+ ......++..+.-+...+|++||.|.|++.+|+.+.+
T Consensus 558 k~~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk~~D~i~V~l~eVr~etR 637 (645)
T COG4776 558 KAGTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANREELVCNQENGTVQIKGETVYKVGDVIDVTLAEVRMETR 637 (645)
T ss_pred ccccCchhhhhhhhhccCceEEEeccCCcceecchhhhccchhheEecCCCceEEEccEEEEeeccEEEEEeHHHHHhhh
Confidence 45566779999999999999999842 1135666655542 2333444443333334699999999999999998665
No 122
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=79.25 E-value=13 Score=25.64 Aligned_cols=54 Identities=24% Similarity=0.188 Sum_probs=38.7
Q ss_pred EEEEEEEEEecceEE-EEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 88 VLDGTVHKVLKHGVF-LKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 88 v~~g~V~~v~~~Gif-v~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
.++|+|+.+-+.+.| |.|. ..+-+-|+|--+.-+. ..+.+||.|.|-+..-|..
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~r--------------IrIl~GD~V~VE~spYDlt 63 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHR--------------IRILAGDRVTLELSPYDLT 63 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeee--------------EEecCCCEEEEEECcccCC
Confidence 478999999999988 5775 3555666665443211 3688999999988876653
No 123
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=78.18 E-value=6 Score=29.81 Aligned_cols=63 Identities=13% Similarity=0.247 Sum_probs=47.1
Q ss_pred EEEEeeecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 77 SGITFKIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 77 k~~~f~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
+++-+-|..|.++.|+|-.+.+.-+|++.|. |..+.-.+.+ +...|..|..||.|+++....
T Consensus 74 kl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~-----------------n~e~Y~~GaRVrlRl~DlELs 136 (173)
T KOG4078|consen 74 KLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPAL-----------------NGEAYQKGARVRLRLIDLELS 136 (173)
T ss_pred ccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCc-----------------CHHHhhcCceEEEEEcChhHh
Confidence 5566778999999999999999999999985 4322222211 125788899999999887764
Q ss_pred c
Q 030170 156 E 156 (182)
Q Consensus 156 ~ 156 (182)
+
T Consensus 137 ~ 137 (173)
T KOG4078|consen 137 E 137 (173)
T ss_pred h
Confidence 4
No 124
>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=73.07 E-value=23 Score=23.20 Aligned_cols=53 Identities=17% Similarity=0.140 Sum_probs=36.7
Q ss_pred EEEEEEEEEecceEE-EEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 88 VLDGTVHKVLKHGVF-LKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 88 v~~g~V~~v~~~Gif-v~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
.++|+|++.-+.|.| |.|. ..+-+-|++-.+.-+ ...+.+||.|.|.+-.-+.
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~--------------rI~I~~GD~V~Ve~spyd~ 60 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMH--------------YIRILPGDKVKVELSPYDL 60 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhc--------------cEEECCCCEEEEEECcccC
Confidence 478999999999888 5765 455566666544311 1368889999988766554
No 125
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=72.21 E-value=10 Score=37.62 Aligned_cols=62 Identities=18% Similarity=0.134 Sum_probs=47.8
Q ss_pred cCCCEEEEEEEEEecce---EEEEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 84 FRGEVLDGTVHKVLKHG---VFLKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 84 ~~gEv~~g~V~~v~~~G---ifv~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
++|-++.++|++++..- +.|.+. ++.|+++.+.+.+..+. +....+++|++|-+||+.++..
T Consensus 984 ~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~----------~p~~~v~vgq~v~~kvi~id~e 1049 (1299)
T KOG1856|consen 984 YEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVR----------RPENRVKVGQTVYCKVIKIDKE 1049 (1299)
T ss_pred ccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhcc----------CHHHhhccCceEEEEeeeeeHh
Confidence 68999999999999875 445665 57899998887763332 2235677999999999999974
No 126
>PRK15464 cold shock-like protein CspH; Provisional
Probab=67.50 E-value=24 Score=23.12 Aligned_cols=50 Identities=14% Similarity=0.116 Sum_probs=32.6
Q ss_pred EEEEEEEEecc-eE-EEEec--CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEE
Q 030170 89 LDGTVHKVLKH-GV-FLKCG--PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGT 152 (182)
Q Consensus 89 ~~g~V~~v~~~-Gi-fv~lg--~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 152 (182)
+.|+|+.-+.. |. |+.-. .-|-++|.+.+-.+-. +.+..|+.|.+.+..-
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g~--------------~~l~~G~~V~f~v~~~ 58 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRDA--------------EVLIPGLRVEFCRVNG 58 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcCC--------------CCCCCCCEEEEEEEEC
Confidence 47888888873 44 45443 3466778777632211 4688899999988763
No 127
>PRK15463 cold shock-like protein CspF; Provisional
Probab=64.52 E-value=28 Score=22.72 Aligned_cols=49 Identities=10% Similarity=0.055 Sum_probs=31.4
Q ss_pred EEEEEEEEecc-eE-EEEec--CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEE
Q 030170 89 LDGTVHKVLKH-GV-FLKCG--PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIG 151 (182)
Q Consensus 89 ~~g~V~~v~~~-Gi-fv~lg--~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 151 (182)
+.|+|+.-+.. |. |++-. .-|-++|.+.+..+- .+.++.|+.|.+.+..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g--------------~~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRD--------------AEELTTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcC--------------CCCCCCCCEEEEEEEE
Confidence 47888888873 43 34332 346677777763221 1578889999997765
No 128
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=64.51 E-value=40 Score=22.57 Aligned_cols=54 Identities=26% Similarity=0.247 Sum_probs=39.5
Q ss_pred CEEEEEEEEEecceEE-EEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEe
Q 030170 87 EVLDGTVHKVLKHGVF-LKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKW 154 (182)
Q Consensus 87 Ev~~g~V~~v~~~Gif-v~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 154 (182)
-.++|+|.+.-+.|.| |++. .++-+-|+|.-+.-.. ..+.+||.|.|.....+.
T Consensus 7 ~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~~~--------------i~I~~GD~V~Ve~~~~d~ 62 (75)
T COG0361 7 IEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNR--------------IRILPGDVVLVELSPYDL 62 (75)
T ss_pred cEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchhee--------------EEeCCCCEEEEEeccccc
Confidence 3578999999999887 7775 4667777776553211 368889999998877764
No 129
>PRK09750 hypothetical protein; Provisional
Probab=61.02 E-value=7.3 Score=24.85 Aligned_cols=20 Identities=10% Similarity=0.154 Sum_probs=17.8
Q ss_pred ceEEEEeccCCCccccCCCC
Q 030170 160 EFQALVSLEGDFLGPVSCEN 179 (182)
Q Consensus 160 ~~~i~gs~~~~gLG~i~w~~ 179 (182)
.|+|.++++-+|=+|.+|-+
T Consensus 3 kY~I~Ati~KpGg~P~~W~r 22 (64)
T PRK09750 3 MYKITATIEKEGGTPTNWTR 22 (64)
T ss_pred eeEEEEEEECCCCCccceeE
Confidence 47899999999999999963
No 130
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=55.57 E-value=56 Score=21.57 Aligned_cols=50 Identities=18% Similarity=0.084 Sum_probs=30.2
Q ss_pred EEEEEEEec-ceE-EEEe-c-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEE
Q 030170 90 DGTVHKVLK-HGV-FLKC-G-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 90 ~g~V~~v~~-~Gi-fv~l-g-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 153 (182)
.|+|+--+. .|. |+.- + .-+-++|.+.+..+-+ +.+..|+.|.+.+..-.
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g~--------------~~l~~G~~V~f~~~~~~ 56 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDGY--------------RTLKAGQSVQFDVHQGP 56 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccCC--------------CCCCCCCEEEEEEEECC
Confidence 367777666 233 3433 2 3566777776632211 57888999999887644
No 131
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=53.46 E-value=1.2e+02 Score=25.44 Aligned_cols=71 Identities=24% Similarity=0.323 Sum_probs=44.4
Q ss_pred eecCCCEEEEEEEEEecceEEEEecCcc-eEEEcCC-cCCC----------ceeecCCCcEEEc-CCCceEcCCCeEEEE
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCGPVE-NIYLTCS-KMPD----------YRYVQAENPVFLS-EKNPKIEKDVVVRVI 148 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg~~~-gl~~~s~-~~~d----------~~~~~~~~~~~~~-~~~~~~~~Gd~Vrvr 148 (182)
...+|+.....|.+.++||.|+.-+..+ .++.+.. ...+ +.|.|.+.. +.. ...-..++|+-=..+
T Consensus 2 ~~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~~e~evGdev~vFiY~D~~~r-l~aTt~~p~~tvg~~g~~~ 80 (287)
T COG2996 2 MIKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEEDELEVGDEVTVFIYVDSEDR-LIATTREPKATVGEYGWLK 80 (287)
T ss_pred cccccceEEEEEEEeeceeEEEecCCCceEEeccccCCcCCccccCcEEEEEEEECCCCc-eeheeecceEeecceeEEE
Confidence 3468999999999999999999988653 3444333 2221 122232221 111 111367788888888
Q ss_pred EEEEE
Q 030170 149 VIGTK 153 (182)
Q Consensus 149 V~~v~ 153 (182)
|++++
T Consensus 81 Vv~v~ 85 (287)
T COG2996 81 VVEVN 85 (287)
T ss_pred EEEEc
Confidence 88887
No 132
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=50.05 E-value=68 Score=20.73 Aligned_cols=51 Identities=10% Similarity=0.096 Sum_probs=30.4
Q ss_pred EEEEEEEEec-ceE-EEEe-c-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEE
Q 030170 89 LDGTVHKVLK-HGV-FLKC-G-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 89 ~~g~V~~v~~-~Gi-fv~l-g-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 153 (182)
+.|+|+.-+. .|. |+.- + .-|-++|.+.+..+.. +.++.|+.|.+.+..-+
T Consensus 4 ~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g~--------------~~l~~G~~V~f~~~~~~ 58 (69)
T PRK09507 4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNGF--------------KTLAEGQRVEFEITNGA 58 (69)
T ss_pred cceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccCC--------------CCCCCCCEEEEEEEECC
Confidence 4678887765 233 3333 2 2455667666532211 57788999999876644
No 133
>PRK10943 cold shock-like protein CspC; Provisional
Probab=49.85 E-value=66 Score=20.80 Aligned_cols=51 Identities=10% Similarity=0.082 Sum_probs=30.9
Q ss_pred EEEEEEEEec-ceE-EEEe-c-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEE
Q 030170 89 LDGTVHKVLK-HGV-FLKC-G-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 89 ~~g~V~~v~~-~Gi-fv~l-g-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 153 (182)
+.|+|+.-+. .|. |++- + .-+-++|.+.+..+.+ +.+..|+.|.+.+..-+
T Consensus 4 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g~--------------~~l~~G~~V~f~~~~~~ 58 (69)
T PRK10943 4 IKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNGF--------------KTLAEGQNVEFEIQDGQ 58 (69)
T ss_pred cceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccCC--------------CCCCCCCEEEEEEEECC
Confidence 5688887776 232 3333 2 3455777776532211 56788999999876543
No 134
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=48.79 E-value=39 Score=28.22 Aligned_cols=27 Identities=26% Similarity=0.267 Sum_probs=24.2
Q ss_pred eecCCCEEEEEEEEEecceEEEEecCc
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKCGPV 108 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~lg~~ 108 (182)
+|..||+-+|.|.+..+.|.+|.+|--
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG~~ 128 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIGKD 128 (272)
T ss_pred CccceeecceEEEEecCCceEEEecCC
Confidence 468999999999999999999999853
No 135
>PRK09890 cold shock protein CspG; Provisional
Probab=48.03 E-value=75 Score=20.60 Aligned_cols=49 Identities=10% Similarity=0.093 Sum_probs=29.9
Q ss_pred EEEEEEEEec-ceE-EEEec--CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEE
Q 030170 89 LDGTVHKVLK-HGV-FLKCG--PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIG 151 (182)
Q Consensus 89 ~~g~V~~v~~-~Gi-fv~lg--~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 151 (182)
+.|+|+.-++ .|. |++-. .-|-++|.+.+..+-+ +.++.|+.|++.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~--------------~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEF--------------RTLNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCC--------------CCCCCCCEEEEEEEE
Confidence 4788888765 232 33332 2455677776532211 467889999997754
No 136
>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=42.24 E-value=86 Score=20.13 Aligned_cols=50 Identities=16% Similarity=0.072 Sum_probs=28.9
Q ss_pred EEEEEEEec-ceE-EEEe-c-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEE
Q 030170 90 DGTVHKVLK-HGV-FLKC-G-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 90 ~g~V~~v~~-~Gi-fv~l-g-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 153 (182)
.|+|+.-+. .|. |+.- + .-+-++|.|.+..+- -+.++.|+.|++.+..-+
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g--------------~~~l~~G~~V~f~~~~~~ 56 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDG--------------YRTLKAGQKVQFEVVQGP 56 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcC--------------CCCCCCCCEEEEEEEECC
Confidence 367777664 233 3333 2 345566666653211 157888999999776543
No 137
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=42.02 E-value=51 Score=20.44 Aligned_cols=14 Identities=14% Similarity=-0.111 Sum_probs=9.9
Q ss_pred eEcCCCeEEEEEEE
Q 030170 138 KIEKDVVVRVIVIG 151 (182)
Q Consensus 138 ~~~~Gd~VrvrV~~ 151 (182)
.--.||+|.|++..
T Consensus 31 ~A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 31 GAMDGDKVLVRITP 44 (58)
T ss_dssp TS-TT-EEEEEEEE
T ss_pred CCCCCCEEEEEEec
Confidence 34459999999998
No 138
>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=41.88 E-value=85 Score=19.51 Aligned_cols=16 Identities=13% Similarity=0.011 Sum_probs=13.2
Q ss_pred ceEcCCCeEEEEEEEE
Q 030170 137 PKIEKDVVVRVIVIGT 152 (182)
Q Consensus 137 ~~~~~Gd~VrvrV~~v 152 (182)
..++.|+.|.+.+..-
T Consensus 39 ~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 39 RSLEEGDRVEFELEEG 54 (65)
T ss_pred CcCCCCCEEEEEEEEC
Confidence 5788999999988765
No 139
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=41.01 E-value=98 Score=19.97 Aligned_cols=49 Identities=10% Similarity=0.064 Sum_probs=30.6
Q ss_pred EEEEEEEEec---ceEEEEec--CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEE
Q 030170 89 LDGTVHKVLK---HGVFLKCG--PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGT 152 (182)
Q Consensus 89 ~~g~V~~v~~---~Gifv~lg--~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 152 (182)
..|+|+.-++ ||+ ++-. .-|-++|.+.+..+.+ +.++.|+.|.+.+..-
T Consensus 5 ~~G~Vk~f~~~kGfGF-I~~~~g~~dvfvH~s~l~~~g~--------------~~l~~G~~V~f~~~~~ 58 (70)
T PRK10354 5 MTGIVKWFNADKGFGF-ITPDDGSKDVFVHFSAIQNDGY--------------KSLDEGQKVSFTIESG 58 (70)
T ss_pred ceEEEEEEeCCCCcEE-EecCCCCccEEEEEeeccccCC--------------CCCCCCCEEEEEEEEC
Confidence 3788887765 343 4332 2456777776632211 5788899999987653
No 140
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=39.02 E-value=54 Score=27.33 Aligned_cols=42 Identities=17% Similarity=0.238 Sum_probs=33.3
Q ss_pred EEeeecCCCEEEEEEEEEecceEEEEecC-cceEEEcCCc-CCC
Q 030170 79 ITFKIFRGEVLDGTVHKVLKHGVFLKCGP-VENIYLTCSK-MPD 120 (182)
Q Consensus 79 ~~f~p~~gEv~~g~V~~v~~~Gifv~lg~-~~gl~~~s~~-~~d 120 (182)
.-|.|.+|+++.|+|..|.+.-.-|+++. .++++..++. +|+
T Consensus 79 ~rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPG 122 (301)
T KOG3013|consen 79 SRYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPG 122 (301)
T ss_pred hhcCCccCCEEEEEeeeeecceeEEecccccceEEEeecccCCc
Confidence 34668999999999999999999999996 5666665543 553
No 141
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=38.80 E-value=51 Score=20.37 Aligned_cols=24 Identities=21% Similarity=0.175 Sum_probs=17.6
Q ss_pred eecCCCEEEEEEEEEecceEEEEe
Q 030170 82 KIFRGEVLDGTVHKVLKHGVFLKC 105 (182)
Q Consensus 82 ~p~~gEv~~g~V~~v~~~Gifv~l 105 (182)
.|.+|+.+..+|++.+++-++.++
T Consensus 37 ~~~iG~~v~v~I~~~~~~~l~G~~ 60 (61)
T PF01938_consen 37 LPLIGEFVKVRITKAKKNYLFGEL 60 (61)
T ss_dssp -T--TEEEEEEEEEE-SSEEEEEE
T ss_pred CCCCCCEEEEEEEEeeCCcEEEEE
Confidence 466899999999999998887654
No 142
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=38.73 E-value=37 Score=22.04 Aligned_cols=52 Identities=17% Similarity=0.222 Sum_probs=27.0
Q ss_pred EEEEEEe--cceEEEEecCcceEEEcCCcCCCc--eeecCCCcEEEcCCC-ceEcCCCeEEEEEEEEE
Q 030170 91 GTVHKVL--KHGVFLKCGPVENIYLTCSKMPDY--RYVQAENPVFLSEKN-PKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 91 g~V~~v~--~~Gifv~lg~~~gl~~~s~~~~d~--~~~~~~~~~~~~~~~-~~~~~Gd~VrvrV~~v~ 153 (182)
|+|.+++ ..-+-++-+++.++- +|.. .|.-. +... ..++.||.|+|.+...+
T Consensus 1 G~V~~vd~~~~~iti~H~pIp~l~-----wpaMTM~F~v~------~~~~l~~l~~Gd~V~F~~~~~~ 57 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISHEPIPELG-----WPAMTMDFPVA------DPVDLAGLKPGDKVRFTFERTD 57 (70)
T ss_dssp EEEEEEETTTTEEEEEE--BCCCT-----B-SEEEEEE--------TTSEESS-STT-EEEEEEEEET
T ss_pred CEEEEEecCCCEEEEecCccccCC-----CCCeEEEEEcC------ChhhhhcCCCCCEEEEEEEECC
Confidence 7888888 445666667774321 2221 11111 0111 58999999999998754
No 143
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=38.46 E-value=1.1e+02 Score=19.86 Aligned_cols=33 Identities=15% Similarity=0.150 Sum_probs=25.7
Q ss_pred EEEEEEEeeecCCCEEEEEEEEEecceEEEEec
Q 030170 74 VVFSGITFKIFRGEVLDGTVHKVLKHGVFLKCG 106 (182)
Q Consensus 74 v~fk~~~f~p~~gEv~~g~V~~v~~~Gifv~lg 106 (182)
+...+.......+..+.|++.+++..|+.+.+.
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~diS~~G~~~~~~ 42 (102)
T PF07238_consen 10 VNLPIRVILDPGGSSFQGTIVDISEGGCAFRSP 42 (102)
T ss_dssp EEEEEE-EEEETTEEEEEEEEEETTSEEEEEEC
T ss_pred ccceEEEEEecCCcEEEEEEEEECccceEEEEC
Confidence 334444466778889999999999999999885
No 144
>PF06688 DUF1187: Protein of unknown function (DUF1187); InterPro: IPR009572 This family consists of several short, hypothetical bacterial proteins of around 62 residues in length. Members of this family are found in Escherichia coli and Salmonella typhi. The function of this family is unknown.
Probab=38.18 E-value=19 Score=22.94 Aligned_cols=18 Identities=11% Similarity=0.111 Sum_probs=16.1
Q ss_pred eEEEEeccCCCccccCCC
Q 030170 161 FQALVSLEGDFLGPVSCE 178 (182)
Q Consensus 161 ~~i~gs~~~~gLG~i~w~ 178 (182)
|.|.|+|.-+|=.|++|=
T Consensus 1 YkItAtI~KpG~~Pv~W~ 18 (61)
T PF06688_consen 1 YKITATIIKPGNTPVNWT 18 (61)
T ss_pred CceEEEEEcCCCCCeeeE
Confidence 468999999999999995
No 145
>COG3323 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.00 E-value=59 Score=23.35 Aligned_cols=67 Identities=22% Similarity=0.270 Sum_probs=41.2
Q ss_pred eEEEcCCCCCCCCCChHHHHHHHHHHhHhcCeeeCCccEEEEEEeeeeeCceEEecCCCceEEEEEEEEEEeeecCCCEE
Q 030170 10 NVVVPAENLDAKGPMLQRSIVVRLLDDFARRKATKDLGYFLAVTTLENIGEGRVRENTGEVLFPVVFSGITFKIFRGEVL 89 (182)
Q Consensus 10 ~v~i~P~~l~~~~~~~~~~i~~~l~~~~~~~k~~~~~G~~v~i~~i~~~~~g~i~~~~g~~~~~v~fk~~~f~p~~gEv~ 89 (182)
.|.||+++... +.+.|-+.= .|++ .++-.|.. ...+.|.-+|.+|.- |++||+
T Consensus 9 ~vyVP~~~~e~--------vr~aL~~aG-ag~i-G~Y~~C~~----~~~g~G~frP~egAn------------P~iGev- 61 (109)
T COG3323 9 EVYVPEEYVEQ--------VRDALFEAG-AGHI-GNYDHCTF----SSEGTGQFRPLEGAN------------PFIGEV- 61 (109)
T ss_pred EEEeCHHHHHH--------HHHHHHhcC-Ccce-eccceEEE----EeeeeEEEeecCCCC------------Cccccc-
Confidence 35566666533 434443332 4553 56666665 445678888888764 999997
Q ss_pred EEEEEEEecceEEEE
Q 030170 90 DGTVHKVLKHGVFLK 104 (182)
Q Consensus 90 ~g~V~~v~~~Gifv~ 104 (182)
|+++.+.+--+-+.
T Consensus 62 -gk~e~v~E~kiE~v 75 (109)
T COG3323 62 -GKLEFVAEVKIEFV 75 (109)
T ss_pred -ceEEeeeeeEEEEE
Confidence 77777776555433
No 146
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=34.87 E-value=71 Score=18.93 Aligned_cols=19 Identities=16% Similarity=0.352 Sum_probs=16.9
Q ss_pred CCCEEEEEEEEEecceEEE
Q 030170 85 RGEVLDGTVHKVLKHGVFL 103 (182)
Q Consensus 85 ~gEv~~g~V~~v~~~Gifv 103 (182)
-++.++|++.++++.|..+
T Consensus 11 ~~~~~~G~~~gId~~G~L~ 29 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDDGALL 29 (48)
T ss_dssp TSCEEEEEEEEEETTSEEE
T ss_pred CCeEEEEEEEEECCCCEEE
Confidence 6788999999999999875
No 147
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=30.64 E-value=1.9e+02 Score=20.28 Aligned_cols=58 Identities=24% Similarity=0.149 Sum_probs=38.1
Q ss_pred EeeecCCCEEEEEEEEEecceEE-EEec-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEE
Q 030170 80 TFKIFRGEVLDGTVHKVLKHGVF-LKCG-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 80 ~f~p~~gEv~~g~V~~v~~~Gif-v~lg-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 153 (182)
...|..|| +.|+|+.....+.| |.+. ...-+.+++.-+... .-+..||.|.|.....+
T Consensus 15 ~~~p~e~e-~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~---------------IwI~~GD~VlVe~~~~~ 74 (100)
T PRK04012 15 LPMPEEGE-VFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKKR---------------MWIREGDVVIVAPWDFQ 74 (100)
T ss_pred ccCCCCCE-EEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhccc---------------EEecCCCEEEEEecccC
Confidence 34455555 78999999999988 4654 455666666544321 35677888887765544
No 148
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=29.81 E-value=1.7e+02 Score=19.32 Aligned_cols=17 Identities=24% Similarity=0.604 Sum_probs=12.7
Q ss_pred EEEEEEEEec----ceEEEEe
Q 030170 89 LDGTVHKVLK----HGVFLKC 105 (182)
Q Consensus 89 ~~g~V~~v~~----~Gifv~l 105 (182)
++|+|+.+.+ .|+|+.-
T Consensus 2 v~GvVTa~~~~~~~~GffiQd 22 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQD 22 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEc
Confidence 6899999888 5666654
No 149
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=27.57 E-value=2e+02 Score=20.77 Aligned_cols=55 Identities=13% Similarity=0.162 Sum_probs=33.2
Q ss_pred EEEEEEEEecce--EEEEecCcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEE
Q 030170 89 LDGTVHKVLKHG--VFLKCGPVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIG 151 (182)
Q Consensus 89 ~~g~V~~v~~~G--ifv~lg~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 151 (182)
.+|+|.+++... +.++-+|+..+=-+.--+ ++.. ... ..-..++.||.|+|.+..
T Consensus 45 ~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM-~F~v--~~~-----~~l~~lk~G~~V~F~~~~ 101 (115)
T PRK09838 45 GTGVVKGIDLESKKITIHHEPIPAVNWPEMTM-RFTI--TPQ-----TKMSEIKTGDKVAFNFVQ 101 (115)
T ss_pred EEEEEEEEeCCCCEEEEeecccccCCCCCccc-cccC--CCh-----hhhccCCCCCEEEEEEEE
Confidence 489999998877 888888874331111111 1111 100 011479999999999874
No 150
>PRK14998 cold shock-like protein CspD; Provisional
Probab=26.01 E-value=2e+02 Score=18.85 Aligned_cols=50 Identities=20% Similarity=0.105 Sum_probs=29.4
Q ss_pred EEEEEEEec-ceE-EEEe-c-CcceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEE
Q 030170 90 DGTVHKVLK-HGV-FLKC-G-PVENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 90 ~g~V~~v~~-~Gi-fv~l-g-~~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 153 (182)
.|+|+--+. .|. |+.- + .-|-++|.|.+-.+- -+.+..|+.|.+.+..-.
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g--------------~~~l~~G~~V~f~~~~~~ 56 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG--------------YRTLKAGQSVRFDVHQGP 56 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccC--------------CCCCCCCCEEEEEEEECC
Confidence 367776665 232 3333 2 245567776653211 157888999999987644
No 151
>KOG0459 consensus Polypeptide release factor 3 [Translation, ribosomal structure and biogenesis]
Probab=25.57 E-value=1.4e+02 Score=26.90 Aligned_cols=33 Identities=12% Similarity=0.076 Sum_probs=25.4
Q ss_pred ceEcCCCeEEEEEEEEEecccccceEEEEeccCC
Q 030170 137 PKIEKDVVVRVIVIGTKWLEAEREFQALVSLEGD 170 (182)
Q Consensus 137 ~~~~~Gd~VrvrV~~v~~~~~~~~~~i~gs~~~~ 170 (182)
+...+|+.|++|+.+++-++.... .++++-+.+
T Consensus 360 ~~~~pGenvk~rlkgieeedi~~G-fiL~~~~n~ 392 (501)
T KOG0459|consen 360 DRVAPGENVKLRLKGIEEEDISPG-FILCSPNNP 392 (501)
T ss_pred eeccCCcceEEEecccchhhccCc-eEEecCCCc
Confidence 688999999999999988776444 466665543
No 152
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=24.65 E-value=1.7e+02 Score=19.31 Aligned_cols=14 Identities=21% Similarity=0.038 Sum_probs=11.9
Q ss_pred eEcCCCeEEEEEEE
Q 030170 138 KIEKDVVVRVIVIG 151 (182)
Q Consensus 138 ~~~~Gd~VrvrV~~ 151 (182)
.|+.||.+++++..
T Consensus 2 ~~~~Ge~v~~~~~~ 15 (83)
T PF14326_consen 2 VYRVGERVRFRVTS 15 (83)
T ss_pred cccCCCEEEEEEEe
Confidence 57889999999877
No 153
>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=23.92 E-value=1.5e+02 Score=19.39 Aligned_cols=55 Identities=15% Similarity=0.124 Sum_probs=33.4
Q ss_pred EEEEEEEecceEEEEecC---cceEEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEEec
Q 030170 90 DGTVHKVLKHGVFLKCGP---VENIYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 90 ~g~V~~v~~~Gifv~lg~---~~gl~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 155 (182)
.++|--+.+.=+-|++-. + ..+..++.+++-..+ +++.+++|+.+.|.+...+.+
T Consensus 5 tA~VQh~~kdfAvvSL~~t~~L-~a~p~~sHLNdtfrf----------~seklkvG~~l~v~lk~~~~~ 62 (69)
T cd05701 5 TAIVQHADKDFAIVSLATTGDL-AAFPTRSHLNDTFRF----------DSEKLSVGQCLDVTLKDPNCL 62 (69)
T ss_pred chhhhhhhhceEEEEeeccccE-EEEEchhhccccccc----------cceeeeccceEEEEEecCccC
Confidence 344445555555566542 2 344555555554432 236899999999999887764
No 154
>PF01629 DUF22: Domain of unknown function DUF22; InterPro: IPR002572 This region is found in 1 to 3 copies in archaeal proteins whose function is unknown. It only appears in multiple copies in proteins from Archaeoglobus fulgidus.
Probab=23.70 E-value=2.1e+02 Score=20.55 Aligned_cols=26 Identities=8% Similarity=0.143 Sum_probs=21.5
Q ss_pred EcCCCceEcCCCeEEEEEEEEEeccc
Q 030170 132 LSEKNPKIEKDVVVRVIVIGTKWLEA 157 (182)
Q Consensus 132 ~~~~~~~~~~Gd~VrvrV~~v~~~~~ 157 (182)
+.+++..++.|+..+++|..+.+.++
T Consensus 42 IAdEdvevk~Ge~~~IkIk~I~iP~~ 67 (112)
T PF01629_consen 42 IADEDVEVKKGEVKIIKIKKIEIPPN 67 (112)
T ss_pred EEcCeeEEecCCEEEEEEEEEecCCC
Confidence 34555799999999999999999654
No 155
>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=22.35 E-value=1.9e+02 Score=19.37 Aligned_cols=19 Identities=16% Similarity=0.018 Sum_probs=14.6
Q ss_pred ceEcCCCeEEEEEEEEEec
Q 030170 137 PKIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 137 ~~~~~Gd~VrvrV~~v~~~ 155 (182)
..|++||+|.+|+.-.+..
T Consensus 9 ~iYrPGetV~~~~~~~~~~ 27 (99)
T PF01835_consen 9 PIYRPGETVHFRAIVRDLD 27 (99)
T ss_dssp SEE-TTSEEEEEEEEEEEC
T ss_pred cCcCCCCEEEEEEEEeccc
Confidence 5899999999999955553
No 156
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.79 E-value=1.9e+02 Score=22.25 Aligned_cols=42 Identities=12% Similarity=0.177 Sum_probs=27.7
Q ss_pred EEEcCCcCCCceeecCCCcEEEcCCCceEcCCCeEEEEEEEEE
Q 030170 111 IYLTCSKMPDYRYVQAENPVFLSEKNPKIEKDVVVRVIVIGTK 153 (182)
Q Consensus 111 l~~~s~~~~d~~~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 153 (182)
+++.|.-| ++.|....-.+++++....++.||.|-++|.+=+
T Consensus 51 VVVLSgSM-ePaF~RGDlLfL~N~~~~p~~vGdivVf~vegR~ 92 (180)
T KOG3342|consen 51 VVVLSGSM-EPAFHRGDLLFLTNRNEDPIRVGDIVVFKVEGRE 92 (180)
T ss_pred EEEEcCCc-CcccccccEEEEecCCCCcceeccEEEEEECCcc
Confidence 33444333 4444444446788877789999999999998433
No 157
>PF00394 Cu-oxidase: Multicopper oxidase; InterPro: IPR001117 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 1 (blue) domains. These domains are also present in proteins that have lost the ability to bind copper.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1RZP_A 2AVF_D 1NIA_A 1KCB_A 2NRD_A 1NIB_A 2BW4_A 1RZQ_C 2BWD_A 2BWI_A ....
Probab=20.22 E-value=1.9e+02 Score=21.40 Aligned_cols=18 Identities=17% Similarity=0.115 Sum_probs=15.6
Q ss_pred eEcCCCeEEEEEEEEEec
Q 030170 138 KIEKDVVVRVIVIGTKWL 155 (182)
Q Consensus 138 ~~~~Gd~VrvrV~~v~~~ 155 (182)
.++.|+++|+|+++....
T Consensus 63 ~v~~g~~~rlRliNa~~~ 80 (159)
T PF00394_consen 63 KVKPGERYRLRLINAGAS 80 (159)
T ss_dssp EEETTTEEEEEEEEESSS
T ss_pred EEcCCcEEEEEEEeccCC
Confidence 799999999999987664
Done!