Query psy13107
Match_columns 170
No_of_seqs 153 out of 1735
Neff 8.1
Searched_HMMs 46136
Date Fri Aug 16 19:41:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13107.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13107hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00162 DNA-directed RNA poly 100.0 1.7E-53 3.7E-58 321.6 21.8 170 1-170 1-170 (176)
2 COG1095 RPB7 DNA-directed RNA 100.0 1.1E-48 2.4E-53 291.5 20.4 169 1-170 1-172 (183)
3 TIGR00448 rpoE DNA-directed RN 100.0 1.3E-46 2.9E-51 285.7 20.9 168 1-170 1-172 (179)
4 KOG3297|consensus 100.0 6.8E-47 1.5E-51 279.2 16.6 170 1-170 1-195 (202)
5 PRK08563 DNA-directed RNA poly 100.0 3.7E-44 8E-49 274.0 21.6 168 1-170 1-172 (187)
6 KOG3298|consensus 100.0 1.8E-41 3.8E-46 246.2 19.6 169 1-170 1-169 (170)
7 cd04330 RNAP_III_Rpc25_N RNAP_ 99.9 3.3E-25 7.2E-30 147.2 10.5 80 2-81 1-80 (80)
8 cd04462 S1_RNAPII_Rpb7 S1_RNAP 99.9 9E-25 2E-29 147.7 12.4 88 81-169 1-88 (88)
9 cd00655 RNAP_Rpb7_N_like RNAP_ 99.9 7.1E-25 1.5E-29 145.6 10.5 80 2-81 1-80 (80)
10 cd04329 RNAP_II_Rpb7_N RNAP_II 99.9 6.1E-25 1.3E-29 145.9 10.0 80 2-81 1-80 (80)
11 cd04331 RNAP_E_N RNAP_E_N: Rpo 99.9 1.3E-24 2.9E-29 144.2 9.7 79 2-80 1-79 (80)
12 PF08292 RNA_pol_Rbc25: RNA po 99.9 2E-23 4.4E-28 148.6 12.9 92 79-170 1-118 (122)
13 PF03876 SHS2_Rpb7-N: SHS2 dom 99.8 7.4E-18 1.6E-22 109.2 10.1 70 8-77 1-70 (70)
14 cd04328 RNAP_I_Rpa43_N RNAP_I_ 99.7 1.3E-15 2.9E-20 103.1 9.8 79 1-81 8-89 (89)
15 cd04460 S1_RpoE S1_RpoE: RpoE, 99.5 5.2E-14 1.1E-18 97.0 9.6 86 83-170 1-90 (99)
16 cd04471 S1_RNase_R S1_RNase_R: 99.4 1.5E-12 3.3E-17 86.2 10.3 76 81-158 1-79 (83)
17 KOG4134|consensus 99.4 2.6E-12 5.6E-17 98.5 10.4 114 5-118 30-145 (253)
18 PF00575 S1: S1 RNA binding do 99.3 1.2E-11 2.5E-16 80.4 8.0 70 78-159 1-71 (74)
19 PRK11642 exoribonuclease R; Pr 99.3 5.6E-12 1.2E-16 114.5 8.6 96 72-169 634-735 (813)
20 cd05686 S1_pNO40 S1_pNO40: pNO 99.3 4.2E-11 9.1E-16 77.9 8.8 67 79-158 1-69 (73)
21 cd05698 S1_Rrp5_repeat_hs6_sc5 99.2 6.3E-11 1.4E-15 76.1 6.9 65 82-158 1-66 (70)
22 cd05705 S1_Rrp5_repeat_hs14 S1 99.2 9.4E-11 2E-15 76.6 7.5 70 80-158 2-72 (74)
23 cd05690 S1_RPS1_repeat_ec5 S1_ 99.2 9.1E-11 2E-15 75.1 7.4 66 82-158 1-67 (69)
24 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.2 7.4E-11 1.6E-15 75.7 6.9 65 82-158 1-66 (69)
25 PLN00207 polyribonucleotide nu 99.2 2.8E-13 6.2E-18 122.5 -6.1 140 6-158 667-819 (891)
26 TIGR00358 3_prime_RNase VacB a 99.2 3.6E-11 7.8E-16 107.4 7.3 85 72-158 563-650 (654)
27 cd05706 S1_Rrp5_repeat_sc10 S1 99.2 2.2E-10 4.9E-15 74.2 9.1 67 80-158 2-69 (73)
28 TIGR02063 RNase_R ribonuclease 99.2 6.5E-11 1.4E-15 106.7 8.7 85 72-158 618-705 (709)
29 TIGR03591 polynuc_phos polyrib 99.2 7.3E-13 1.6E-17 118.5 -3.8 136 9-157 536-682 (684)
30 cd04461 S1_Rrp5_repeat_hs8_sc7 99.2 1.1E-10 2.4E-15 77.7 7.1 70 78-159 11-81 (83)
31 cd05707 S1_Rrp5_repeat_sc11 S1 99.2 1.8E-10 3.8E-15 73.8 7.1 65 82-158 1-66 (68)
32 TIGR02696 pppGpp_PNP guanosine 99.2 1.8E-12 4E-17 115.1 -2.9 140 7-158 562-716 (719)
33 cd05689 S1_RPS1_repeat_ec4 S1_ 99.1 4.5E-10 9.8E-15 72.6 8.8 68 80-158 2-70 (72)
34 cd05708 S1_Rrp5_repeat_sc12 S1 99.1 4.4E-10 9.5E-15 73.2 8.7 67 81-159 2-70 (77)
35 PRK08582 hypothetical protein; 99.1 4.1E-10 8.8E-15 82.2 9.0 68 78-158 2-70 (139)
36 COG1098 VacB Predicted RNA bin 99.1 8E-11 1.7E-15 82.8 4.2 68 78-158 2-70 (129)
37 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.1 6E-10 1.3E-14 72.2 7.7 66 82-159 1-69 (71)
38 cd04452 S1_IF2_alpha S1_IF2_al 99.1 9.1E-10 2E-14 71.7 8.4 69 79-159 1-72 (76)
39 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.1 5.4E-10 1.2E-14 74.7 7.3 83 77-170 2-85 (86)
40 COG0539 RpsA Ribosomal protein 99.1 1.9E-09 4.2E-14 93.3 12.0 68 80-159 191-258 (541)
41 PRK11824 polynucleotide phosph 99.1 2.4E-11 5.3E-16 108.9 -0.0 137 7-158 537-686 (693)
42 cd05703 S1_Rrp5_repeat_hs12_sc 99.0 8.9E-10 1.9E-14 71.7 7.1 68 82-159 1-69 (73)
43 cd05685 S1_Tex S1_Tex: The C-t 99.0 8.6E-10 1.9E-14 69.8 6.6 65 82-158 1-66 (68)
44 cd05688 S1_RPS1_repeat_ec3 S1_ 99.0 1.9E-09 4E-14 68.4 8.1 66 81-158 1-66 (68)
45 cd05684 S1_DHX8_helicase S1_DH 99.0 4.6E-09 1E-13 69.1 10.0 64 82-158 1-68 (79)
46 cd04454 S1_Rrp4_like S1_Rrp4_l 99.0 2.2E-09 4.8E-14 71.2 8.4 79 77-170 2-81 (82)
47 COG1185 Pnp Polyribonucleotide 99.0 3.8E-12 8.2E-17 111.4 -6.9 138 1-152 529-679 (692)
48 cd05692 S1_RPS1_repeat_hs4 S1_ 99.0 1.4E-09 3.1E-14 68.9 6.8 64 82-158 1-65 (69)
49 cd05691 S1_RPS1_repeat_ec6 S1_ 99.0 2.2E-09 4.8E-14 69.2 7.5 65 82-158 1-66 (73)
50 PRK07252 hypothetical protein; 99.0 3.1E-09 6.7E-14 75.7 8.7 67 80-158 2-69 (120)
51 PRK05807 hypothetical protein; 99.0 3.9E-09 8.4E-14 76.8 9.0 68 78-158 2-69 (136)
52 cd05704 S1_Rrp5_repeat_hs13 S1 98.9 2.6E-09 5.6E-14 69.3 5.6 60 80-151 2-63 (72)
53 cd04472 S1_PNPase S1_PNPase: P 98.9 6.8E-09 1.5E-13 65.9 7.4 64 82-158 1-65 (68)
54 smart00316 S1 Ribosomal protei 98.9 1.1E-08 2.3E-13 64.9 8.3 67 81-159 2-69 (72)
55 cd05694 S1_Rrp5_repeat_hs2_sc2 98.9 1.1E-08 2.3E-13 66.9 8.3 62 80-159 3-66 (74)
56 PRK08059 general stress protei 98.9 7E-09 1.5E-13 74.2 8.1 69 78-158 4-73 (123)
57 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.9 8.9E-09 1.9E-13 65.7 7.6 63 82-158 1-64 (66)
58 PRK07400 30S ribosomal protein 98.9 9E-08 2E-12 78.8 14.8 68 79-158 194-261 (318)
59 cd05687 S1_RPS1_repeat_ec1_hs1 98.9 1.3E-08 2.9E-13 65.2 7.3 64 82-157 1-65 (70)
60 PRK12269 bifunctional cytidyla 98.9 3.9E-08 8.5E-13 90.0 12.6 137 9-159 642-822 (863)
61 cd04453 S1_RNase_E S1_RNase_E: 98.8 2.2E-08 4.7E-13 67.5 8.0 78 78-164 4-84 (88)
62 PTZ00248 eukaryotic translatio 98.8 1.2E-08 2.7E-13 83.4 6.9 68 79-158 15-85 (319)
63 PRK07899 rpsA 30S ribosomal pr 98.8 7.4E-08 1.6E-12 83.4 11.9 68 80-159 207-274 (486)
64 cd04465 S1_RPS1_repeat_ec2_hs2 98.8 3.8E-08 8.3E-13 62.7 7.5 63 82-158 1-63 (67)
65 PRK05054 exoribonuclease II; P 98.8 4.6E-08 1E-12 87.4 10.6 85 72-159 550-641 (644)
66 cd04473 S1_RecJ_like S1_RecJ_l 98.8 5.5E-08 1.2E-12 63.8 8.0 61 77-158 12-73 (77)
67 cd05702 S1_Rrp5_repeat_hs11_sc 98.7 5.8E-08 1.3E-12 62.4 7.1 63 82-154 1-64 (70)
68 TIGR02062 RNase_B exoribonucle 98.7 9.1E-08 2E-12 85.5 9.5 85 72-159 546-637 (639)
69 COG0557 VacB Exoribonuclease R 98.7 5E-08 1.1E-12 88.1 7.7 85 72-158 613-700 (706)
70 cd04455 S1_NusA S1_NusA: N-uti 98.7 2.7E-07 5.8E-12 58.9 8.6 62 80-159 2-63 (67)
71 PRK03987 translation initiatio 98.6 1E-07 2.2E-12 76.5 7.6 69 78-158 5-76 (262)
72 COG0539 RpsA Ribosomal protein 98.6 5.4E-08 1.2E-12 84.5 6.2 68 80-159 276-344 (541)
73 cd00164 S1_like S1_like: Ribos 98.6 2.3E-07 5E-12 57.5 6.6 61 85-157 1-62 (65)
74 PRK04163 exosome complex RNA-b 98.6 7.3E-07 1.6E-11 70.5 10.9 82 77-170 59-142 (235)
75 PHA02945 interferon resistance 98.6 6.6E-07 1.4E-11 59.5 8.7 65 78-157 8-77 (88)
76 cd05693 S1_Rrp5_repeat_hs1_sc1 98.6 1.4E-07 2.9E-12 65.2 5.6 74 80-153 2-83 (100)
77 COG2183 Tex Transcriptional ac 98.6 1.1E-07 2.4E-12 84.9 6.2 68 80-159 657-725 (780)
78 PRK09521 exosome complex RNA-b 98.6 2.6E-07 5.6E-12 70.8 7.2 78 75-169 58-146 (189)
79 PRK13806 rpsA 30S ribosomal pr 98.5 4.9E-07 1.1E-11 78.6 8.3 69 80-159 291-360 (491)
80 PRK13806 rpsA 30S ribosomal pr 98.5 5.1E-07 1.1E-11 78.5 8.0 136 10-158 270-445 (491)
81 PRK07899 rpsA 30S ribosomal pr 98.5 6.9E-07 1.5E-11 77.4 8.6 67 81-159 293-360 (486)
82 PRK06676 rpsA 30S ribosomal pr 98.4 7E-07 1.5E-11 75.4 7.4 68 79-158 190-257 (390)
83 PRK12269 bifunctional cytidyla 98.4 9.7E-07 2.1E-11 81.0 7.8 69 80-159 664-733 (863)
84 PRK07400 30S ribosomal protein 98.3 2E-06 4.4E-11 70.9 7.6 68 78-157 28-96 (318)
85 PRK06299 rpsA 30S ribosomal pr 98.3 1.6E-06 3.5E-11 76.5 7.2 68 80-158 372-440 (565)
86 TIGR00717 rpsA ribosomal prote 98.3 2E-06 4.4E-11 75.0 7.7 68 80-158 358-426 (516)
87 PRK06299 rpsA 30S ribosomal pr 98.3 3.2E-06 6.9E-11 74.6 8.3 68 79-158 199-266 (565)
88 PRK06676 rpsA 30S ribosomal pr 98.2 5.1E-06 1.1E-10 70.1 8.4 68 80-159 276-344 (390)
89 TIGR00717 rpsA ribosomal prote 98.2 4.1E-06 8.8E-11 73.1 7.9 67 80-158 445-512 (516)
90 PRK09202 nusA transcription el 98.2 3.3E-06 7.2E-11 72.9 7.1 67 80-164 133-199 (470)
91 COG1093 SUI2 Translation initi 98.2 1.1E-06 2.4E-11 69.5 3.3 67 79-157 9-78 (269)
92 PRK12327 nusA transcription el 98.2 5E-06 1.1E-10 69.6 7.2 71 78-166 131-201 (362)
93 PRK00087 4-hydroxy-3-methylbut 98.2 6.7E-06 1.5E-10 73.8 8.0 67 80-158 561-628 (647)
94 PRK00087 4-hydroxy-3-methylbut 98.1 6.5E-06 1.4E-10 73.9 7.2 67 80-158 476-542 (647)
95 cd05790 S1_Rrp40 S1_Rrp40: Rrp 98.1 2.2E-05 4.8E-10 52.6 7.7 81 77-170 2-85 (86)
96 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.1 1.6E-05 3.5E-10 54.0 7.2 80 77-169 2-90 (92)
97 TIGR01953 NusA transcription t 98.0 2.4E-05 5.2E-10 65.1 7.1 70 79-166 129-199 (341)
98 PF03293 Pox_RNA_pol: Poxvirus 98.0 0.0025 5.4E-08 46.0 16.1 149 6-164 7-159 (160)
99 KOG1067|consensus 97.7 9.1E-06 2E-10 70.5 0.3 64 81-156 668-732 (760)
100 COG1097 RRP4 RNA-binding prote 97.5 0.00062 1.3E-08 53.6 8.5 84 76-170 59-143 (239)
101 TIGR00757 RNaseEG ribonuclease 97.5 0.00041 9E-09 59.2 7.4 86 78-164 22-111 (414)
102 PRK12328 nusA transcription el 97.4 0.00047 1E-08 57.8 7.0 73 77-167 134-208 (374)
103 PF13509 S1_2: S1 domain; PDB: 97.2 0.0022 4.9E-08 40.0 6.4 48 81-148 1-49 (61)
104 PF10447 EXOSC1: Exosome compo 97.0 0.0015 3.3E-08 43.3 4.5 62 79-150 2-82 (82)
105 COG1096 Predicted RNA-binding 96.8 0.015 3.3E-07 44.2 9.4 63 76-150 59-132 (188)
106 PRK12329 nusA transcription el 96.8 0.0051 1.1E-07 52.7 6.9 72 77-166 148-226 (449)
107 KOG1070|consensus 96.7 0.0022 4.7E-08 61.1 4.4 67 80-158 598-665 (1710)
108 cd05699 S1_Rrp5_repeat_hs7 S1_ 96.6 0.0095 2.1E-07 38.5 5.6 57 82-148 1-60 (72)
109 PRK11712 ribonuclease G; Provi 96.2 0.026 5.6E-07 49.3 8.0 87 77-164 34-124 (489)
110 PRK10811 rne ribonuclease E; R 96.0 0.04 8.7E-07 51.4 8.5 82 78-163 35-120 (1068)
111 KOG1070|consensus 95.2 0.094 2E-06 50.6 8.1 68 80-159 1161-1229(1710)
112 COG1107 Archaea-specific RecJ- 95.0 0.018 3.8E-07 50.8 2.7 61 79-157 120-181 (715)
113 KOG3409|consensus 94.0 0.36 7.9E-06 36.4 7.3 64 78-151 65-137 (193)
114 PF00313 CSD: 'Cold-shock' DNA 93.7 0.71 1.5E-05 28.7 7.4 56 85-159 1-60 (66)
115 KOG1004|consensus 93.6 1.1 2.4E-05 34.8 9.5 93 64-169 48-143 (230)
116 COG2996 Predicted RNA-bindinin 93.4 0.27 5.8E-06 39.7 6.1 53 81-153 155-208 (287)
117 PHA02858 EIF2a-like PKR inhibi 93.4 0.098 2.1E-06 34.7 3.0 67 76-156 11-80 (86)
118 PF10246 MRP-S35: Mitochondria 93.2 0.61 1.3E-05 32.1 6.8 57 77-152 19-76 (104)
119 COG4776 Rnb Exoribonuclease II 92.5 0.062 1.4E-06 46.3 1.4 77 78-157 558-639 (645)
120 PRK15463 cold shock-like prote 90.2 1.1 2.3E-05 28.7 5.1 49 85-149 5-57 (70)
121 COG1530 CafA Ribonucleases G a 89.9 2.6 5.6E-05 37.0 8.9 85 63-155 19-106 (487)
122 PF07076 DUF1344: Protein of u 89.7 1.5 3.3E-05 27.3 5.3 50 83-151 3-52 (61)
123 PRK15464 cold shock-like prote 89.5 1.4 3E-05 28.2 5.2 49 85-149 5-57 (70)
124 PRK09890 cold shock protein Cs 87.6 2.6 5.6E-05 26.8 5.6 49 85-149 5-57 (70)
125 PRK10943 cold shock-like prote 86.8 2.6 5.6E-05 26.8 5.2 51 84-150 3-57 (69)
126 PRK09507 cspE cold shock prote 86.4 3.2 6.9E-05 26.3 5.5 50 85-150 4-57 (69)
127 PRK10354 RNA chaperone/anti-te 84.6 4.2 9.2E-05 25.8 5.5 49 85-149 5-57 (70)
128 COG2996 Predicted RNA-bindinin 84.6 5.2 0.00011 32.4 7.0 71 79-151 3-85 (287)
129 PRK12442 translation initiatio 84.6 9.3 0.0002 25.5 7.1 58 84-157 8-67 (87)
130 PRK09937 stationary phase/star 83.7 4.1 8.9E-05 26.3 5.1 49 86-150 3-55 (74)
131 PRK14998 cold shock-like prote 80.0 6.4 0.00014 25.3 5.0 49 86-150 3-55 (73)
132 TIGR02381 cspD cold shock doma 79.7 4.4 9.5E-05 25.6 4.1 49 86-150 3-55 (68)
133 cd04458 CSP_CDS Cold-Shock Pro 79.4 6.6 0.00014 24.1 4.9 49 86-150 2-54 (65)
134 KOG2916|consensus 79.4 0.89 1.9E-05 36.6 0.9 65 79-155 14-81 (304)
135 KOG1856|consensus 77.2 6 0.00013 38.1 5.7 63 80-154 984-1050(1299)
136 COG0361 InfA Translation initi 74.4 19 0.00041 23.4 5.9 59 84-157 8-67 (75)
137 KOG4078|consensus 74.1 7.2 0.00016 28.5 4.3 64 72-154 73-137 (173)
138 PF01629 DUF22: Domain of unkn 72.6 15 0.00033 25.7 5.6 45 125-169 37-81 (112)
139 TIGR00008 infA translation ini 66.3 31 0.00067 21.9 7.1 58 84-157 6-65 (68)
140 PF08206 OB_RNB: Ribonuclease 61.3 31 0.00066 20.8 4.8 42 87-149 1-44 (58)
141 COG1278 CspC Cold shock protei 59.5 28 0.0006 22.1 4.4 48 86-149 3-54 (67)
142 KOG3013|consensus 55.0 23 0.00051 28.6 4.3 68 76-150 80-153 (301)
143 PF01330 RuvA_N: RuvA N termin 54.1 44 0.00095 20.3 4.6 29 85-113 5-35 (61)
144 PF03459 TOBE: TOBE domain; I 51.6 23 0.00051 21.3 3.2 47 84-149 6-59 (64)
145 cd04486 YhcR_OBF_like YhcR_OBF 49.1 70 0.0015 20.6 5.8 49 85-146 2-54 (78)
146 COG1417 Uncharacterized conser 48.9 54 0.0012 26.6 5.4 45 125-169 66-110 (288)
147 smart00357 CSP Cold shock prot 48.0 56 0.0012 19.1 4.5 15 136-150 36-50 (64)
148 PF07238 PilZ: PilZ domain; I 46.0 67 0.0015 20.4 5.0 35 68-102 8-42 (102)
149 PF01938 TRAM: TRAM domain; I 43.7 40 0.00088 20.2 3.3 24 78-101 37-60 (61)
150 COG2106 Uncharacterized conser 41.4 81 0.0017 25.6 5.4 25 78-102 102-126 (272)
151 PRK06763 F0F1 ATP synthase sub 39.0 98 0.0021 24.1 5.3 20 83-102 40-59 (213)
152 PF11604 CusF_Ec: Copper bindi 38.2 39 0.00084 21.3 2.6 16 135-150 41-56 (70)
153 PRK14600 ruvA Holliday junctio 35.6 1.5E+02 0.0033 22.5 6.0 30 84-113 4-35 (186)
154 PRK09838 periplasmic copper-bi 34.5 74 0.0016 22.3 3.8 54 85-149 45-101 (115)
155 TIGR02866 CoxB cytochrome c ox 33.2 70 0.0015 24.4 3.9 21 133-153 117-137 (201)
156 PF02237 BPL_C: Biotin protein 32.7 90 0.0019 17.9 3.4 19 81-99 11-29 (48)
157 TIGR00084 ruvA Holliday juncti 31.2 1.7E+02 0.0036 22.3 5.6 30 84-113 4-35 (191)
158 COG3175 COX11 Cytochrome oxida 30.8 2.4E+02 0.0052 21.6 6.2 42 123-164 75-116 (195)
159 PF07177 Neuralized: Neuralize 30.8 96 0.0021 19.5 3.6 30 135-164 37-66 (69)
160 PRK04012 translation initiatio 29.8 1.8E+02 0.004 19.8 7.2 57 77-151 16-74 (100)
161 PRK14603 ruvA Holliday junctio 28.0 1.4E+02 0.0031 22.8 4.8 29 84-112 4-34 (197)
162 PF01835 A2M_N: MG2 domain; I 26.4 1E+02 0.0023 20.1 3.4 18 136-153 10-27 (99)
163 PF14326 DUF4384: Domain of un 21.8 85 0.0018 20.2 2.2 14 136-149 2-15 (83)
164 PRK13901 ruvA Holliday junctio 20.4 2.1E+02 0.0047 22.0 4.4 30 84-113 4-35 (196)
165 TIGR01433 CyoA cytochrome o ub 20.2 1.6E+02 0.0035 23.1 3.8 21 133-153 139-159 (226)
No 1
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=100.00 E-value=1.7e-53 Score=321.59 Aligned_cols=170 Identities=46% Similarity=0.826 Sum_probs=166.7
Q ss_pred CeEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEeecC
Q psy13107 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPF 80 (170)
Q Consensus 1 Mf~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f~p~ 80 (170)
||++++++|+|+|||++|++++.+++.++|+++|+||+.++.|+||+++||.++++|+|.+|||+++|+|+|+|++|+|+
T Consensus 1 MF~~~~l~d~v~i~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf 80 (176)
T PTZ00162 1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPF 80 (176)
T ss_pred CcEEEEEEEEEEECHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEEE
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAI 160 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~i 160 (170)
+||+++|+|++++++|+|+++||+++|||.++||+++.||++++.|+|.+++++.+++.|+.||+||.+++++.+.++++
T Consensus 81 ~gEVv~g~V~~v~~~G~~v~~Gp~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~~~i 160 (176)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAI 160 (176)
T ss_pred CCCEEEEEEEEEecceEEEEeeCeEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCcEEE
Confidence 99999999999999999999999999999999999999999999999997777899999999999999999999999999
Q ss_pred EEecCCCCCC
Q psy13107 161 GTLMDDYLGL 170 (170)
Q Consensus 161 g~~~~~~LG~ 170 (170)
|||++||||+
T Consensus 161 ~T~~~~~LG~ 170 (176)
T PTZ00162 161 ATINSDYLGP 170 (176)
T ss_pred EEecCCCcCc
Confidence 9999999997
No 2
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=100.00 E-value=1.1e-48 Score=291.52 Aligned_cols=169 Identities=33% Similarity=0.546 Sum_probs=160.7
Q ss_pred CeEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEeecC
Q psy13107 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPF 80 (170)
Q Consensus 1 Mf~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f~p~ 80 (170)
||++.+++|+|+|||++|++++.+++..+|+++|+|++.++.|+||+++|++++++|+|.+|||+++++|+|++++|+|+
T Consensus 1 My~l~~~~d~VripP~~fg~~~~~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~ 80 (183)
T COG1095 1 MYKLVELEDTVRIPPSYFGEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPF 80 (183)
T ss_pred CcEEEEEeeEEEeCHHHcCccHHHHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCc---e
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASG---I 157 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~---i 157 (170)
.||+++|.|++++++|+||.+||++||+|.+++++| .++.+.+.|.|.+++++++++.||.||+||.++++...+ .
T Consensus 81 ~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd-~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~~ 159 (183)
T COG1095 81 RGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDD-YIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRES 159 (183)
T ss_pred cccEEEEEEEEEeecceEEEeccccccccHhhccCc-ccccCcccceeeecccceEEecCCEEEEEEEEEecccCccccc
Confidence 999999999999999999999999999999999999 334445558999999999999999999999999997764 7
Q ss_pred EEEEEecCCCCCC
Q psy13107 158 FAIGTLMDDYLGL 170 (170)
Q Consensus 158 ~~ig~~~~~~LG~ 170 (170)
.+.+||+|||||+
T Consensus 160 ~I~lTmrq~~LGk 172 (183)
T COG1095 160 KIGLTMRQPGLGK 172 (183)
T ss_pred eEEEEeccccCCc
Confidence 7999999999995
No 3
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=100.00 E-value=1.3e-46 Score=285.68 Aligned_cols=168 Identities=26% Similarity=0.481 Sum_probs=158.0
Q ss_pred CeEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEeecC
Q psy13107 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPF 80 (170)
Q Consensus 1 Mf~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f~p~ 80 (170)
||++++++|+|+|||++|++++.+++.++|+++|+||++++.|+||+++||.++++|+|.||||+++++|+|++++|+|+
T Consensus 1 Mf~~~~l~d~v~i~P~~~~~~~~~~i~~~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~ 80 (179)
T TIGR00448 1 MYILSKIADTVRIPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPE 80 (179)
T ss_pred CeEEEEEeeEEEECHHHhCccHHHHHHHHHHHHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCC-ceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCC---c
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTD-MQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDAS---G 156 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~-~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~---~ 156 (170)
+||+++|+|++++++|+|+++||++|++|.+++.++ +.||+.++.|.| ++++.+++.||.|||||.++++++. .
T Consensus 81 ~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~--~~~~~~~~~Gd~VrvrV~~v~~~~~~~~~ 158 (179)
T TIGR00448 81 LGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIG--KETKKVLDEGDKVRARIVALSLKDRRPEG 158 (179)
T ss_pred CCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEE--ccCCeEEcCCCEEEEEEEEEEccCCCCCc
Confidence 999999999999999999999999999999998766 889999987777 4556799999999999999998544 3
Q ss_pred eEEEEEecCCCCCC
Q psy13107 157 IFAIGTLMDDYLGL 170 (170)
Q Consensus 157 i~~ig~~~~~~LG~ 170 (170)
..+.+||++|||||
T Consensus 159 ~~I~lt~k~~~LG~ 172 (179)
T TIGR00448 159 SKIGLTMRQPLLGK 172 (179)
T ss_pred ceEEEEeccCcCCc
Confidence 35799999999997
No 4
>KOG3297|consensus
Probab=100.00 E-value=6.8e-47 Score=279.20 Aligned_cols=170 Identities=25% Similarity=0.466 Sum_probs=161.6
Q ss_pred CeEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEeecC
Q psy13107 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPF 80 (170)
Q Consensus 1 Mf~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f~p~ 80 (170)
||++++++|+|+|||++|++++.++|+++|++||.||++++.|+|||++||..+++|+|.||||+.+++|.||+++||||
T Consensus 1 MF~Lsel~D~VrI~P~qf~~~~~~ai~~eL~~k~anKvl~nvGLCI~vyDi~~v~e~~v~pGDGas~~~V~FR~vVFrPF 80 (202)
T KOG3297|consen 1 MFYLSELEDTVRIPPSQFEKPLEDAIKEELNRKLANKVLPNVGLCICVYDILEVEEGIVLPGDGASYARVWFRVVVFRPF 80 (202)
T ss_pred CeeehhcccceecChHHhCchHHHHHHHHHHHHHHhhhcccccEEEEEeEeeeecceEEecCCCceEEEEEEEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEec-----CceeEEcCCCeEEEEEEEEEecC
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSV-----HGEVVIQEDDEIRLKIVGTRVDA 154 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~-----~~~~~~~~Gd~VrvrV~~v~~~~ 154 (170)
+||++.|+|.++++.|+.+++++| |+|||.+.||++..|++.++.|.|.++ .++++++.|+.|||||.+..|..
T Consensus 81 ~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~f~d 160 (202)
T KOG3297|consen 81 VGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDESFVD 160 (202)
T ss_pred cceEEEEEeecCCccceEEEEEeeeceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeeecccc
Confidence 999999999999999999999999 999999999999999999999999987 56799999999999999996521
Q ss_pred ------------------Cc-eEEEEEecCCCCCC
Q psy13107 155 ------------------SG-IFAIGTLMDDYLGL 170 (170)
Q Consensus 155 ------------------~~-i~~ig~~~~~~LG~ 170 (170)
.. +.++|+|+++||||
T Consensus 161 ~~p~~~~~~~t~~e~~e~~~py~l~gs~~~~GLG~ 195 (202)
T KOG3297|consen 161 VSPEGNSTAITGAEDPEKESPYTLLGSMNEDGLGP 195 (202)
T ss_pred cCccccccccccccccccCCCeEEEEEecCCCCcc
Confidence 12 46999999999997
No 5
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=100.00 E-value=3.7e-44 Score=274.02 Aligned_cols=168 Identities=27% Similarity=0.443 Sum_probs=158.3
Q ss_pred CeEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEeecC
Q psy13107 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPF 80 (170)
Q Consensus 1 Mf~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f~p~ 80 (170)
||++++++|+|+|||++|++++.+++.++|+++|+||++++.|+||+++||.++++|+|.||||.++++|+|++++|+|+
T Consensus 1 MF~~~~l~d~v~i~P~~~~~~~~~~i~~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~ 80 (187)
T PRK08563 1 MYKLVKLEDVVRIPPEMFGEDLEEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPE 80 (187)
T ss_pred CeEEEEEeEEEEECHHHcCccHHHHHHHHHHHHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCC-ceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce--
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTD-MQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI-- 157 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~-~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i-- 157 (170)
+||+++|+|++++++|+|++++++++++|.++++++ +.||+.++.|.| ++.+.+++.||.|||||.+++++.+.+
T Consensus 81 ~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~--~~~~~~i~~Gd~VrvrV~~v~~~~~~~~~ 158 (187)
T PRK08563 81 LQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIG--KESKRVLKVGDVVRARIVAVSLKERRPRG 158 (187)
T ss_pred CCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEE--ccCCeEEcCCCEEEEEEEEEEcccCCCCC
Confidence 999999999999999999999999999999999887 889998886554 455679999999999999999987654
Q ss_pred -EEEEEecCCCCCC
Q psy13107 158 -FAIGTLMDDYLGL 170 (170)
Q Consensus 158 -~~ig~~~~~~LG~ 170 (170)
.+.+||++||||+
T Consensus 159 ~~I~ls~~~~~LG~ 172 (187)
T PRK08563 159 SKIGLTMRQPGLGK 172 (187)
T ss_pred CEEEEEecCCCCCc
Confidence 5666999999996
No 6
>KOG3298|consensus
Probab=100.00 E-value=1.8e-41 Score=246.23 Aligned_cols=169 Identities=59% Similarity=1.040 Sum_probs=163.4
Q ss_pred CeEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEeecC
Q psy13107 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPF 80 (170)
Q Consensus 1 Mf~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f~p~ 80 (170)
||+...++..+.++|++++++.++.+++.|.++.+|+|.++.|++|++.+++++++|+|.+++|.+.|.|+|+|++|+|+
T Consensus 1 mff~~~l~~~i~l~p~~~gp~~~~~l~~~L~~~veg~ctg~~Gyvi~vt~ld~Ig~g~I~~~~G~v~FpVky~av~Fkpf 80 (170)
T KOG3298|consen 1 MFFHKDLDLNICLHPSYFGPNLQAILKRKLLAEVEGKCTGKYGYVIAVTTLDNIGEGRIRPGTGFVTFPVKYKAVTFKPF 80 (170)
T ss_pred CcceeeeeeeeeecccccCchHHHHHHHHHHHHhhccccccccEEEEEEEhhhccCCccccCCceEEEEEEEEEEEEeec
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEEE
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAI 160 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~i 160 (170)
+||+++|+|+++++.|+|+++||++.|++...+|+||+|++.+++..|..++.. .+++|++||++|.++++++..++|+
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~GPl~~f~sshl~ppd~~f~p~~n~P~f~~~d~s-~I~~~~~VR~kiigtr~~~~~i~al 159 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSGPLEVFYSSHLKPPDYEFDPGENPPNFQTEDES-VIQKGVEVRLKIIGTRVDETEIFAL 159 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEeccceEeeeecccCCCCcccCCCCCCCcccccccc-eeeeCcEEEEEEEEEEEeeeeEEEE
Confidence 999999999999999999999999999999999999999999886677776654 9999999999999999999999999
Q ss_pred EEecCCCCCC
Q psy13107 161 GTLMDDYLGL 170 (170)
Q Consensus 161 g~~~~~~LG~ 170 (170)
||+++|+|||
T Consensus 160 gtl~~D~LG~ 169 (170)
T KOG3298|consen 160 GTLKGDYLGP 169 (170)
T ss_pred EEecCccccc
Confidence 9999999997
No 7
>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.
Probab=99.93 E-value=3.3e-25 Score=147.17 Aligned_cols=80 Identities=28% Similarity=0.539 Sum_probs=78.5
Q ss_pred eEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEeecCC
Q psy13107 2 FYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFK 81 (170)
Q Consensus 2 f~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f~p~~ 81 (170)
|++++++|+|++||++|++++.+++.++|+++|+||++++.|+||+++|+.++++|+|.+|||+++++|+|++++|+|++
T Consensus 1 F~~~~l~d~v~i~P~~fg~~~~~~i~~~L~~ky~gkv~~~~Gl~v~v~di~~i~eG~I~~gdG~~~~~V~Fr~lvFrPf~ 80 (80)
T cd04330 1 FILSEIEDTVRIPPSQFSRPLNDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80 (80)
T ss_pred CEEEEEEEEEEECHHHcCcCHHHHHHHHHHHHhCCcEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEECCC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999984
No 8
>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=99.93 E-value=9e-25 Score=147.68 Aligned_cols=88 Identities=66% Similarity=1.124 Sum_probs=83.1
Q ss_pred CCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEEE
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAI 160 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~i 160 (170)
+||+++|+|++++++|+|+++||+++|+|.+++|+++.|+++++.|+|..+ ++.+++.|+.|||||.+++++.+.++++
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~~ip~~~~~~~~~~~~~~~~~-~~~~i~~g~~VR~rV~~v~~~~~~~~~i 79 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTSN-EDIVIKKDTEVRLKIIGTRVDATDIFAI 79 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEeeecCccceECCcCCCCeEeCC-CcEEECCCCEEEEEEEEEEEccCceEEE
Confidence 589999999999999999999999999999999999999997788999744 6789999999999999999999999999
Q ss_pred EEecCCCCC
Q psy13107 161 GTLMDDYLG 169 (170)
Q Consensus 161 g~~~~~~LG 169 (170)
|||++||||
T Consensus 80 gt~~~~~LG 88 (88)
T cd04462 80 GTIKDDYLG 88 (88)
T ss_pred EEccCCCCC
Confidence 999999998
No 9
>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=99.92 E-value=7.1e-25 Score=145.62 Aligned_cols=80 Identities=31% Similarity=0.561 Sum_probs=78.4
Q ss_pred eEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEeecCC
Q psy13107 2 FYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFK 81 (170)
Q Consensus 2 f~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f~p~~ 81 (170)
|++++++|+|+|||++|++++.+++.++|+++|+||++++.|+||+++|+.++++|+|.+|||+++++|+|++++|+|+.
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~~ivFrPf~ 80 (80)
T cd00655 1 FQILEIADLVSVPPKYFGDDCKGVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPFS 80 (80)
T ss_pred CEEEEEEEEEEECHHHhCccHHHHHHHHHHHHhCCeEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEEcCC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999984
No 10
>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=99.92 E-value=6.1e-25 Score=145.88 Aligned_cols=80 Identities=68% Similarity=1.216 Sum_probs=78.5
Q ss_pred eEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEeecCC
Q psy13107 2 FYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPFK 81 (170)
Q Consensus 2 f~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f~p~~ 81 (170)
|++++++|+|+|||++|++++.+++.++|+++|+||+.++.|+||+++||.++++|+|.+|||+++++|+|+|++|+|++
T Consensus 1 F~~~~l~d~v~i~P~~fg~~l~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~~G~I~~gdG~~~~~V~F~aivfrPf~ 80 (80)
T cd04329 1 FFKIELEHNILLHPSYFGPNLKEYLEQKLLEEVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPFK 80 (80)
T ss_pred CEEEEEEEEEEECHHHhCccHHHHHHHHHHHHhCCcCcCceeEEEEEEEeeEecCcEEEcCCCCEEEEEEEEEEEEEccC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999985
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=99.92 E-value=1.3e-24 Score=144.15 Aligned_cols=79 Identities=30% Similarity=0.538 Sum_probs=77.8
Q ss_pred eEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEeecC
Q psy13107 2 FYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVFRPF 80 (170)
Q Consensus 2 f~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f~p~ 80 (170)
|++++++|+|++||++|++++.+++.++|+++|+||+.++.|+||+++||.++++|+|.+|||+++++|+|+|++|+|.
T Consensus 1 f~~~~l~d~vri~P~~fg~~~~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~eG~I~~gdG~~~~~V~F~~ivFrP~ 79 (80)
T cd04331 1 YKLVELEDVVRVPPELFGEDLEEAVLEILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFKPE 79 (80)
T ss_pred CEEEEEEEeEEECHHHcCcCHHHHHHHHHHHHhcCcCcCCCCEEEEEEEEEEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence 7899999999999999999999999999999999999999999999999999999999999999999999999999996
No 12
>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=99.91 E-value=2e-23 Score=148.62 Aligned_cols=92 Identities=24% Similarity=0.408 Sum_probs=77.4
Q ss_pred cCCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEe-cCceeEEcCCCeEEEEEEEEEecC--
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKS-VHGEVVIQEDDEIRLKIVGTRVDA-- 154 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~-~~~~~~~~~Gd~VrvrV~~v~~~~-- 154 (170)
||+||++.|+|+++++.|+.|++||| |+|||.+.||++..||++++.|.|.+ +++.+++..|++|||||.++.|..
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 89999999999999999999999999 99999999999999999999999999 888899999999999999999921
Q ss_pred -----------------C-----ceEEEEEecCCCCCC
Q psy13107 155 -----------------S-----GIFAIGTLMDDYLGL 170 (170)
Q Consensus 155 -----------------~-----~i~~ig~~~~~~LG~ 170 (170)
. -+.++|||+++||||
T Consensus 81 p~~~~~~~~~~~~~~~~~~~~~~Py~I~gs~~~~GLG~ 118 (122)
T PF08292_consen 81 PTPPPSAEASGEEEEEEEDEPKPPYQIIGSINEDGLGL 118 (122)
T ss_dssp -----------------------SEEEEEEB-STT-EE
T ss_pred CCCcccccccccccccccccCCCCeEEEEEecCCCCcc
Confidence 0 156999999999996
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=99.76 E-value=7.4e-18 Score=109.16 Aligned_cols=70 Identities=44% Similarity=0.804 Sum_probs=66.3
Q ss_pred EEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeCCeeEecCCCceEEeEEEEEEEe
Q psy13107 8 EHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPVKYRAIVF 77 (170)
Q Consensus 8 ~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~~g~I~~~~g~~~~~v~f~~i~f 77 (170)
+++|+|||++|++++.+++.++|.++|+||+.++.|++|+++||..+++|+|.+++|+++++|+|++++|
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 EDTVRLPPSYLGPDLKDGIKEQLLDKYEGKYIPELGVVIAVTDIKEISEGKIIPGDGFVYFKVTFRALVF 70 (70)
T ss_dssp EEEEEE-GGGTTSTHHHHHHHHHHHHHTTEEETTTEEEEEEEEEEEESCEEE-TTTSSEEEEEEEEEEEE
T ss_pred CcEEEECHHHhCcCHHHHHHHHHHHHHhCcCcCCceEEEEEeeeeEecCcEEECCCCCEEEEEEEEEEEC
Confidence 6899999999999999999999999999999999999999999999999999999999999999999998
No 14
>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=99.65 E-value=1.3e-15 Score=103.11 Aligned_cols=79 Identities=24% Similarity=0.396 Sum_probs=74.2
Q ss_pred CeEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCe-eEEEEEceeceeCC--eeEecCCCceEEeEEEEEEEe
Q psy13107 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKY-GFVIAVTTIDSIGA--GLIQPGQGFVVYPVKYRAIVF 77 (170)
Q Consensus 1 Mf~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~-G~~i~i~~i~~~~~--g~I~~~~g~~~~~v~f~~i~f 77 (170)
||.+.+++++|+++|+++++.. ++++++|++++. |+..+. |+|++++|+...++ |+|.+++|..+++|+|++++|
T Consensus 8 ~f~~~~~~~~v~l~P~~~~~~~-~~i~~~l~~~l~-ky~~~l~Gv~l~~~di~~~~~~~~~i~~~~~~~~~~V~~~~lVF 85 (89)
T cd04328 8 CFETLTVSLYVSLAPKYLGNPL-TGIKAQLLNPLL-KYSPKLKGVVLAYSNIKLLEGELAKIVDDSPFIFVWISADFLVF 85 (89)
T ss_pred cEEEEEEEEEEEECchhhcCHh-HHHHHHHhhhHh-hhcccCCeEEEEecceEeccccceeeeCCCcEEEEEEEEEEEEE
Confidence 8999999999999999998755 499999999999 999988 99999999998855 999999999999999999999
Q ss_pred ecCC
Q psy13107 78 RPFK 81 (170)
Q Consensus 78 ~p~~ 81 (170)
+|++
T Consensus 86 rP~~ 89 (89)
T cd04328 86 RPKI 89 (89)
T ss_pred ecCC
Confidence 9984
No 15
>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=99.55 E-value=5.2e-14 Score=97.01 Aligned_cols=86 Identities=26% Similarity=0.407 Sum_probs=74.0
Q ss_pred CEEEEEEEEEecccEEEEecCeeEEEEcCCCCCC-ceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCc--eEE
Q psy13107 83 EVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTD-MQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASG--IFA 159 (170)
Q Consensus 83 ev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~-~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~--i~~ 159 (170)
+++.|+|++++++|+||++++.+|++|.++++++ +.|++... +|.+++.+..|++||.|+|+|.+++.+.+. +..
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~--~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~ 78 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNK--RLIGEETKRVLKVGDVVRARIVAVSLKERRPRESK 78 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhhe--eecccCcCCEECCCCEEEEEEEEEeHHHCcCCCce
Confidence 5899999999999999999878999999999877 77776654 678877777999999999999999976554 444
Q ss_pred EE-EecCCCCCC
Q psy13107 160 IG-TLMDDYLGL 170 (170)
Q Consensus 160 ig-~~~~~~LG~ 170 (170)
++ |+++++|||
T Consensus 79 i~ls~k~~~~g~ 90 (99)
T cd04460 79 IGLTMRQPGLGK 90 (99)
T ss_pred EEEEEecCCCCc
Confidence 55 999999997
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=99.44 E-value=1.5e-12 Score=86.23 Aligned_cols=76 Identities=20% Similarity=0.387 Sum_probs=65.4
Q ss_pred CCCEEEEEEEEEecccEEEEecC--eeEEEEcCCCCCC-ceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGP--LSCFISHHSIPTD-MQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~--~~~~i~~~~l~~~-~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
.|++++|+|++++++|+|+++++ .+|++|.++++++ +.||+.+. ++.++.....|++||.|+|+|.+++.+++++
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~--~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i 78 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENH--ALVGERTGKVFRLGDKVKVRVVRVDLDRRKI 78 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccce--EEEeccCCCEEcCCCEEEEEEEEeccccCEE
Confidence 38999999999999999999997 5999999999877 88887664 5666665679999999999999999876665
Q ss_pred E
Q psy13107 158 F 158 (170)
Q Consensus 158 ~ 158 (170)
.
T Consensus 79 ~ 79 (83)
T cd04471 79 D 79 (83)
T ss_pred E
Confidence 4
No 17
>KOG4134|consensus
Probab=99.40 E-value=2.6e-12 Score=98.53 Aligned_cols=114 Identities=25% Similarity=0.405 Sum_probs=100.6
Q ss_pred EEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceeceeC-CeeEecCCCceEEeEEEEEEEeecCCCC
Q psy13107 5 ISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIG-AGLIQPGQGFVVYPVKYRAIVFRPFKGE 83 (170)
Q Consensus 5 ~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~~-~g~I~~~~g~~~~~v~f~~i~f~p~~ge 83 (170)
.+....+++.|-+|..++...+++.|+.++.-+-.+-.|+++++.+|+.++ .++|.+.+++.+..++....+|+|..|+
T Consensus 30 ~t~dlhlalaP~yl~npl~~~i~ehld~~vl~y~~~l~GivLgydnIKvLg~~aki~~D~pf~hlwi~adfyVf~Pk~Gd 109 (253)
T KOG4134|consen 30 ITTDLHLALAPYYLANPLHALIEEHLDTKVLFYDSGLDGIVLGYDNIKVLGQTAKIRADDPFMHLWINADFYVFRPKAGD 109 (253)
T ss_pred eeeheeeeecchhhcchhHHHHHHHhhHHHhhhccCCCceEEeecceEeeccccceecCCCceEEEEeeeEEEECCCCCC
Confidence 346678999999999888778899999887655556679999999999887 7999999999999999999999999999
Q ss_pred EEEEEEEEEecccEEEEe-cCeeEEEEcCCCCCCce
Q psy13107 84 VLDAVVTQVNKVGMFAEI-GPLSCFISHHSIPTDMQ 118 (170)
Q Consensus 84 v~~g~V~~i~~~Gifv~l-g~~~~~i~~~~l~~~~~ 118 (170)
+++|.|..+++.+|-+-+ |.|+..||..++|.||.
T Consensus 110 ~LeG~Vn~vS~sHIglLIhg~FNASIpk~nip~dw~ 145 (253)
T KOG4134|consen 110 ILEGVVNHVSRSHIGLLIHGVFNASIPKTNIPADWE 145 (253)
T ss_pred eeeeeeeecchhhhceeehhhhhccCCCCCCcccee
Confidence 999999999999999877 55799999999987644
No 18
>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=99.31 E-value=1.2e-11 Score=80.42 Aligned_cols=70 Identities=20% Similarity=0.378 Sum_probs=58.7
Q ss_pred ecCCCCEEEEEEEEEecccEEEEec-CeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCc
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEIG-PLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASG 156 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~lg-~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~ 156 (170)
++..|++++|+|++++++|+|+.++ ..+||+|.+++++++. .+....+++||.++++|.+++.++++
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~------------~~~~~~~~~G~~v~v~v~~vd~~~~~ 68 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRI------------DDPSEVYKIGQTVRVKVIKVDKEKGR 68 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEE------------SSSHGTCETTCEEEEEEEEEETTTTE
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccc------------cccccccCCCCEEEEEEEEEECCCCe
Confidence 5789999999999999999999999 5699999999986522 11223889999999999999988887
Q ss_pred eEE
Q psy13107 157 IFA 159 (170)
Q Consensus 157 i~~ 159 (170)
+..
T Consensus 69 i~l 71 (74)
T PF00575_consen 69 IRL 71 (74)
T ss_dssp EEE
T ss_pred EEE
Confidence 654
No 19
>PRK11642 exoribonuclease R; Provisional
Probab=99.31 E-value=5.6e-12 Score=114.49 Aligned_cols=96 Identities=15% Similarity=0.245 Sum_probs=81.6
Q ss_pred EEEEEeecCCCCEEEEEEEEEecccEEEEecC--eeEEEEcCCCCCC-ceecCCCCCeEEEecCceeEEcCCCeEEEEEE
Q psy13107 72 YRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGP--LSCFISHHSIPTD-MQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIV 148 (170)
Q Consensus 72 f~~i~f~p~~gev~~g~V~~i~~~Gifv~lg~--~~~~i~~~~l~~~-~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~ 148 (170)
+++.+++.++|++++|+|++++++|+||+|+. .+|+||.++|++| |.||+..+ ++.+++++..|++||.|+|+|.
T Consensus 634 ~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~--~L~g~~~~~~~~lGD~V~VkV~ 711 (813)
T PRK11642 634 LKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQ--RLIGESSGQTYRLGDRVEVRVE 711 (813)
T ss_pred HHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEecchhe--EEecccCCcEECCCCEEEEEEE
Confidence 55666788999999999999999999999975 5999999999988 88887776 6788887889999999999999
Q ss_pred EEEecCCceE--EEEEec-CCCCC
Q psy13107 149 GTRVDASGIF--AIGTLM-DDYLG 169 (170)
Q Consensus 149 ~v~~~~~~i~--~ig~~~-~~~LG 169 (170)
+++.+++++. ++.+.+ .+|+|
T Consensus 712 ~vD~~~rkI~f~l~~~~~~~~~~~ 735 (813)
T PRK11642 712 AVNMDERKIDFSLISSERAPRNVG 735 (813)
T ss_pred EeecCCCeEEEEEecccccCCCCC
Confidence 9999888765 344444 66676
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=99.27 E-value=4.2e-11 Score=77.94 Aligned_cols=67 Identities=13% Similarity=0.276 Sum_probs=54.6
Q ss_pred cCCCCEEEEEEEEEecccEEEEecC--eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCc
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIGP--LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASG 156 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg~--~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~ 156 (170)
|..|++++|+|+++.++|+|+++.. .+||+|.++++++ .++ +.+..++.||+|+++|.+++.+. +
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~-~~~-----------~~~~~~~~Gd~v~vkv~~vd~~~-k 67 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSC-RVD-----------DPSEVVDVGEKVWVKVIGREMKD-K 67 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCC-ccc-----------CHhhEECCCCEEEEEEEEECCCC-c
Confidence 5689999999999999999999955 4999999999754 221 22348999999999999998754 5
Q ss_pred eE
Q psy13107 157 IF 158 (170)
Q Consensus 157 i~ 158 (170)
+.
T Consensus 68 i~ 69 (73)
T cd05686 68 MK 69 (73)
T ss_pred EE
Confidence 44
No 21
>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=99.20 E-value=6.3e-11 Score=76.14 Aligned_cols=65 Identities=11% Similarity=0.230 Sum_probs=54.6
Q ss_pred CCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
|+++.|+|+++.++|+||++++ .+||+|.++|++++..++ ...+++||.++++|.+++.+.+++.
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~------------~~~~~~G~~i~v~v~~~d~~~~~i~ 66 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDP------------EEHFRVGQVVKVKVLSCDPEQQRLL 66 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCH------------HHcccCCCEEEEEEEEEcCCCCEEE
Confidence 7899999999999999999976 599999999986643322 1379999999999999988777654
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=99.20 E-value=9.4e-11 Score=76.62 Aligned_cols=70 Identities=14% Similarity=0.183 Sum_probs=56.2
Q ss_pred CCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
.+|+++.|+|++++++|+||++++. +|++|.++|.+++.-++ ++-...|++||.|+++|.+++.+++++.
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~---------~~~~~~~~~G~~v~~kVl~id~~~~~i~ 72 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDP---------SLYNKYLPEGKLLTAKVLSVNSEKNLVE 72 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccCh---------hhHhcccCCCCEEEEEEEEEECCCCEEe
Confidence 4799999999999999999999875 99999999975421111 1112489999999999999998877654
No 23
>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=99.20 E-value=9.1e-11 Score=75.07 Aligned_cols=66 Identities=14% Similarity=0.277 Sum_probs=54.0
Q ss_pred CCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
|+++.|+|+++.++|+|+++++. +|++|.++|+.+ ...++....|++||.|+++|.+++.+++++.
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~-----------~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~ 67 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWT-----------QRVRHPSEIYKKGQEVEAVVLNIDVERERIS 67 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCc-----------cccCChhhEECCCCEEEEEEEEEECCcCEEe
Confidence 78999999999999999999774 999999999721 0112223489999999999999998877764
No 24
>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=99.20 E-value=7.4e-11 Score=75.75 Aligned_cols=65 Identities=9% Similarity=0.295 Sum_probs=54.8
Q ss_pred CCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
|++++|+|+++.++|+||++++ .+||+|.++|++++. ++....+++||.++++|.+++.+++++.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~------------~~~~~~~~~Gd~i~~~V~~id~~~~~i~ 66 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRL------------KHPEKKFKPGLKVKCRVLSVEPERKRLV 66 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccc------------cCHHHcCCCCCEEEEEEEEEECCCCEEE
Confidence 7899999999999999999976 599999999986521 1122389999999999999998887765
No 25
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.19 E-value=2.8e-13 Score=122.47 Aligned_cols=140 Identities=12% Similarity=0.101 Sum_probs=101.8
Q ss_pred EEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEE--------EE-ceeceeCCeeEecCCCceEEeE--EEEE
Q psy13107 6 SLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVI--------AV-TTIDSIGAGLIQPGQGFVVYPV--KYRA 74 (170)
Q Consensus 6 ~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i--------~i-~~i~~~~~g~I~~~~g~~~~~v--~f~~ 74 (170)
.|+.+++-|..++++..++....++..+..+.+++.+|..| +- +|+.+-+.-+|...+....-++ .++.
T Consensus 667 ~M~~~i~~pr~~~s~~aP~i~~~~i~~~ki~~vIG~GGktIk~I~eetg~~~Idi~ddg~V~I~a~d~~~i~~A~~~I~~ 746 (891)
T PLN00207 667 EMSKCSPPPSKRLSKYAPLIHIMKVKPEKVNMIIGSGGKKVKSIIEETGVEAIDTQDDGTVKITAKDLSSLEKSKAIISS 746 (891)
T ss_pred HHHHHHhhhhhhhcccCCeeEEEEcCHHHHHHHhcCCchhHHHHHHHHCCCccCcCCCeeEEEEeCCHHHHHHHHHHHHH
Confidence 35666777778888888888888888888899999999987 12 5555522233333333222222 2556
Q ss_pred EEeecCCCCEEE-EEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEe
Q psy13107 75 IVFRPFKGEVLD-AVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRV 152 (170)
Q Consensus 75 i~f~p~~gev~~-g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 152 (170)
+++.|.+|++++ |+|+++.+||+||++.+. +||+|.|+|.+++. . +-...|++||.|+|+|.+++.
T Consensus 747 l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv----~--------~~~dv~kvGD~V~VkVi~ID~ 814 (891)
T PLN00207 747 LTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWL----A--------KPEDAFKVGDRIDVKLIEVND 814 (891)
T ss_pred HhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccc----c--------CHHHhcCCCCEEEEEEEEECC
Confidence 667899999996 699999999999999875 99999999975521 1 112389999999999999985
Q ss_pred cCCceE
Q psy13107 153 DASGIF 158 (170)
Q Consensus 153 ~~~~i~ 158 (170)
++++.
T Consensus 815 -~grI~ 819 (891)
T PLN00207 815 -KGQLR 819 (891)
T ss_pred -CCcEE
Confidence 55554
No 26
>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=99.19 E-value=3.6e-11 Score=107.38 Aligned_cols=85 Identities=14% Similarity=0.254 Sum_probs=75.7
Q ss_pred EEEEEeecCCCCEEEEEEEEEecccEEEEec-C-eeEEEEcCCCCCC-ceecCCCCCeEEEecCceeEEcCCCeEEEEEE
Q psy13107 72 YRAIVFRPFKGEVLDAVVTQVNKVGMFAEIG-P-LSCFISHHSIPTD-MQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIV 148 (170)
Q Consensus 72 f~~i~f~p~~gev~~g~V~~i~~~Gifv~lg-~-~~~~i~~~~l~~~-~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~ 148 (170)
+++.+++.+.|++++|+|++++++|+||+++ + .+|+||.++|+++ |.||+... .+.+++++..|++||+|+|+|.
T Consensus 563 ~~~~yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~--~l~g~~~~~~~~lGD~V~Vki~ 640 (654)
T TIGR00358 563 LKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVFDQEKM--ALIGKGTGKVYRIGDRVTVKLT 640 (654)
T ss_pred HHHHhhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEEecccc--EEEeccCCcEECCCCEEEEEEE
Confidence 5566778899999999999999999999997 4 4999999999988 89998876 6778777789999999999999
Q ss_pred EEEecCCceE
Q psy13107 149 GTRVDASGIF 158 (170)
Q Consensus 149 ~v~~~~~~i~ 158 (170)
+++.+++++.
T Consensus 641 ~vd~~~~~I~ 650 (654)
T TIGR00358 641 EVNMETRSII 650 (654)
T ss_pred EEecccCeEE
Confidence 9999888765
No 27
>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=99.19 E-value=2.2e-10 Score=74.20 Aligned_cols=67 Identities=18% Similarity=0.162 Sum_probs=56.0
Q ss_pred CCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
.+|+++.|+|+++.++|+|+++++. +|++|.+++++++. .. ....|++||.++++|.+++.+++++.
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~--~~----------~~~~~~~Gd~v~~~V~~~d~~~~~i~ 69 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYS--EA----------LPYKFKKNDIVRACVLSVDVPNKKIA 69 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccc--cc----------cccccCCCCEEEEEEEEEeCCCCEEE
Confidence 4799999999999999999999874 99999999986632 11 12379999999999999998777655
No 28
>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=99.19 E-value=6.5e-11 Score=106.68 Aligned_cols=85 Identities=18% Similarity=0.302 Sum_probs=75.4
Q ss_pred EEEEEeecCCCCEEEEEEEEEecccEEEEecC--eeEEEEcCCCCCC-ceecCCCCCeEEEecCceeEEcCCCeEEEEEE
Q psy13107 72 YRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGP--LSCFISHHSIPTD-MQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIV 148 (170)
Q Consensus 72 f~~i~f~p~~gev~~g~V~~i~~~Gifv~lg~--~~~~i~~~~l~~~-~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~ 148 (170)
++|.++++.+|++++|+|++++++|+||++.+ .+|++|.++|+++ |.|++..+ .+.+++++..|++||+|+|+|.
T Consensus 618 ~~~~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~d~~~~--~l~g~~~~~~~~lGd~V~Vkv~ 695 (709)
T TIGR02063 618 KKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVFDEKGL--ALVGERTGKVFRLGDRVKVRVV 695 (709)
T ss_pred HHHHhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEEcccce--EEEeccCCcEECCCCEEEEEEE
Confidence 56667888999999999999999999999986 5999999999988 78888776 6777777779999999999999
Q ss_pred EEEecCCceE
Q psy13107 149 GTRVDASGIF 158 (170)
Q Consensus 149 ~v~~~~~~i~ 158 (170)
+++.+++++.
T Consensus 696 ~vd~~~~~I~ 705 (709)
T TIGR02063 696 KADLDTGKID 705 (709)
T ss_pred EEecccCeEE
Confidence 9998888765
No 29
>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=99.19 E-value=7.3e-13 Score=118.48 Aligned_cols=136 Identities=21% Similarity=0.243 Sum_probs=98.6
Q ss_pred EEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEE--------EEceeceeCCeeEecCCCceEEeE--EEEEEEee
Q psy13107 9 HEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVI--------AVTTIDSIGAGLIQPGQGFVVYPV--KYRAIVFR 78 (170)
Q Consensus 9 ~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i--------~i~~i~~~~~g~I~~~~g~~~~~v--~f~~i~f~ 78 (170)
..++-|..++++..++...-+++....+.+++++|..| +-+||.+-+..+|...++..+.++ .++.+...
T Consensus 536 ~~l~~~~~~~~~~~p~~~~~~I~~~kI~~vIG~gGk~Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~ 615 (684)
T TIGR03591 536 KVISEPRAELSPYAPRIETIKINPDKIRDVIGPGGKVIREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGITAE 615 (684)
T ss_pred HHHhhhhccccccCCeEEEEecCHHHHHhhcCCCcHHHHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhhcc
Confidence 33444555566666666666667777888888888877 456677634444555555555444 56666778
Q ss_pred cCCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
|.+|+++.|+|+++.++|+||++.+ .+||+|.|++++++. ++....|++||.|+|+|.+++. ++++
T Consensus 616 ~~~G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v------------~~~~~~~kvGD~V~VkVi~id~-~gki 682 (684)
T TIGR03591 616 PEVGKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERV------------EKVEDVLKEGDEVKVKVLEIDK-QGRI 682 (684)
T ss_pred cccCcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcc------------cChhhccCCCCEEEEEEEEECC-CCCc
Confidence 9999999999999999999999977 499999999974421 1223489999999999999985 4443
No 30
>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=99.17 E-value=1.1e-10 Score=77.67 Aligned_cols=70 Identities=13% Similarity=0.200 Sum_probs=58.3
Q ss_pred ecCCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCc
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASG 156 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~ 156 (170)
....|+++.|+|++++++|+|++++. .+||+|.++++.++.. +....|++||.|+|+|.+++.++++
T Consensus 11 ~~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~------------~~~~~~~~Gd~v~vkV~~id~~~~~ 78 (83)
T cd04461 11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVT------------DPSFGFKKGQSVTAKVTSVDEEKQR 78 (83)
T ss_pred hCCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCccccc------------CHHHhcCCCCEEEEEEEEEcCCCCE
Confidence 46799999999999999999999976 5999999999855211 2234899999999999999988777
Q ss_pred eEE
Q psy13107 157 IFA 159 (170)
Q Consensus 157 i~~ 159 (170)
+..
T Consensus 79 i~l 81 (83)
T cd04461 79 FLL 81 (83)
T ss_pred EEE
Confidence 653
No 31
>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=99.15 E-value=1.8e-10 Score=73.78 Aligned_cols=65 Identities=17% Similarity=0.256 Sum_probs=54.3
Q ss_pred CCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
|+++.|+|+++.++|+||++++ .+||+|.+++++++.- +....|++||.++++|.+++.+++++.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~------------~~~~~~~~Gd~v~~~v~~~d~~~~~i~ 66 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLK------------DWKKRFKVGQLVKGKIVSIDPDNGRIE 66 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhc------------CHhhccCCCCEEEEEEEEEeCCCCEEe
Confidence 7899999999999999999976 5999999999866321 112379999999999999998777654
No 32
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=99.15 E-value=1.8e-12 Score=115.12 Aligned_cols=140 Identities=19% Similarity=0.181 Sum_probs=98.5
Q ss_pred EEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEE--------EEceeceeCCeeEec--CCCceEE--eEEEEE
Q psy13107 7 LEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVI--------AVTTIDSIGAGLIQP--GQGFVVY--PVKYRA 74 (170)
Q Consensus 7 ~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i--------~i~~i~~~~~g~I~~--~~g~~~~--~v~f~~ 74 (170)
|+..++-| .++++.+++...-+++.+..+.+++++|..| +-+||.+ +|.+.- .+....- .-..+.
T Consensus 562 m~~al~~p-~~~s~~aP~~~~~~I~~~ki~~vIG~gGk~I~~i~~~tg~~Idi~d--~G~V~I~a~d~~~~~~A~~~I~~ 638 (719)
T TIGR02696 562 MAEAIDTP-DEMSPYAPRIITVKIPVDKIGEVIGPKGKMINQIQDETGAEISIED--DGTVYIGAADGPSAEAARAMINA 638 (719)
T ss_pred HHHHHhCc-cccccCCCeeEEEEeChHHhhheeCCCcHhHHHHHHHHCCEEEEec--CcEEEEEeCCHHHHHHHHHHHHH
Confidence 44555555 7788888888888888889999999999988 4566666 566552 2321111 111223
Q ss_pred EEe--ecCCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEE
Q psy13107 75 IVF--RPFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTR 151 (170)
Q Consensus 75 i~f--~p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 151 (170)
++. .|.+|++++|+|+++.+||+||++++. +||+|.|+|.+ ..|. .+ .++-...+++||+|+|+|.+++
T Consensus 639 i~~~~~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisd-ls~~------~r-v~~~~dv~kvGd~V~VKVl~ID 710 (719)
T TIGR02696 639 IANPTMPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRK-LAGG------KR-VENVEDVLSVGQKIQVEIADID 710 (719)
T ss_pred hhCcCcCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhccc-cccc------cC-cCCHHHcCCCCCEEEEEEEEEC
Confidence 333 589999999999999999999999774 99999999852 1110 01 1122348999999999999998
Q ss_pred ecCCceE
Q psy13107 152 VDASGIF 158 (170)
Q Consensus 152 ~~~~~i~ 158 (170)
+++++.
T Consensus 711 -~~gKI~ 716 (719)
T TIGR02696 711 -DRGKLS 716 (719)
T ss_pred -CCCCee
Confidence 455654
No 33
>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=99.14 E-value=4.5e-10 Score=72.55 Aligned_cols=68 Identities=18% Similarity=0.271 Sum_probs=54.8
Q ss_pred CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
.+|+++.|+|++++++|+|+++++ .+||+|.++|+.+ ... .+....|++||.|+++|.+++.+++++.
T Consensus 2 ~~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~----~~~-------~~~~~~~~~Gd~v~v~v~~id~~~~~i~ 70 (72)
T cd05689 2 PEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWT----NKN-------IHPSKVVSLGDEVEVMVLDIDEERRRIS 70 (72)
T ss_pred cCCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCc----ccc-------cCcccEeCCCCEEEEEEEEeeCCcCEEe
Confidence 368999999999999999999977 5999999999632 011 1223589999999999999998777653
No 34
>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=99.14 E-value=4.4e-10 Score=73.22 Aligned_cols=67 Identities=19% Similarity=0.336 Sum_probs=55.7
Q ss_pred CCCEEEEEEEEEecccEEEEecC--eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGP--LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~--~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
+|+++.|+|++++++|+|+++.. .+|++|.+++++++.. +....|++||.|+++|.+++.+.+++.
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~------------~~~~~~~~Gd~v~v~i~~vd~~~~~i~ 69 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVA------------DASKLFRVGDKVRAKVLKIDAEKKRIS 69 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccC------------CHhHeecCCCEEEEEEEEEeCCCCEEE
Confidence 69999999999999999999974 5999999999855321 122489999999999999998777765
Q ss_pred E
Q psy13107 159 A 159 (170)
Q Consensus 159 ~ 159 (170)
.
T Consensus 70 l 70 (77)
T cd05708 70 L 70 (77)
T ss_pred E
Confidence 3
No 35
>PRK08582 hypothetical protein; Provisional
Probab=99.13 E-value=4.1e-10 Score=82.22 Aligned_cols=68 Identities=18% Similarity=0.201 Sum_probs=56.0
Q ss_pred ecCCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCc
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASG 156 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~ 156 (170)
+..+|++++|+|++++++|+||.|++. +|+||.+++++++..+. ...|++||.|+|+|.+++.+ ++
T Consensus 2 ~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~------------~~~l~vGD~VkvkV~~id~~-gk 68 (139)
T PRK08582 2 SIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDI------------NDHLKVGDEVEVKVLNVEDD-GK 68 (139)
T ss_pred CCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCccccccc------------ccccCCCCEEEEEEEEECCC-Cc
Confidence 457899999999999999999999875 99999999986643221 23899999999999999853 55
Q ss_pred eE
Q psy13107 157 IF 158 (170)
Q Consensus 157 i~ 158 (170)
+.
T Consensus 69 I~ 70 (139)
T PRK08582 69 IG 70 (139)
T ss_pred EE
Confidence 54
No 36
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.11 E-value=8e-11 Score=82.84 Aligned_cols=68 Identities=15% Similarity=0.169 Sum_probs=57.4
Q ss_pred ecCCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCc
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASG 156 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~ 156 (170)
++.+|++++|+|+++++||+||++... .||||+|++.++|.-|-+ ..+++||+|.|+|.+++- .++
T Consensus 2 ~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~------------d~L~vG~eV~vKVl~ide-~GK 68 (129)
T COG1098 2 SMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIH------------DHLKVGQEVKVKVLDIDE-NGK 68 (129)
T ss_pred CccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHH------------HHhcCCCEEEEEEEeecc-CCC
Confidence 467899999999999999999999876 999999999977653321 288999999999999985 555
Q ss_pred eE
Q psy13107 157 IF 158 (170)
Q Consensus 157 i~ 158 (170)
+.
T Consensus 69 is 70 (129)
T COG1098 69 IS 70 (129)
T ss_pred cc
Confidence 54
No 37
>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=6e-10 Score=72.16 Aligned_cols=66 Identities=20% Similarity=0.250 Sum_probs=53.6
Q ss_pred CCEEE-EEEEEE-ecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 82 GEVLD-AVVTQV-NKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 82 gev~~-g~V~~i-~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
|++++ |+|+++ .++|+||++.+ .+||+|.|+++++. ..+ ....+++||++++||.+++..++++.
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~----~~~--------~~~~~~vG~~v~~kV~~id~~~~~i~ 68 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDK----VPS--------DTGPFKAGTTHKARIIGYSPMDGLLQ 68 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcch----hcC--------cccccCCCCEEEEEEEEEeCCCCEEE
Confidence 78999 999999 69999999976 59999999998541 111 12379999999999999988777665
Q ss_pred E
Q psy13107 159 A 159 (170)
Q Consensus 159 ~ 159 (170)
.
T Consensus 69 l 69 (71)
T cd05696 69 L 69 (71)
T ss_pred E
Confidence 4
No 38
>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=99.09 E-value=9.1e-10 Score=71.69 Aligned_cols=69 Identities=12% Similarity=0.172 Sum_probs=56.1
Q ss_pred cCCCCEEEEEEEEEecccEEEEecC---eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCC
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIGP---LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDAS 155 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg~---~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 155 (170)
|..|+++.|+|+++.++|+|+++.. .+|++|.+++++++. . +-...|+.||.|+++|.+++.+++
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~----~--------~~~~~~~~Gd~v~vkv~~~d~~~~ 68 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRI----R--------SIRKLVKVGRKEVVKVIRVDKEKG 68 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCccc----C--------CHHHeeCCCCEEEEEEEEEECCCC
Confidence 5689999999999999999999952 699999999985521 1 112379999999999999988776
Q ss_pred ceEE
Q psy13107 156 GIFA 159 (170)
Q Consensus 156 ~i~~ 159 (170)
++..
T Consensus 69 ~i~l 72 (76)
T cd04452 69 YIDL 72 (76)
T ss_pred EEEE
Confidence 6553
No 39
>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=99.08 E-value=5.4e-10 Score=74.75 Aligned_cols=83 Identities=14% Similarity=0.137 Sum_probs=63.5
Q ss_pred eecCCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCC
Q psy13107 77 FRPFKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDAS 155 (170)
Q Consensus 77 f~p~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 155 (170)
|.|..|++++|+|+++.++|+++.++. .+|++|.+++..+ ..+. + .++....+++||.++++|.+++-+ +
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~----~~~~---~-~~~~~~~l~vGd~i~~~V~~~~~~-~ 72 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLP----RTDE---D-ELNMRSYLDEGDLIVAEVQSVDSD-G 72 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCC----CCcc---c-hHHHHhhCCCCCEEEEEEEEECCC-C
Confidence 578999999999999999999999986 5999999999732 0000 0 111223799999999999998644 4
Q ss_pred ceEEEEEecCCCCCC
Q psy13107 156 GIFAIGTLMDDYLGL 170 (170)
Q Consensus 156 ~i~~ig~~~~~~LG~ 170 (170)
++.. |+.+++||.
T Consensus 73 ~i~L--S~~~~~~g~ 85 (86)
T cd05789 73 SVSL--HTRSLKYGK 85 (86)
T ss_pred CEEE--EeCcccccC
Confidence 5555 788888883
No 40
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.07 E-value=1.9e-09 Score=93.35 Aligned_cols=68 Identities=21% Similarity=0.377 Sum_probs=58.3
Q ss_pred CCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFA 159 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ 159 (170)
.+|++++|+|++++++|+||.+|.++|++|.++|+.. .... -..++++||+|+|+|.++|.++++++.
T Consensus 191 ~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~----rv~~--------P~~vvkvGd~VkvkVi~~D~e~~RVsL 258 (541)
T COG0539 191 EVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWK----RVDH--------PSEVVKVGDEVKVKVISLDEERGRVSL 258 (541)
T ss_pred CCCceEEEEEEEeecCcEEEEecCeeeEEehhhcccc----ccCC--------HHHhcccCCEEEEEEEEEccCCCeEEE
Confidence 5899999999999999999999999999999999732 1111 123899999999999999998888775
No 41
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.06 E-value=2.4e-11 Score=108.95 Aligned_cols=137 Identities=20% Similarity=0.249 Sum_probs=95.7
Q ss_pred EEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEE--------EEceeceeCCeeEecC--CCceE--EeEEEEE
Q psy13107 7 LEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVI--------AVTTIDSIGAGLIQPG--QGFVV--YPVKYRA 74 (170)
Q Consensus 7 ~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i--------~i~~i~~~~~g~I~~~--~g~~~--~~v~f~~ 74 (170)
|++.+.-|+.++++..++....+++....+.+++.+|..| +-.|+.+ +|.+... +.... .+-..+.
T Consensus 537 M~~aI~~~r~~~~~~ap~~~~~~I~~~kI~~vIG~gg~~ik~I~~~~~~~idi~d--~G~v~i~~~~~~~~~~a~~~I~~ 614 (693)
T PRK11824 537 MNEAISEPRAELSPYAPRIETIKIPPDKIRDVIGPGGKTIREITEETGAKIDIED--DGTVKIAATDGEAAEAAKERIEG 614 (693)
T ss_pred HHHHhcCChhhhcccCchheeecCCHHHHHHHhcCCchhHHHHHHHHCCccccCC--CceEEEEcccHHHHHHHHHHHHH
Confidence 5556777778888887777777777777788888888876 2333333 4544421 11100 0001233
Q ss_pred EEeecCCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEec
Q psy13107 75 IVFRPFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVD 153 (170)
Q Consensus 75 i~f~p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 153 (170)
+...+.+|+++.|+|+++.++|+||++.+. +|++|.|+|++++. ++....|++||.|+|+|.+++.+
T Consensus 615 ~~~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v------------~~~~~v~kvGD~V~VkV~~iD~~ 682 (693)
T PRK11824 615 ITAEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERV------------EKVEDVLKEGDEVKVKVLEIDKR 682 (693)
T ss_pred hcccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccc------------cCccceeCCCCEEEEEEEEECCC
Confidence 445689999999999999999999999875 99999999985421 11124899999999999999865
Q ss_pred CCceE
Q psy13107 154 ASGIF 158 (170)
Q Consensus 154 ~~~i~ 158 (170)
+++.
T Consensus 683 -grI~ 686 (693)
T PRK11824 683 -GRIR 686 (693)
T ss_pred -CcEE
Confidence 5554
No 42
>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=99.05 E-value=8.9e-10 Score=71.75 Aligned_cols=68 Identities=19% Similarity=0.258 Sum_probs=55.4
Q ss_pred CCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFA 159 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ 159 (170)
|+++.|+|+++.++|+||++++ ++|++|.++|+++.... ++-...|++||.|+++|.+++.+++++..
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~----------~~~~~~~~vG~~v~~kV~~id~~~~~i~L 69 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVL----------EHPEKKFPIGQALKAKVVGVDKEHKLLRL 69 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccc----------cCHHHhCCCCCEEEEEEEEEeCCCCEEEE
Confidence 7899999999999999999987 59999999998441111 11124899999999999999988887764
No 43
>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=99.04 E-value=8.6e-10 Score=69.84 Aligned_cols=65 Identities=26% Similarity=0.399 Sum_probs=53.6
Q ss_pred CCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
|+++.|+|++++++|+|+++++. +|++|.+++++++.- +....+++||.++++|.+++.+++++.
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~------------~~~~~~~~Gd~v~v~i~~vd~~~~~i~ 66 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVS------------HPSDVVSVGDIVEVKVISIDEERGRIS 66 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCcccc------------CHHHhcCCCCEEEEEEEEEECCCCEEe
Confidence 68999999999999999999875 999999999755211 112479999999999999998766553
No 44
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.04 E-value=1.9e-09 Score=68.41 Aligned_cols=66 Identities=18% Similarity=0.387 Sum_probs=54.1
Q ss_pred CCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
+|+++.|+|++++++|+|+.++..+|++|.++++.... +.....|++||.|+++|.+++.+++++.
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e~~~~~~------------~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ 66 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRV------------KHPSEVVNVGDEVEVKVLKIDKERKRIS 66 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccc------------cCHhHEECCCCEEEEEEEEEECCCCEEe
Confidence 48999999999999999999987899999999973211 1122479999999999999988776654
No 45
>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=99.03 E-value=4.6e-09 Score=69.13 Aligned_cols=64 Identities=13% Similarity=0.309 Sum_probs=51.9
Q ss_pred CCEEEEEEEEEecccEEEEec----CeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIG----PLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg----~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
|++++|+|+++.++|+|++++ +.+||+|.+++++++. .++....|+.||+|+++|.+++ ++++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~-----------~~~~~~~~~~Gd~v~v~v~~vd--~~~i 67 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGR-----------VANPSDVVKRGQKVKVKVISIQ--NGKI 67 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCC-----------cCChhheeCCCCEEEEEEEEEe--CCEE
Confidence 789999999999999999998 3599999999985521 0122348999999999999998 5555
Q ss_pred E
Q psy13107 158 F 158 (170)
Q Consensus 158 ~ 158 (170)
.
T Consensus 68 ~ 68 (79)
T cd05684 68 S 68 (79)
T ss_pred E
Confidence 4
No 46
>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=99.02 E-value=2.2e-09 Score=71.19 Aligned_cols=79 Identities=22% Similarity=0.218 Sum_probs=63.5
Q ss_pred eecCCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCC
Q psy13107 77 FRPFKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDAS 155 (170)
Q Consensus 77 f~p~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 155 (170)
|.|..|+++.|+|+++++.+++|.++. .+|++|.++++.+.. ++....+++||.++++|.+++-+ +
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~------------~~~~~~~~~GD~i~~~V~~~~~~-~ 68 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDK------------KEIRKSLQPGDLILAKVISLGDD-M 68 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcch------------HHHHhcCCCCCEEEEEEEEeCCC-C
Confidence 579999999999999999999999976 499999999975421 11123789999999999998754 4
Q ss_pred ceEEEEEecCCCCCC
Q psy13107 156 GIFAIGTLMDDYLGL 170 (170)
Q Consensus 156 ~i~~ig~~~~~~LG~ 170 (170)
.+.. |+.++.||.
T Consensus 69 ~i~L--S~~~~~~Gv 81 (82)
T cd04454 69 NVLL--TTADNELGV 81 (82)
T ss_pred CEEE--EECCCCCcc
Confidence 4444 788888884
No 47
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.01 E-value=3.8e-12 Score=111.35 Aligned_cols=138 Identities=19% Similarity=0.250 Sum_probs=105.1
Q ss_pred CeEEEEEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEE--------EEceeceeCCeeEe--cCCCceEEeE
Q psy13107 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVI--------AVTTIDSIGAGLIQ--PGQGFVVYPV 70 (170)
Q Consensus 1 Mf~~~~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i--------~i~~i~~~~~g~I~--~~~g~~~~~v 70 (170)
|+++..|.++++-|..++++..++....+++......++++.|..| +..||.+ +|.+. ..++......
T Consensus 529 lhIL~~M~~ai~~pr~els~~aPri~t~~i~~dKI~dvIG~gGk~I~~I~eetg~~Idied--dGtv~i~~s~~~~~~~a 606 (692)
T COG1185 529 LHILIVMNEAISEPRKELSPYAPRIETIKIDPDKIRDVIGPGGKTIKAITEETGVKIDIED--DGTVKIAASDGESAKKA 606 (692)
T ss_pred HHHHHHHHHHHhhhhhhhhccCCceEEEccCHHHHhhccCCcccchhhhhhhhCcEEEecC--CCcEEEEecchHHHHHH
Confidence 3456667888899999999998888888888888889999999887 4555554 44444 3343222222
Q ss_pred --EEEEEEeecCCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEE
Q psy13107 71 --KYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKI 147 (170)
Q Consensus 71 --~f~~i~f~p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV 147 (170)
..+.++-.+.+||+|.|+|+++.+||+|+++.+. +|++|.|++... .. ++-+.+++.||.|+||+
T Consensus 607 k~~I~~i~~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~----rv--------~kv~dvlk~Gd~v~Vkv 674 (692)
T COG1185 607 KERIEAITREVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKE----RV--------EKVEDVLKEGDEVKVKV 674 (692)
T ss_pred HHHHHHHHhhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhh----hh--------hcccceeecCceEEEEE
Confidence 3455567889999999999999999999999886 999999999844 11 11224999999999999
Q ss_pred EEEEe
Q psy13107 148 VGTRV 152 (170)
Q Consensus 148 ~~v~~ 152 (170)
.++|-
T Consensus 675 ~~iD~ 679 (692)
T COG1185 675 IEIDK 679 (692)
T ss_pred eeecc
Confidence 99863
No 48
>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=99.01 E-value=1.4e-09 Score=68.94 Aligned_cols=64 Identities=23% Similarity=0.411 Sum_probs=52.3
Q ss_pred CCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
|+++.|+|+++.++|+|+.++. .+||+|.+++++++..++ ...+++||.++++|.+++. .+++.
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~------------~~~~~~Gd~v~v~v~~~~~-~~~i~ 65 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDV------------KDVLKEGDKVKVKVLSIDA-RGRIS 65 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCH------------HHccCCCCEEEEEEEEECC-CCcEE
Confidence 7899999999999999999986 499999999986542211 1378999999999999976 45544
No 49
>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=99.00 E-value=2.2e-09 Score=69.20 Aligned_cols=65 Identities=20% Similarity=0.308 Sum_probs=54.2
Q ss_pred CCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
|+++.|+|+++.++|+|+++++ .+|++|.+++++++. ++....|++||.++++|.+++.+++++.
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~------------~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ 66 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRV------------EDATERFKVGDEVEAKITNVDRKNRKIS 66 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccc------------cCHHHccCCCCEEEEEEEEEeCCCCEEE
Confidence 7899999999999999999966 599999999986632 1112378999999999999998776655
No 50
>PRK07252 hypothetical protein; Provisional
Probab=99.00 E-value=3.1e-09 Score=75.72 Aligned_cols=67 Identities=15% Similarity=0.193 Sum_probs=55.7
Q ss_pred CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
.+|+++.|+|+++.++|+||+++. .+|++|.++|++++. . +-...|++||.|+|+|.+++.+.+++.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~-~-----------~~~~~~~vGD~V~VkI~~iD~~~~ri~ 69 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFI-D-----------NIHQLLKVGEEVLVQVVDFDEYTGKAS 69 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccc-c-----------ChhhccCCCCEEEEEEEEEeCCCCEEE
Confidence 369999999999999999999976 599999999985521 1 112379999999999999998777765
No 51
>PRK05807 hypothetical protein; Provisional
Probab=98.98 E-value=3.9e-09 Score=76.79 Aligned_cols=68 Identities=15% Similarity=0.269 Sum_probs=55.3
Q ss_pred ecCCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
+..+|++++|+|++++++|+||.+...+|+||.+++++++..+. ...+++||.|+|+|.+++. .+++
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~------------~~~~kvGd~V~VkV~~id~-~gkI 68 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDI------------REHLKEQDKVKVKVISIDD-NGKI 68 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCc------------cccCCCCCEEEEEEEEECC-CCcE
Confidence 34679999999999999999999965699999999986543221 1278999999999999986 4555
Q ss_pred E
Q psy13107 158 F 158 (170)
Q Consensus 158 ~ 158 (170)
.
T Consensus 69 ~ 69 (136)
T PRK05807 69 S 69 (136)
T ss_pred E
Confidence 4
No 52
>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=98.92 E-value=2.6e-09 Score=69.34 Aligned_cols=60 Identities=17% Similarity=0.149 Sum_probs=49.7
Q ss_pred CCCCEEEEEEEEEec-ccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEE
Q psy13107 80 FKGEVLDAVVTQVNK-VGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTR 151 (170)
Q Consensus 80 ~~gev~~g~V~~i~~-~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 151 (170)
.+|+++.|+|+++.+ +|+|+++++. +|++|.+++.+++. + + -...+++||.||++|.+++
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~--~--~--------~~~~~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYT--E--N--------PLEGFKPGKIVRCCILSKK 63 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCccc--C--C--------HHHhCCCCCEEEEEEEEec
Confidence 479999999999986 8999999885 99999999986531 1 1 0127899999999999985
No 53
>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=98.92 E-value=6.8e-09 Score=65.85 Aligned_cols=64 Identities=20% Similarity=0.347 Sum_probs=52.0
Q ss_pred CCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
|+++.|+|+++.++|+|++++.. +||+|.++++.++.. +....|++||.|+|+|.+++. ++++.
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~------------~~~~~~~~Gd~v~v~v~~~d~-~~~i~ 65 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVE------------KVEDVLKVGDEVKVKVIEVDD-RGRIS 65 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCcccc------------CHHHccCCCCEEEEEEEEECC-CCcEE
Confidence 68999999999999999999874 999999999755211 112389999999999999986 55543
No 54
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.92 E-value=1.1e-08 Score=64.91 Aligned_cols=67 Identities=21% Similarity=0.441 Sum_probs=55.3
Q ss_pred CCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEE
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFA 159 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ 159 (170)
.|+++.|+|.+++++|+|+.+++ .+|++|.+++++++ ..+....|++||.++++|.+++.+++++.+
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~------------~~~~~~~~~~G~~v~~~V~~~~~~~~~i~l 69 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKR------------VKDPEEVLKVGDEVKVKVLSVDEEKGRIIL 69 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccc------------cCCHHHeecCCCEEEEEEEEEeCCCCEEEE
Confidence 69999999999999999999985 59999999998553 111224799999999999999877666543
No 55
>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=98.92 E-value=1.1e-08 Score=66.89 Aligned_cols=62 Identities=16% Similarity=0.216 Sum_probs=53.4
Q ss_pred CCCCEEEEEEEEEecccEEEEec--CeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIG--PLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg--~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
..|+++.|+|+++.++|+|+++| .++||+|.++++.+ ..+++|+.+.++|.+++-+.+++
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~------------------~~~~~Gq~v~~~V~~vd~~~~~v 64 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF------------------SKLKVGQLLLCVVEKVKDDGRVV 64 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc------------------cccCCCCEEEEEEEEEECCCCEE
Confidence 47899999999999999999997 36999999998722 27899999999999998777666
Q ss_pred EE
Q psy13107 158 FA 159 (170)
Q Consensus 158 ~~ 159 (170)
..
T Consensus 65 ~l 66 (74)
T cd05694 65 SL 66 (74)
T ss_pred EE
Confidence 54
No 56
>PRK08059 general stress protein 13; Validated
Probab=98.92 E-value=7e-09 Score=74.19 Aligned_cols=69 Identities=16% Similarity=0.217 Sum_probs=56.8
Q ss_pred ecCCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCc
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASG 156 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~ 156 (170)
+..+|+++.|+|+++.++|+||.++.. +|++|.++++.++.. +....|++||.|+|+|.+++.+.++
T Consensus 4 ~~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~------------~~~~~~~vGD~I~vkI~~id~~~~~ 71 (123)
T PRK08059 4 QYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVK------------DIHDFLSVGDEVKVKVLSVDEEKGK 71 (123)
T ss_pred cCCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCccccc------------CHHHcCCCCCEEEEEEEEEECCCCe
Confidence 356899999999999999999999874 999999999865321 1123789999999999999876666
Q ss_pred eE
Q psy13107 157 IF 158 (170)
Q Consensus 157 i~ 158 (170)
+.
T Consensus 72 i~ 73 (123)
T PRK08059 72 IS 73 (123)
T ss_pred EE
Confidence 55
No 57
>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=98.91 E-value=8.9e-09 Score=65.68 Aligned_cols=63 Identities=13% Similarity=0.210 Sum_probs=52.2
Q ss_pred CCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
|++++|+|+++.++|+++++.+ ++||+|.++++++.. . ...|++|++|++||.+++.+++++.
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~~~--~------------~~~~~~G~~i~~kVi~id~~~~~i~ 64 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKS--S------------KSTYKEGQKVRARILYVDPSTKVVG 64 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCccC--c------------ccCcCCCCEEEEEEEEEeCCCCEEe
Confidence 7899999999999999999954 699999999974411 0 2379999999999999998776653
No 58
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.89 E-value=9e-08 Score=78.85 Aligned_cols=68 Identities=22% Similarity=0.328 Sum_probs=57.5
Q ss_pred cCCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
...|+++.|+|++++++|+||+++..+|++|.++++.+.. . +....|++||.|+++|.+++.+++++.
T Consensus 194 ~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~~~----~--------~~~~~~~vGd~VkvkVl~iD~e~~rI~ 261 (318)
T PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHI----E--------TPHSVFNVNDEMKVMIIDLDAERGRIS 261 (318)
T ss_pred CCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccccc----c--------ChhhccCCCCEEEEEEEEEeCCCCEEE
Confidence 4689999999999999999999987899999999985421 1 122489999999999999998877775
No 59
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.86 E-value=1.3e-08 Score=65.21 Aligned_cols=64 Identities=17% Similarity=0.320 Sum_probs=51.3
Q ss_pred CCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
|+++.|+|.++.++|+|++++. .+|++|.+++.+++.- +-...+++||.++++|.+++-+.+++
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~------------~~~~~~~~Gd~i~~~i~~~~~~~~~i 65 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIE------------NGEDEVKVGDEVEVYVLRVEDEEGNV 65 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccC------------CHhHcCCCCCEEEEEEEEEECCCCeE
Confidence 7899999999999999999976 5999999999754221 11237899999999999998544443
No 60
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.85 E-value=3.9e-08 Score=90.02 Aligned_cols=137 Identities=13% Similarity=0.187 Sum_probs=91.4
Q ss_pred EEEEEcCCCCCCCHHHHHHHHH--HhhhcceEeC--CeeEEEEEce-eceeCCeeEe------------------cCCCc
Q psy13107 9 HEILLHPRYFGPQLYETVKQKL--YSEVEGTCTG--KYGFVIAVTT-IDSIGAGLIQ------------------PGQGF 65 (170)
Q Consensus 9 ~~i~i~P~~l~~~~~~~i~~~l--~~~~~gk~~~--~~G~~i~i~~-i~~~~~g~I~------------------~~~g~ 65 (170)
..++++.+++..++.+.+.+.+ .+.+.|++.. ++|+++.+.. + +|+|. .|+ .
T Consensus 642 ~rIsLS~K~l~~~Pw~~~~~~~~vG~~v~G~V~~i~~~G~fV~l~~gV----~GlIh~sels~~~~~~~~~~~~kvGq-~ 716 (863)
T PRK12269 642 GRVSLGLKQVTANPWEEIEARYPVGARFTRRIVKVTNAGAFIEMEEGI----DGFLHVDDLSWVKRTRPADHELEVGK-E 716 (863)
T ss_pred CceEEEehhcccCchHHHHHhCCCCCEEEEEEEEEecceEEEEeCCCc----EEEEEhHHhhccccccchhhccCCCC-E
Confidence 4788888888777666665554 3667777754 7888887642 1 12222 111 1
Q ss_pred eEEeE------------EEEEEEe-------e-cCCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCC
Q psy13107 66 VVYPV------------KYRAIVF-------R-PFKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSN 124 (170)
Q Consensus 66 ~~~~v------------~f~~i~f-------~-p~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~ 124 (170)
+.++| ..+.+.- + ..+|++++|+|++++++|+||++++ ++|++|.++|++++..+..+
T Consensus 717 VkvkVl~ID~e~rrI~LS~K~l~~dpw~~~~~~~~vG~iV~GkV~~v~~~GvFVeL~~gVeGlI~~s~lsdd~~~~~~~- 795 (863)
T PRK12269 717 IECMVIECDPQARRIRLGVKQLSDNPWQVFANAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGE- 795 (863)
T ss_pred EEEEEEEEeccCCEEEEEecccccChHHHHHhhCCCCCEEEEEEEEEecCeEEEEcCCCeEEEEEHHHcCCcccccchh-
Confidence 11211 1111110 1 2479999999999999999999976 59999999999764221111
Q ss_pred CeEEEecCceeEEcCCCeEEEEEEEEEecCCceEE
Q psy13107 125 PVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFA 159 (170)
Q Consensus 125 ~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ 159 (170)
....|++||.|+|+|.+++.+++++..
T Consensus 796 --------~~~~f~vGD~V~v~Vl~iD~~~rkI~L 822 (863)
T PRK12269 796 --------ALRKYAVGDRVKAVIVDMNVKDRKVAF 822 (863)
T ss_pred --------hccccCCCCEEEEEEEEEEcCCCEEEE
Confidence 124799999999999999988777653
No 61
>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=2.2e-08 Score=67.55 Aligned_cols=78 Identities=18% Similarity=0.270 Sum_probs=59.1
Q ss_pred ecCCCCEEEEEEEEEecc--cEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecC
Q psy13107 78 RPFKGEVLDAVVTQVNKV--GMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDA 154 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~--Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 154 (170)
++..|+++.|+|+++.++ |+||++++. +||+|.+++.... |+... +-...++.||.|.|+|.......
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~-~~~v~--------~~~~~~~~Gd~v~VqV~~~~~~~ 74 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAY-FKKHK--------KIAKLLKEGQEILVQVVKEPIGT 74 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchh-ccccC--------CHHHcCCCCCEEEEEEEEecCCC
Confidence 467999999999999997 999999875 9999999986321 11111 11238999999999999988777
Q ss_pred CceEEEEEec
Q psy13107 155 SGIFAIGTLM 164 (170)
Q Consensus 155 ~~i~~ig~~~ 164 (170)
....+...+.
T Consensus 75 K~~~lt~~~~ 84 (88)
T cd04453 75 KGPRLTTNIS 84 (88)
T ss_pred CCceEEEEEE
Confidence 7666554443
No 62
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.80 E-value=1.2e-08 Score=83.41 Aligned_cols=68 Identities=9% Similarity=0.105 Sum_probs=55.8
Q ss_pred cCCCCEEEEEEEEEecccEEEEec---CeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCC
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIG---PLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDAS 155 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg---~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 155 (170)
|.+|+++.|+|+++.++|+||.|+ ..+||||.|.|.. .|. ++-...+++|++|.|+|.+++.+.+
T Consensus 15 P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~-----------~ri-~~i~d~vkvGd~v~vkVl~VD~ekg 82 (319)
T PTZ00248 15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSK-----------RRI-RSINKLIRVGRHEVVVVLRVDKEKG 82 (319)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcc-----------ccc-CCHHHhcCCCCEEEEEEEEEeCCCC
Confidence 568999999999999999999995 4699999999972 222 1223489999999999999988776
Q ss_pred ceE
Q psy13107 156 GIF 158 (170)
Q Consensus 156 ~i~ 158 (170)
++.
T Consensus 83 ~Id 85 (319)
T PTZ00248 83 YID 85 (319)
T ss_pred EEE
Confidence 654
No 63
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.80 E-value=7.4e-08 Score=83.35 Aligned_cols=68 Identities=18% Similarity=0.346 Sum_probs=56.1
Q ss_pred CCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFA 159 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ 159 (170)
..|+++.|+|++++++|+||.++..+||||.++|+... . ++-...+++||.|+++|.+++.+++++..
T Consensus 207 k~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~-----------v-~~~~~~~kvGd~V~vkVl~iD~e~~rI~L 274 (486)
T PRK07899 207 QKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKH-----------I-DHPSEVVEVGQEVTVEVLDVDMDRERVSL 274 (486)
T ss_pred cCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcc-----------c-CCHHHhcCCCCEEEEEEEEEECCCCEEEE
Confidence 37999999999999999999998889999999997321 1 11124799999999999999988777653
No 64
>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=98.79 E-value=3.8e-08 Score=62.67 Aligned_cols=63 Identities=21% Similarity=0.371 Sum_probs=49.9
Q ss_pred CCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
|++++|+|+++.++|++++++..+||+|.++|+.... .. ... .+|+.++++|.+++.+.+++.
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~g~~gfip~s~~~~~~~----~~-------~~~---~vG~~i~~~i~~vd~~~~~i~ 63 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPV----ED-------LDE---YVGKELKFKIIEIDRERNNIV 63 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCccc----CC-------hHH---hCCCEEEEEEEEEeCCCCEEE
Confidence 7899999999999999999966799999999974311 11 011 389999999999987666554
No 65
>PRK05054 exoribonuclease II; Provisional
Probab=98.78 E-value=4.6e-08 Score=87.40 Aligned_cols=85 Identities=19% Similarity=0.250 Sum_probs=66.4
Q ss_pred EEEEEeecCCCC--EEEEEEEEEecccEEEEecC--eeEEEEcCCCCCC---ceecCCCCCeEEEecCceeEEcCCCeEE
Q psy13107 72 YRAIVFRPFKGE--VLDAVVTQVNKVGMFAEIGP--LSCFISHHSIPTD---MQFCPNSNPVCYKSVHGEVVIQEDDEIR 144 (170)
Q Consensus 72 f~~i~f~p~~ge--v~~g~V~~i~~~Gifv~lg~--~~~~i~~~~l~~~---~~~d~~~~~~~~~~~~~~~~~~~Gd~Vr 144 (170)
+++.+++.+.|+ .++|.|++++++|+||++.. .+|+||.+.|+++ |.|+.++..-.+ .+++.|++||+|+
T Consensus 550 ~~~~y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~---~~~~~~~lGd~V~ 626 (644)
T PRK05054 550 LYARYLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQI---KGETVYKLGDVID 626 (644)
T ss_pred HHHHHHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccceEEE---eCCEEEcCCCEEE
Confidence 444467778865 99999999999999999965 4999999999886 445544432122 2336999999999
Q ss_pred EEEEEEEecCCceEE
Q psy13107 145 LKIVGTRVDASGIFA 159 (170)
Q Consensus 145 vrV~~v~~~~~~i~~ 159 (170)
|+|.+++..++++..
T Consensus 627 V~v~~vd~~~~~i~~ 641 (644)
T PRK05054 627 VTLAEVRMETRSIIA 641 (644)
T ss_pred EEEEEEccccCeEEE
Confidence 999999998887753
No 66
>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=98.77 E-value=5.5e-08 Score=63.85 Aligned_cols=61 Identities=16% Similarity=0.235 Sum_probs=52.4
Q ss_pred eecCCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCC
Q psy13107 77 FRPFKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDAS 155 (170)
Q Consensus 77 f~p~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 155 (170)
.....|+.++|+|++++++|+|+++.+ .+|++|.++++ ..++.||.++++|.++ .+++
T Consensus 12 ~~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~~--------------------~~~~iGd~v~v~I~~i-~e~~ 70 (77)
T cd04473 12 EDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLL--------------------RDYEVGDEVIVQVTDI-PENG 70 (77)
T ss_pred hhCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhcc--------------------CcCCCCCEEEEEEEEE-CCCC
Confidence 456789999999999999999999977 59999999863 1589999999999999 6666
Q ss_pred ceE
Q psy13107 156 GIF 158 (170)
Q Consensus 156 ~i~ 158 (170)
++.
T Consensus 71 ~i~ 73 (77)
T cd04473 71 NID 73 (77)
T ss_pred cEE
Confidence 654
No 67
>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=98.73 E-value=5.8e-08 Score=62.44 Aligned_cols=63 Identities=11% Similarity=0.185 Sum_probs=50.4
Q ss_pred CCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecC
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDA 154 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 154 (170)
|+++.|+|+++.++|++++++. ++|++|.++++++|. .. ++....|++||.|+++|.+++-++
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~--~~--------~~~~~~~~~Gd~i~~kVl~~d~~~ 64 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWP--DG--------KNPLSKFKIGQKIKARVIGGHDAK 64 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccc--cc--------cChhHhCCCCCEEEEEEEEEeCcc
Confidence 7899999999999999999976 599999999975531 01 111237899999999999997544
No 68
>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=98.69 E-value=9.1e-08 Score=85.46 Aligned_cols=85 Identities=16% Similarity=0.200 Sum_probs=67.9
Q ss_pred EEEEEeecCCCC--EEEEEEEEEecccEEEEecC--eeEEEEcCCCCC--C-ceecCCCCCeEEEecCceeEEcCCCeEE
Q psy13107 72 YRAIVFRPFKGE--VLDAVVTQVNKVGMFAEIGP--LSCFISHHSIPT--D-MQFCPNSNPVCYKSVHGEVVIQEDDEIR 144 (170)
Q Consensus 72 f~~i~f~p~~ge--v~~g~V~~i~~~Gifv~lg~--~~~~i~~~~l~~--~-~~~d~~~~~~~~~~~~~~~~~~~Gd~Vr 144 (170)
+.+.+++.++|+ .++|.|++++++|+||.+.. ++|+||.+.|++ + |.|++++..-.+.++ ..|++||+|+
T Consensus 546 ~~~~yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~---~~~~lgd~v~ 622 (639)
T TIGR02062 546 LYARFLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGE---TVYKIGDVID 622 (639)
T ss_pred HHHHHHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEecc---EEEecCCEEE
Confidence 344456778864 99999999999999999943 499999999987 5 778877653244443 3899999999
Q ss_pred EEEEEEEecCCceEE
Q psy13107 145 LKIVGTRVDASGIFA 159 (170)
Q Consensus 145 vrV~~v~~~~~~i~~ 159 (170)
|+|.+++.+.+++..
T Consensus 623 V~v~~vd~~~~~i~~ 637 (639)
T TIGR02062 623 VVLTEVRMETRSIIA 637 (639)
T ss_pred EEEEEeccccCcEee
Confidence 999999998887653
No 69
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=98.69 E-value=5e-08 Score=88.10 Aligned_cols=85 Identities=26% Similarity=0.392 Sum_probs=73.7
Q ss_pred EEEEEeecCCCCEEEEEEEEEecccEEEEecC--eeEEEEcCCCCCC-ceecCCCCCeEEEecCceeEEcCCCeEEEEEE
Q psy13107 72 YRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGP--LSCFISHHSIPTD-MQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIV 148 (170)
Q Consensus 72 f~~i~f~p~~gev~~g~V~~i~~~Gifv~lg~--~~~~i~~~~l~~~-~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~ 148 (170)
.+|-+++-++|++++|+|++++.+|+||.+.. ++|+||.+.|+++ |.|++..+ .+.++.++..++.||.|+|++.
T Consensus 613 ~~~~~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~--~l~~~~~~~~~~lgd~v~v~v~ 690 (706)
T COG0557 613 LKAEYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHFDERGQ--ALVGEKSGKVYRLGDEVKVKVT 690 (706)
T ss_pred HHHHHHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeeeccccc--eeeccccccccccCCEEEEEEE
Confidence 34445677899999999999999999999966 3999999999988 88988765 6778888899999999999999
Q ss_pred EEEecCCceE
Q psy13107 149 GTRVDASGIF 158 (170)
Q Consensus 149 ~v~~~~~~i~ 158 (170)
+++.+.+++-
T Consensus 691 ~v~~~~~~i~ 700 (706)
T COG0557 691 SVDLDERKID 700 (706)
T ss_pred EEcccccceE
Confidence 9998777653
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=98.67 E-value=2.7e-07 Score=58.90 Aligned_cols=62 Identities=15% Similarity=0.326 Sum_probs=51.7
Q ss_pred CCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFA 159 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ 159 (170)
..|++++|+|.++++.|+|+.++..+|++|.+++.. . ..+++||+|++.|.+++-+.+...+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~------~------------~~~~~Gd~v~v~v~~v~~~~~~~~i 63 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIP------G------------ESYRPGDRIKAYVLEVRKTSKGPQI 63 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCC------C------------CcCCCCCEEEEEEEEEecCCCCCEE
Confidence 579999999999999999999988899999988751 0 1569999999999999865554443
No 71
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.65 E-value=1e-07 Score=76.48 Aligned_cols=69 Identities=17% Similarity=0.261 Sum_probs=56.7
Q ss_pred ecCCCCEEEEEEEEEecccEEEEecC---eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecC
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEIGP---LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDA 154 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~lg~---~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 154 (170)
-|.+|+++.|+|+++.++|+||++.. .+||+|.+++++++. . +-...+++||.|+++|.+++.++
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i----~--------~i~~~~kvGd~V~vkVi~VD~~k 72 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWV----K--------NIRDHVKEGQKVVCKVIRVDPRK 72 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccc----c--------CHHHhCCCCCEEEEEEEEEeccc
Confidence 38899999999999999999999963 599999999985521 0 11238899999999999999877
Q ss_pred CceE
Q psy13107 155 SGIF 158 (170)
Q Consensus 155 ~~i~ 158 (170)
+.+.
T Consensus 73 ~~I~ 76 (262)
T PRK03987 73 GHID 76 (262)
T ss_pred CeEE
Confidence 7654
No 72
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.64 E-value=5.4e-08 Score=84.49 Aligned_cols=68 Identities=21% Similarity=0.274 Sum_probs=58.1
Q ss_pred CCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
.+|+.+.|+|++++++|+|+++.+. +||+|.|+|. |..... -..+++.||+|.|+|.+++.++++++
T Consensus 276 ~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEis-----------w~~~~~-P~evv~~Gq~V~V~Vl~id~e~rRIs 343 (541)
T COG0539 276 PVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEIS-----------WTKKNV-PSEVVKVGQEVEVKVLDIDPERRRIS 343 (541)
T ss_pred CCCCEEEEEEEEeecCcEEEEecCCccceeechhhc-----------ccccCC-HHHhcccCCEEEEEEEeeCchhceEE
Confidence 5899999999999999999999886 9999999997 222222 23489999999999999999999887
Q ss_pred E
Q psy13107 159 A 159 (170)
Q Consensus 159 ~ 159 (170)
+
T Consensus 344 L 344 (541)
T COG0539 344 L 344 (541)
T ss_pred e
Confidence 5
No 73
>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=98.59 E-value=2.3e-07 Score=57.52 Aligned_cols=61 Identities=16% Similarity=0.305 Sum_probs=49.0
Q ss_pred EEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 85 LDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 85 ~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
++|+|+++.++|+|+.++.. +|++|.+++++++. .+....+++||.|+++|.+++.+++.+
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~~~------------~~~~~~~~~G~~v~~~v~~~d~~~~~i 62 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFV------------KDPSEVFKVGDEVEVKVLEVDPEKGRI 62 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCccc------------cCHhhEeCCCCEEEEEEEEEcCCcCEE
Confidence 47999999999999999864 99999999985521 111247999999999999998765554
No 74
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.59 E-value=7.3e-07 Score=70.53 Aligned_cols=82 Identities=17% Similarity=0.156 Sum_probs=63.8
Q ss_pred eecCCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCce-ecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecC
Q psy13107 77 FRPFKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQ-FCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDA 154 (170)
Q Consensus 77 f~p~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~-~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 154 (170)
+.|.+|+++.|+|++++++|++++++. ++|++|.+++...+. .|. .+....+++||.|++||.+++-+.
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~---------~~~~~~~~~GDlV~akV~~i~~~~ 129 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEG---------TDLRKYLDIGDYIIAKVKDVDRTR 129 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccch---------hhhHhhCCCCCEEEEEEEEECCCC
Confidence 889999999999999999999999985 699999999974321 111 112347999999999999997432
Q ss_pred CceEEEEEecCCCCCC
Q psy13107 155 SGIFAIGTLMDDYLGL 170 (170)
Q Consensus 155 ~~i~~ig~~~~~~LG~ 170 (170)
.+.. |+.+++||.
T Consensus 130 -~~~L--S~k~~~lG~ 142 (235)
T PRK04163 130 -DVVL--TLKGKGLGK 142 (235)
T ss_pred -cEEE--EEcCCCCCc
Confidence 3334 667888884
No 75
>PHA02945 interferon resistance protein; Provisional
Probab=98.58 E-value=6.6e-07 Score=59.52 Aligned_cols=65 Identities=14% Similarity=0.220 Sum_probs=52.2
Q ss_pred ecCCCCEEEEEEEEEecccEEEEecC---eeEEEEcCCC--CCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEe
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEIGP---LSCFISHHSI--PTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRV 152 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~lg~---~~~~i~~~~l--~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 152 (170)
-|..||++.|+|.. .++|+|+.|.. .+||+|.|.. .+. |.-. ..++ .|++|.+||..+|.
T Consensus 8 ~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~-----------wvK~--rd~l-~GqkvV~KVirVd~ 72 (88)
T PHA02945 8 LPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNR-----------YFKY--RDKL-VGKTVKVKVIRVDY 72 (88)
T ss_pred CCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccc-----------eEee--eeEe-cCCEEEEEEEEECC
Confidence 59999999999999 99999999954 4999999955 422 3322 2377 99999999999987
Q ss_pred cCCce
Q psy13107 153 DASGI 157 (170)
Q Consensus 153 ~~~~i 157 (170)
.++.+
T Consensus 73 ~kg~I 77 (88)
T PHA02945 73 TKGYI 77 (88)
T ss_pred CCCEE
Confidence 76654
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=98.58 E-value=1.4e-07 Score=65.17 Aligned_cols=74 Identities=12% Similarity=0.118 Sum_probs=53.3
Q ss_pred CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCce-ecCCC----CCe--EEEecCceeEEcCCCeEEEEEEEEE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQ-FCPNS----NPV--CYKSVHGEVVIQEDDEIRLKIVGTR 151 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~-~d~~~----~~~--~~~~~~~~~~~~~Gd~VrvrV~~v~ 151 (170)
.+|+++.|+|++++++|+|+.+++ .+|++|.+++.++|. +.++. +.- .-...+-...|++||.|+++|.+++
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 479999999999999999999976 599999999986531 10000 000 0001111247999999999999998
Q ss_pred ec
Q psy13107 152 VD 153 (170)
Q Consensus 152 ~~ 153 (170)
.+
T Consensus 82 ~~ 83 (100)
T cd05693 82 KS 83 (100)
T ss_pred CC
Confidence 75
No 77
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.57 E-value=1.1e-07 Score=84.94 Aligned_cols=68 Identities=21% Similarity=0.355 Sum_probs=61.6
Q ss_pred CCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
+.|++++|+|+++..||+||.+|-. +|+||.|++.+.|.+++.+ +++.||.|.|+|.+++..++++.
T Consensus 657 k~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~------------vv~vGdiV~v~V~~vD~~r~rI~ 724 (780)
T COG2183 657 KPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNE------------VVKVGDIVKVKVIEVDTARKRIA 724 (780)
T ss_pred cCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHH------------hcccCCEEEEEEEEEecccCeee
Confidence 6899999999999999999999997 9999999999878777632 88999999999999999888776
Q ss_pred E
Q psy13107 159 A 159 (170)
Q Consensus 159 ~ 159 (170)
.
T Consensus 725 L 725 (780)
T COG2183 725 L 725 (780)
T ss_pred e
Confidence 4
No 78
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.55 E-value=2.6e-07 Score=70.77 Aligned_cols=78 Identities=14% Similarity=0.122 Sum_probs=59.4
Q ss_pred EEeecCCCCEEEEEEEEEecccEEEEec-----------CeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeE
Q psy13107 75 IVFRPFKGEVLDAVVTQVNKVGMFAEIG-----------PLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEI 143 (170)
Q Consensus 75 i~f~p~~gev~~g~V~~i~~~Gifv~lg-----------~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V 143 (170)
....|.+|+++.|+|+++.++|++|+++ +++|++|.+++.++.. . +-...+++||.|
T Consensus 58 ~~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~----~--------~~~~~~~~GD~V 125 (189)
T PRK09521 58 TPPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYV----E--------SLTDAFKIGDIV 125 (189)
T ss_pred CCCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhh----h--------hHHhccCCCCEE
Confidence 3467889999999999999999999995 3589999999874311 1 112378999999
Q ss_pred EEEEEEEEecCCceEEEEEecCCCCC
Q psy13107 144 RLKIVGTRVDASGIFAIGTLMDDYLG 169 (170)
Q Consensus 144 rvrV~~v~~~~~~i~~ig~~~~~~LG 169 (170)
++||.+++ +++.. |+.++.||
T Consensus 126 ~akV~~i~---~~i~L--S~k~~~lG 146 (189)
T PRK09521 126 RAKVISYT---DPLQL--STKGKDLG 146 (189)
T ss_pred EEEEEecC---CcEEE--EEecCCce
Confidence 99999986 33333 55666666
No 79
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.49 E-value=4.9e-07 Score=78.57 Aligned_cols=69 Identities=19% Similarity=0.251 Sum_probs=55.7
Q ss_pred CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
..|+++.|+|+++.++|+||++++ .+||+|.++|+.. . ...+-...+++||.|+|+|.+++.+.+++.
T Consensus 291 ~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~----~-------~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~ 359 (491)
T PRK13806 291 KAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWT----R-------RVNKPEDVVAPGDAVAVKIKDIDPAKRRIS 359 (491)
T ss_pred CCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcc----c-------ccCCHHHcCCCCCEEEEEEEEEEccCCEEE
Confidence 479999999999999999999986 5999999999721 0 011223479999999999999998877765
Q ss_pred E
Q psy13107 159 A 159 (170)
Q Consensus 159 ~ 159 (170)
.
T Consensus 360 L 360 (491)
T PRK13806 360 L 360 (491)
T ss_pred E
Confidence 3
No 80
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=98.48 E-value=5.1e-07 Score=78.46 Aligned_cols=136 Identities=18% Similarity=0.300 Sum_probs=86.9
Q ss_pred EEEEcCCCCCCCHHHHHHHHHH--hhhcceEeC--CeeEEEEEce-e------ceeCC-eeE-------ecCCCceEEeE
Q psy13107 10 EILLHPRYFGPQLYETVKQKLY--SEVEGTCTG--KYGFVIAVTT-I------DSIGA-GLI-------QPGQGFVVYPV 70 (170)
Q Consensus 10 ~i~i~P~~l~~~~~~~i~~~l~--~~~~gk~~~--~~G~~i~i~~-i------~~~~~-g~I-------~~~~g~~~~~v 70 (170)
++.++.+.+..++.+.+.+.+. +.+.|++.. +.|+++.+.. + .+++. ..+ ..|+ .+.++|
T Consensus 270 ri~lS~K~~~~~p~~~~~~~~~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd-~v~vkV 348 (491)
T PRK13806 270 RISLSIKQAGGDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGD-AVAVKI 348 (491)
T ss_pred EEEEEehhhhcccchhhhccCCCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCC-EEEEEE
Confidence 4667776665655555555543 667777754 7888886642 1 11111 111 1111 122222
Q ss_pred ------------EEEEEEeec--------CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEE
Q psy13107 71 ------------KYRAIVFRP--------FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYK 129 (170)
Q Consensus 71 ------------~f~~i~f~p--------~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~ 129 (170)
..+...-.| .+|++++|+|+++.++|+||++.+ ++||+|.++++++. ..
T Consensus 349 l~iD~e~~ri~Ls~K~~~~~p~~~~~~~~~vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~~----~~------ 418 (491)
T PRK13806 349 KDIDPAKRRISLSLRDAEGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAG----KP------ 418 (491)
T ss_pred EEEEccCCEEEEEEeecccChhHHhhhhCCCCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCccc----cc------
Confidence 111111122 379999999999999999999976 59999999998431 11
Q ss_pred ecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 130 SVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 130 ~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
+....++.||+|+++|.+++.++++++
T Consensus 419 --~~~~~~~~Gd~v~~~V~~id~e~~ri~ 445 (491)
T PRK13806 419 --ATYEKLKPGDSVTLVVEEIDTAKRKIS 445 (491)
T ss_pred --chhhcCCCCCEEEEEEEEEeCCCCEEE
Confidence 112378999999999999998887765
No 81
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.47 E-value=6.9e-07 Score=77.41 Aligned_cols=67 Identities=18% Similarity=0.309 Sum_probs=56.1
Q ss_pred CCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEE
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFA 159 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ 159 (170)
+|+++.|+|+++.++|+||++.+ ++||+|.++|+++.. . .....|++||+|+|+|.+++.+++++..
T Consensus 293 vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v----~--------~~~~~~kvGd~V~VkIi~ID~e~rrI~L 360 (486)
T PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHV----E--------VPEQVVQVGDEVFVKVIDIDLERRRISL 360 (486)
T ss_pred CCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccc----c--------CccceeCCCCEEEEEEEEEECCCCEEEE
Confidence 79999999999999999999975 599999999985421 1 1124899999999999999988887763
No 82
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.43 E-value=7e-07 Score=75.36 Aligned_cols=68 Identities=16% Similarity=0.348 Sum_probs=55.8
Q ss_pred cCCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
...|++++|+|++++++|+|+.++..+||+|.++++.++. ++-...+++||.|+++|.+++.+++++.
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~------------~~~~~~~~vGd~i~~~Vl~vd~~~~~i~ 257 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERV------------EKPSEVVSVGQEVEVKVLSIDWETERIS 257 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCcccc------------CCHHHhcCCCCEEEEEEEEEeCCCCEEE
Confidence 4689999999999999999999987899999999984311 1112378999999999999987766654
No 83
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=98.39 E-value=9.7e-07 Score=81.04 Aligned_cols=69 Identities=14% Similarity=0.251 Sum_probs=55.6
Q ss_pred CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
.+|++++|+|++++++|+||++++ .+||||.++|. |... .+.....|++||.|+++|.++|.+++++.
T Consensus 664 ~vG~~v~G~V~~i~~~G~fV~l~~gV~GlIh~sels----~~~~-------~~~~~~~~kvGq~VkvkVl~ID~e~rrI~ 732 (863)
T PRK12269 664 PVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLS----WVKR-------TRPADHELEVGKEIECMVIECDPQARRIR 732 (863)
T ss_pred CCCCEEEEEEEEEecceEEEEeCCCcEEEEEhHHhh----cccc-------ccchhhccCCCCEEEEEEEEEeccCCEEE
Confidence 479999999999999999999976 59999999885 2111 11112379999999999999999888765
Q ss_pred E
Q psy13107 159 A 159 (170)
Q Consensus 159 ~ 159 (170)
.
T Consensus 733 L 733 (863)
T PRK12269 733 L 733 (863)
T ss_pred E
Confidence 4
No 84
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.32 E-value=2e-06 Score=70.87 Aligned_cols=68 Identities=15% Similarity=0.271 Sum_probs=55.2
Q ss_pred ecCCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCc
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASG 156 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~ 156 (170)
+...|+++.|+|.++.+.|++|.+|.. +||+|.++++.++.-+ ....+++||.|+|+|.+++-+.++
T Consensus 28 ~~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~------------~~~~~~~G~~v~~~Vi~~~~~~~~ 95 (318)
T PRK07400 28 HFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEG------------PEEVLQPNETREFFILSDENEDGQ 95 (318)
T ss_pred hcCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccC------------HHHccCCCCEEEEEEEEEeCCCCe
Confidence 358899999999999999999999985 9999999997543211 113789999999999998766554
Q ss_pred e
Q psy13107 157 I 157 (170)
Q Consensus 157 i 157 (170)
+
T Consensus 96 i 96 (318)
T PRK07400 96 L 96 (318)
T ss_pred E
Confidence 4
No 85
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.31 E-value=1.6e-06 Score=76.50 Aligned_cols=68 Identities=16% Similarity=0.295 Sum_probs=55.8
Q ss_pred CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
..|+++.|+|++++++|+||+++. .+|++|.++|+.++. .++....|++||.|+++|.+++.+.+++.
T Consensus 372 ~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~-----------~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ 440 (565)
T PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKK-----------GEEAVELYKKGDEVEAVVLKVDVEKERIS 440 (565)
T ss_pred CCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCcccc-----------ccChHhhCCCCCEEEEEEEEEeCCCCEEE
Confidence 479999999999999999999985 699999999984321 12223489999999999999998777664
No 86
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=98.31 E-value=2e-06 Score=74.99 Aligned_cols=68 Identities=16% Similarity=0.262 Sum_probs=55.6
Q ss_pred CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
.+|+++.|+|++++++|+||++++ .+||+|.++|+.++.. ......+++||.|.++|.+++.+.+++.
T Consensus 358 ~~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~-----------~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ 426 (516)
T TIGR00717 358 PVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDG-----------READHLYKKGDEIEAVVLAVDKEKKRIS 426 (516)
T ss_pred CCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccC-----------CCHhHccCCCCEEEEEEEEEeCcCCEEE
Confidence 379999999999999999999986 5999999999844221 1112489999999999999998777654
No 87
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.28 E-value=3.2e-06 Score=74.61 Aligned_cols=68 Identities=19% Similarity=0.376 Sum_probs=55.5
Q ss_pred cCCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
...|++++|+|+++.++|+||.++..+|++|.++++.+ ... +-...+++||.|+++|.+++.+.+++.
T Consensus 199 l~~G~iv~g~V~~v~~~G~~V~i~g~~glv~~se~s~~----~~~--------~~~~~~kvG~~v~v~V~~~d~~~~~i~ 266 (565)
T PRK06299 199 LEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWK----RVN--------HPSEVVNVGDEVKVKVLKFDKEKKRVS 266 (565)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEECCEEEEEEHHHhccc----ccC--------CHhhcCCCCCEEEEEEEEEeCCCCeEE
Confidence 46899999999999999999999977999999999632 111 112368999999999999987777654
No 88
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=98.24 E-value=5.1e-06 Score=70.14 Aligned_cols=68 Identities=19% Similarity=0.392 Sum_probs=55.4
Q ss_pred CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
.+|+++.|+|+++.++|+||++.+ ++|++|.++++++.. . +....|+.||.|+++|.+++.+.+++.
T Consensus 276 ~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~----~--------~~~~~~~~Gd~v~v~V~~id~e~~~i~ 343 (390)
T PRK06676 276 PEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHI----A--------TPSEVLEEGQEVKVKVLEVNEEEKRIS 343 (390)
T ss_pred cCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCcccc----C--------ChhhccCCCCEEEEEEEEEECCCCEEE
Confidence 479999999999999999999975 599999999974311 1 112378999999999999998777665
Q ss_pred E
Q psy13107 159 A 159 (170)
Q Consensus 159 ~ 159 (170)
.
T Consensus 344 l 344 (390)
T PRK06676 344 L 344 (390)
T ss_pred E
Confidence 3
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=98.24 E-value=4.1e-06 Score=73.10 Aligned_cols=67 Identities=19% Similarity=0.297 Sum_probs=56.4
Q ss_pred CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
.+|+++.|+|++++++|+||.++. .+|++|.+++++++. ++....|+.||.++++|.+++.+.+++.
T Consensus 445 ~~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~~~------------~~~~~~~~~Gd~v~~~V~~id~~~~~i~ 512 (516)
T TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRD------------EDKTDEIKVGDEVEAKVVDIDKKNRKVS 512 (516)
T ss_pred CcceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCcccc------------ccccccCCCCCEEEEEEEEEeCCCCEEE
Confidence 479999999999999999999987 599999999985531 1123489999999999999998877765
No 90
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.23 E-value=3.3e-06 Score=72.87 Aligned_cols=67 Identities=19% Similarity=0.315 Sum_probs=56.5
Q ss_pred CCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFA 159 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ 159 (170)
..|+++.|+|.++++.|++|.+|..++|+|.+++. +. ..|++||+|++.|.+++.+++...+
T Consensus 133 ~~GeIV~G~V~ri~~~giiVDLggvea~LP~sE~i------p~------------E~~~~GdrIka~I~~Vd~~~kg~qI 194 (470)
T PRK09202 133 RVGEIITGVVKRVERGNIIVDLGRAEAILPRKEQI------PR------------ENFRPGDRVRAYVYEVRKEARGPQI 194 (470)
T ss_pred hcCCEEEEEEEEEecCCEEEEECCeEEEecHHHcC------CC------------ccCCCCCEEEEEEEEEecCCCCCeE
Confidence 48999999999999999999999889999999874 11 2779999999999999987776665
Q ss_pred EEEec
Q psy13107 160 IGTLM 164 (170)
Q Consensus 160 ig~~~ 164 (170)
+=|-.
T Consensus 195 ilSRt 199 (470)
T PRK09202 195 ILSRT 199 (470)
T ss_pred EEEeC
Confidence 54443
No 91
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=98.20 E-value=1.1e-06 Score=69.50 Aligned_cols=67 Identities=19% Similarity=0.296 Sum_probs=54.8
Q ss_pred cCCCCEEEEEEEEEecccEEEEec---CeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCC
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIG---PLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDAS 155 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg---~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 155 (170)
|..||++-|+|.+|.++|+|+.|. ..+||+|.|.+...+. ++-..+++.|+++-++|.+||..++
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wV------------knIrd~vkegqkvV~kVlrVd~~rg 76 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWV------------KNIRDYVKEGQKVVAKVLRVDPKRG 76 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHH------------HHHHHHhhcCCeEEEEEEEEcCCCC
Confidence 889999999999999999999995 3599999999974421 1112389999999999999987665
Q ss_pred ce
Q psy13107 156 GI 157 (170)
Q Consensus 156 ~i 157 (170)
.+
T Consensus 77 ~I 78 (269)
T COG1093 77 HI 78 (269)
T ss_pred eE
Confidence 43
No 92
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.19 E-value=5e-06 Score=69.55 Aligned_cols=71 Identities=11% Similarity=0.203 Sum_probs=57.7
Q ss_pred ecCCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
++..|+++.|+|.+..+.|+++.+|..++++|.+++.+ +..|++||.+++.|.+++.+++..
T Consensus 131 ~~k~GeiV~G~V~~~~~~~~~Vdlg~vEa~LP~~E~ip------------------~e~~~~Gd~Ika~V~~V~~~~kgp 192 (362)
T PRK12327 131 SEREGDIVTGVVQRRDNRFVYVNLGKIEAVLPPAEQIP------------------GETYKHGDRIKVYVVKVEKTTKGP 192 (362)
T ss_pred HHhcCCEEEEEEEEEeCCcEEEEeCCeEEEecHHHcCC------------------CCCCCCCCEEEEEEEEEecCCCCC
Confidence 33699999999999999999999998999999655421 126899999999999999888777
Q ss_pred EEEEEecCC
Q psy13107 158 FAIGTLMDD 166 (170)
Q Consensus 158 ~~ig~~~~~ 166 (170)
.++=|-..|
T Consensus 193 ~IivSRt~p 201 (362)
T PRK12327 193 QIFVSRTHP 201 (362)
T ss_pred eEEEEeCCH
Confidence 666555443
No 93
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.17 E-value=6.7e-06 Score=73.76 Aligned_cols=67 Identities=21% Similarity=0.309 Sum_probs=55.8
Q ss_pred CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
..|+++.|+|++++++|+|+.+++ .+||+|.++++++.. ++....|++||.|+++|.+++.+++++.
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~------------~~~~~~~kvGd~V~vkV~~id~e~~rI~ 628 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRI------------DKPEDVLSEGEEVKAKILEVDPEEKRIR 628 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCcccc------------CCHhhcCCCCCEEEEEEEEEeCCCCEEE
Confidence 479999999999999999999976 599999999984421 1122378999999999999998877765
No 94
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.14 E-value=6.5e-06 Score=73.88 Aligned_cols=67 Identities=19% Similarity=0.341 Sum_probs=54.5
Q ss_pred CCCCEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
..|+++.|+|+++.++|+|+.++..+||+|.+++++++. . +-...|++||.|+++|.+++.+++++.
T Consensus 476 ~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~~~----~--------~~~~~~~vGd~V~vkV~~id~~~~~I~ 542 (647)
T PRK00087 476 EEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRV----E--------KPSDVLKVGDEIKVYILDIDKENKKLS 542 (647)
T ss_pred CCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCcccc----C--------CHHHhcCCCCEEEEEEEEEECCCCEEE
Confidence 479999999999999999999976799999999974321 1 112378999999999999987666554
No 95
>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=98.11 E-value=2.2e-05 Score=52.60 Aligned_cols=81 Identities=15% Similarity=0.156 Sum_probs=63.0
Q ss_pred eecCCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecC-
Q psy13107 77 FRPFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDA- 154 (170)
Q Consensus 77 f~p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~- 154 (170)
|.|..|+.+-|+|++++....+|.++.. .+++|.+.++.- .+++...+++||.|-.||.+++.+.
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-------------TKRNRPNLNVGDLVYARVVKANRDME 68 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccc-------------cccccccCCCCCEEEEEEEecCCCCC
Confidence 6799999999999999999999999764 899988776421 1223458999999999999997542
Q ss_pred CceEEEEEec-CCCCCC
Q psy13107 155 SGIFAIGTLM-DDYLGL 170 (170)
Q Consensus 155 ~~i~~ig~~~-~~~LG~ 170 (170)
-.+.|+.+.. ..|||+
T Consensus 69 ~eLtc~~~~~k~~g~G~ 85 (86)
T cd05790 69 PELSCVDSSGKADGFGP 85 (86)
T ss_pred eEEEEeCCCCccccccc
Confidence 2456766443 678885
No 96
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.11 E-value=1.6e-05 Score=53.98 Aligned_cols=80 Identities=20% Similarity=0.201 Sum_probs=59.8
Q ss_pred eecCCCCEEEEEEEEEecccEEEEe--------c-CeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEE
Q psy13107 77 FRPFKGEVLDAVVTQVNKVGMFAEI--------G-PLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKI 147 (170)
Q Consensus 77 f~p~~gev~~g~V~~i~~~Gifv~l--------g-~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV 147 (170)
+.|.+|+++.|+|++++...+.+++ . ++.|++|.+++.+.+. ++.+ -...|++||.|+.||
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~-d~~~---------~~~~f~~GDiV~AkV 71 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEK-DKVE---------MYKCFRPGDIVRAKV 71 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHcccccc-chHH---------HHhhcCCCCEEEEEE
Confidence 4689999999999999999999998 4 3589999998863211 1111 123899999999999
Q ss_pred EEEEecCCceEEEEEecCCCCC
Q psy13107 148 VGTRVDASGIFAIGTLMDDYLG 169 (170)
Q Consensus 148 ~~v~~~~~~i~~ig~~~~~~LG 169 (170)
.+..- ...+.. |+.++.||
T Consensus 72 is~~~-~~~~~L--st~~~~lG 90 (92)
T cd05791 72 ISLGD-ASSYYL--STAENELG 90 (92)
T ss_pred EEcCC-CCCcEE--EecCCCCc
Confidence 99742 234444 78888888
No 97
>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=97.97 E-value=2.4e-05 Score=65.06 Aligned_cols=70 Identities=20% Similarity=0.306 Sum_probs=56.7
Q ss_pred cCCCCEEEEEEEEEeccc-EEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 79 PFKGEVLDAVVTQVNKVG-MFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~G-ifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
...|+++.|+|.++++.| +++.+|..+|++|.+++.. . ..|++||++++.|.+++.+++..
T Consensus 129 ~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP~~E~ip------~------------E~~~~Gd~ik~~V~~V~~~~kg~ 190 (341)
T TIGR01953 129 SKEGEIISGTVKRVNRRGNLYVELGKTEGILPKKEQIP------G------------EKFRIGDRIKAYVYEVRKTAKGP 190 (341)
T ss_pred hhcCCEEEEEEEEEecCCcEEEEECCeEEEecHHHcCC------C------------cCCCCCCEEEEEEEEEEcCCCCC
Confidence 359999999999999988 6999987899999887641 1 14899999999999999877666
Q ss_pred EEEEEecCC
Q psy13107 158 FAIGTLMDD 166 (170)
Q Consensus 158 ~~ig~~~~~ 166 (170)
.++=|-..|
T Consensus 191 qIivSRt~~ 199 (341)
T TIGR01953 191 QIILSRTHP 199 (341)
T ss_pred eEEEEeCcH
Confidence 665555443
No 98
>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=97.96 E-value=0.0025 Score=45.96 Aligned_cols=149 Identities=16% Similarity=0.238 Sum_probs=100.0
Q ss_pred EEEEEEEEcCCCCCCCHHHHHHHHHHhhhcceEeCCeeEEEEEceecee---CCeeEecCCCceEEeEEEEEEEeecCCC
Q psy13107 6 SLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSI---GAGLIQPGQGFVVYPVKYRAIVFRPFKG 82 (170)
Q Consensus 6 ~~~~~i~i~P~~l~~~~~~~i~~~l~~~~~gk~~~~~G~~i~i~~i~~~---~~g~I~~~~g~~~~~v~f~~i~f~p~~g 82 (170)
+.--.|.+.|++|+-++.+.|++...++|..|- ..|+.-.-++|..- .=|.|. ...+..+|-....+-.-+.|
T Consensus 7 ~vYLpV~l~PhELtLd~~~Ni~~aV~~eYLhkE--~~G~MakkIei~~d~~lPLGeiv--NN~ivv~VPC~vtykyYk~G 82 (160)
T PF03293_consen 7 NVYLPVTLQPHELTLDIRKNIKDAVYREYLHKE--SGGIMAKKIEICEDKELPLGEIV--NNHIVVKVPCNVTYKYYKVG 82 (160)
T ss_pred eeEEEEecCcceeeehHHHhHHHHHHHHHhhhc--ccCceeeeEEEEeccccchHhhc--ccEEEEEeeeEEEEEEEeeC
Confidence 345568899999999999999998888887664 35665555554321 125555 33455555444444456899
Q ss_pred CEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE-EEE
Q psy13107 83 EVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF-AIG 161 (170)
Q Consensus 83 ev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~-~ig 161 (170)
+++.|+..--++.-++|.+|.+-.-+..++ ....|+..+ ++|.-+ +..|..|++|.+-+.+.+--....+ -.|
T Consensus 83 DvV~GtLnIedESni~V~CgDLiCkl~rds--GtVSf~dsK--YCfirN--g~vY~ngs~Vsv~LkEaq~g~~S~FvFla 156 (160)
T PF03293_consen 83 DVVRGTLNIEDESNITVQCGDLICKLSRDS--GTVSFNDSK--YCFIRN--GVVYDNGSEVSVVLKEAQQGMESNFVFLA 156 (160)
T ss_pred CEEEEEEEecccCceEEEcCcEEEEeeccC--CeEEecCce--EEEEEC--CEEecCCCEEEEEehhhhcCCcceEEEEE
Confidence 999999999999999999987544443332 225565444 366533 4699999999999988765433333 456
Q ss_pred Eec
Q psy13107 162 TLM 164 (170)
Q Consensus 162 ~~~ 164 (170)
++.
T Consensus 157 ~I~ 159 (160)
T PF03293_consen 157 SII 159 (160)
T ss_pred Eec
Confidence 654
No 99
>KOG1067|consensus
Probab=97.70 E-value=9.1e-06 Score=70.48 Aligned_cols=64 Identities=16% Similarity=0.330 Sum_probs=52.3
Q ss_pred CCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCc
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASG 156 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~ 156 (170)
.|-++.|+|+++.+.|+||++-|. .+++|.++|.+. |..+-+. .+++|+.|.|+..+.|...+.
T Consensus 668 ~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL~~e-----------~iakpsd-~levGq~I~vk~ie~d~~g~~ 732 (760)
T KOG1067|consen 668 FGGVYTATITEIRDTGVMVELYPMQQGLLHNSQLDQE-----------KIAKPSD-LLEVGQEIQVKYIERDPRGGI 732 (760)
T ss_pred eeeEEEEEEeeecccceEEEecCCchhhccchhcccc-----------cccChHH-HHhhcceeEEEEEeecCccce
Confidence 566789999999999999999888 999999999744 3333333 499999999999999865443
No 100
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.54 E-value=0.00062 Score=53.58 Aligned_cols=84 Identities=21% Similarity=0.268 Sum_probs=63.4
Q ss_pred EeecCCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecC
Q psy13107 76 VFRPFKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDA 154 (170)
Q Consensus 76 ~f~p~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 154 (170)
-|.|..|+++-|+|..+.+.+..|+++. ..+++|.|+++.- .++.. .++...++++||.|-.||.+++-+
T Consensus 59 ~YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r-~~~~~-------~~~~r~~l~vGD~v~AkV~~vd~~- 129 (239)
T COG1097 59 RYIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRR-KFENA-------EKDLRPFLNVGDLVYAKVVDVDRD- 129 (239)
T ss_pred cccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcc-ccccc-------ccccccccccCCEEEEEEEEccCC-
Confidence 5889999999999999999999999976 6999999998533 11111 123345999999999999998642
Q ss_pred CceEEEEEecCCCCCC
Q psy13107 155 SGIFAIGTLMDDYLGL 170 (170)
Q Consensus 155 ~~i~~ig~~~~~~LG~ 170 (170)
....+ ++.+.+||+
T Consensus 130 ~~~~L--~~k~~~~Gk 143 (239)
T COG1097 130 GEVEL--TLKDEGLGK 143 (239)
T ss_pred CceEE--EeecCCCcc
Confidence 23333 447788774
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=97.48 E-value=0.00041 Score=59.19 Aligned_cols=86 Identities=14% Similarity=0.204 Sum_probs=59.0
Q ss_pred ecCCCCEEEEEEEEEecc--cEEEEecCe-eEEEEcCCCCCCceecCC-CCCeEEEecCceeEEcCCCeEEEEEEEEEec
Q psy13107 78 RPFKGEVLDAVVTQVNKV--GMFAEIGPL-SCFISHHSIPTDMQFCPN-SNPVCYKSVHGEVVIQEDDEIRLKIVGTRVD 153 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~--Gifv~lg~~-~~~i~~~~l~~~~~~d~~-~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 153 (170)
++.+|.+|.|+|.++.+. |+||++|.- +||+|.+++..++.+... ... .-...+-...++.||+|.|+|..--..
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~-~~~~~~i~~~l~~G~~IlVQV~Ke~~~ 100 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAK-REAGPSISELLRPGQSVLVQVVKEPRG 100 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhcccccccc-ccccCCHHHhCcCCCEEEEEEeeCCcC
Confidence 457999999999999999 999999986 999999999654321111 000 000001112689999999999996655
Q ss_pred CCceEEEEEec
Q psy13107 154 ASGIFAIGTLM 164 (170)
Q Consensus 154 ~~~i~~ig~~~ 164 (170)
+....+.+.+.
T Consensus 101 ~Kgp~lT~~Is 111 (414)
T TIGR00757 101 NKGARLTTDIS 111 (414)
T ss_pred CCCCeEEEEEE
Confidence 55555554443
No 102
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.44 E-value=0.00047 Score=57.80 Aligned_cols=73 Identities=14% Similarity=0.224 Sum_probs=58.4
Q ss_pred eecCCCCEEEEEEEEEecc-cEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCC
Q psy13107 77 FRPFKGEVLDAVVTQVNKV-GMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDAS 155 (170)
Q Consensus 77 f~p~~gev~~g~V~~i~~~-Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 155 (170)
|++.+||++.|+|.++... ++++.+|..++++|.++.. + +..|++||.+++-|.+|+.+++
T Consensus 134 y~~~~Geiv~g~V~r~~~~~~i~vdlg~~ea~LP~~eqi------p------------~E~~~~Gdrik~~i~~V~~~~k 195 (374)
T PRK12328 134 YKKKVGKIVFGTVVRVDNEENTFIEIDEIRAVLPMKNRI------K------------GEKFKVGDVVKAVLKRVKIDKN 195 (374)
T ss_pred HHHhcCcEEEEEEEEEecCCCEEEEcCCeEEEeCHHHcC------C------------CCcCCCCCEEEEEEEEEecCCC
Confidence 4557999999999999974 6999999889999887543 1 1278999999999999998877
Q ss_pred -ceEEEEEecCCC
Q psy13107 156 -GIFAIGTLMDDY 167 (170)
Q Consensus 156 -~i~~ig~~~~~~ 167 (170)
...++=|-..|.
T Consensus 196 ~gp~IilSRt~p~ 208 (374)
T PRK12328 196 NGILIELSRTSPK 208 (374)
T ss_pred CCCEEEEEcCCHH
Confidence 677766655443
No 103
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.18 E-value=0.0022 Score=40.01 Aligned_cols=48 Identities=19% Similarity=0.373 Sum_probs=28.3
Q ss_pred CCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEE
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIV 148 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~ 148 (170)
+|++-..+|++.+++|+|+..+.. +.++|.+++|. .+++||+|.|-|=
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~--------------------~~~~Gd~v~VFvY 49 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPE--------------------PLKVGDEVEVFVY 49 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG--------------------------TTSEEEEEEE
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCC--------------------CCCCCCEEEEEEE
Confidence 488899999999999999999884 99999998762 4577777777763
No 104
>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=96.99 E-value=0.0015 Score=43.34 Aligned_cols=62 Identities=21% Similarity=0.243 Sum_probs=35.6
Q ss_pred cCCCCEEEEEEEEEecccEEEEec-------------------CeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcC
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIG-------------------PLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQE 139 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg-------------------~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~ 139 (170)
|.+|.++.|+|+++++.-+++++- +|.|.|+.+++-.. +-|+... ...|++
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~t-e~Dkv~~---------~~~Frp 71 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRAT-EKDKVKM---------YDCFRP 71 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT--SS----G---------GGT--S
T ss_pred CCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeeccc-ccchhhH---------HhccCC
Confidence 889999999999999999998762 23455555554311 0011000 137899
Q ss_pred CCeEEEEEEEE
Q psy13107 140 DDEIRLKIVGT 150 (170)
Q Consensus 140 Gd~VrvrV~~v 150 (170)
||.||.||.+.
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 105
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=96.85 E-value=0.015 Score=44.18 Aligned_cols=63 Identities=16% Similarity=0.093 Sum_probs=48.7
Q ss_pred EeecCCCCEEEEEEEEEecccEEEEecC-----------eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEE
Q psy13107 76 VFRPFKGEVLDAVVTQVNKVGMFAEIGP-----------LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIR 144 (170)
Q Consensus 76 ~f~p~~gev~~g~V~~i~~~Gifv~lg~-----------~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~Vr 144 (170)
-..|..|.++-|+|+++....+-|++-. +.+-+|.|+..+.|..+ -...|++||.||
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~------------~~d~f~~GDivr 126 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEK------------LSDAFRIGDIVR 126 (188)
T ss_pred CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccc------------cccccccccEEE
Confidence 4467899999999999999999988732 35778888876553321 113899999999
Q ss_pred EEEEEE
Q psy13107 145 LKIVGT 150 (170)
Q Consensus 145 vrV~~v 150 (170)
.||.+.
T Consensus 127 A~Vis~ 132 (188)
T COG1096 127 ARVIST 132 (188)
T ss_pred EEEEec
Confidence 999996
No 106
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=96.75 E-value=0.0051 Score=52.66 Aligned_cols=72 Identities=11% Similarity=0.189 Sum_probs=55.6
Q ss_pred eecCCCCEEEEEEEEEecccEEEEe----cC--eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEE
Q psy13107 77 FRPFKGEVLDAVVTQVNKVGMFAEI----GP--LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGT 150 (170)
Q Consensus 77 f~p~~gev~~g~V~~i~~~Gifv~l----g~--~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 150 (170)
|++.+|+++.|+|.++...++++.+ |. .++++|.++.. + +..|+.||.|++-|.+|
T Consensus 148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p------------~E~y~~Gdrika~i~~V 209 (449)
T PRK12329 148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------P------------NDNYRANATFKVFLKEV 209 (449)
T ss_pred HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------C------------CCcCCCCCEEEEEEEEe
Confidence 5567999999999999999999998 43 58888876542 1 12789999999999999
Q ss_pred EecC-CceEEEEEecCC
Q psy13107 151 RVDA-SGIFAIGTLMDD 166 (170)
Q Consensus 151 ~~~~-~~i~~ig~~~~~ 166 (170)
+... +.+.++=|-..|
T Consensus 210 ~~~~~kGpqIilSRt~p 226 (449)
T PRK12329 210 SEGPRRGPQLFVSRANA 226 (449)
T ss_pred ecCCCCCCEEEEEcCCH
Confidence 8873 666665554443
No 107
>KOG1070|consensus
Probab=96.67 E-value=0.0022 Score=61.11 Aligned_cols=67 Identities=16% Similarity=0.276 Sum_probs=56.8
Q ss_pred CCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
..|+++.|++..+.++|+||++.. ++||.|.+.+.+++.-+.. ..+.+|+++|++|.+++-+.++|.
T Consensus 598 ~pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~~v~~~~------------ehf~vGqTv~~~i~nvd~ek~rm~ 665 (1710)
T KOG1070|consen 598 IPGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDDFVLSDS------------EHFPVGQTVRAKIVNVDDEKRRMP 665 (1710)
T ss_pred CCCceEEEEEeeeccCCeEEEecCccccccchhhhhhhhhcChh------------hhcccccEEEEEEEecCchhceee
Confidence 469999999999999999999954 6999999999988553321 388999999999999998777764
No 108
>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=96.55 E-value=0.0095 Score=38.48 Aligned_cols=57 Identities=23% Similarity=0.277 Sum_probs=46.0
Q ss_pred CCEEEEEEEEEecccEEEEecCe--eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeE-EEEEE
Q psy13107 82 GEVLDAVVTQVNKVGMFAEIGPL--SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEI-RLKIV 148 (170)
Q Consensus 82 gev~~g~V~~i~~~Gifv~lg~~--~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~V-rvrV~ 148 (170)
|++++|+|..-++.++.+++++. .|++|..+|+| .+......| ..+++||++ ++-|.
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--HVSNCPLLW--------HCLQEGDTIPNLMCL 60 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEEEEEccccCC--chhhCHHHH--------hhhhcCCCccceEEE
Confidence 68899999999999999999873 99999999996 333333222 278999999 88887
No 109
>PRK11712 ribonuclease G; Provisional
Probab=96.18 E-value=0.026 Score=49.30 Aligned_cols=87 Identities=14% Similarity=0.231 Sum_probs=58.3
Q ss_pred eecCCCCEEEEEEEEEec--ccEEEEecCe-eEEEEcCCCCCCcee-cCCCCCeEEEecCceeEEcCCCeEEEEEEEEEe
Q psy13107 77 FRPFKGEVLDAVVTQVNK--VGMFAEIGPL-SCFISHHSIPTDMQF-CPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRV 152 (170)
Q Consensus 77 f~p~~gev~~g~V~~i~~--~Gifv~lg~~-~~~i~~~~l~~~~~~-d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 152 (170)
-+..+|.+|.|+|.++.| .++||++|.- +||+|.+++..++.+ ..+... ......-...++.||.|-|.|..--.
T Consensus 34 ~~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~-~~~~~~i~~~l~~Gq~iLVQV~Ke~~ 112 (489)
T PRK11712 34 KRGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQK-QFVVRDISELVRQGQDIMVQVVKDPL 112 (489)
T ss_pred cccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhccccccc-ccccccHHHhccCCCEEEEEEEeCCc
Confidence 345699999999999999 5999999986 999999998433211 111100 00000011258999999999998766
Q ss_pred cCCceEEEEEec
Q psy13107 153 DASGIFAIGTLM 164 (170)
Q Consensus 153 ~~~~i~~ig~~~ 164 (170)
.+....+++.+.
T Consensus 113 ~~KG~~lT~~Is 124 (489)
T PRK11712 113 GTKGARLTTDIT 124 (489)
T ss_pred CCCCCeEEEEEE
Confidence 666655555443
No 110
>PRK10811 rne ribonuclease E; Reviewed
Probab=95.98 E-value=0.04 Score=51.37 Aligned_cols=82 Identities=16% Similarity=0.234 Sum_probs=56.3
Q ss_pred ecCCCCEEEEEEEEEec--ccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEec-CceeEEcCCCeEEEEEEEEEec
Q psy13107 78 RPFKGEVLDAVVTQVNK--VGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSV-HGEVVIQEDDEIRLKIVGTRVD 153 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~--~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~-~~~~~~~~Gd~VrvrV~~v~~~ 153 (170)
.+..|.||.|+|.++.+ .++||.+|.. .||+|.+++...+ |..... -... .-+..++.||.|-|.|..--..
T Consensus 35 e~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~-f~~~~~---~~~~~~i~~~Lk~GqeILVQV~KEa~g 110 (1068)
T PRK10811 35 EQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREY-FPANYS---AHGRPNIKDVLREGQEVIVQIDKEERG 110 (1068)
T ss_pred ccCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccc-cccccc---cccccccccccCCCCEEEEEEeecccC
Confidence 35689999999999999 4999999987 9999999885442 111000 0000 1123689999999999987665
Q ss_pred CCceEEEEEe
Q psy13107 154 ASGIFAIGTL 163 (170)
Q Consensus 154 ~~~i~~ig~~ 163 (170)
.....+.+.+
T Consensus 111 tKGp~LTt~I 120 (1068)
T PRK10811 111 NKGAALTTFI 120 (1068)
T ss_pred CCCCceeeeE
Confidence 5554444333
No 111
>KOG1070|consensus
Probab=95.22 E-value=0.094 Score=50.57 Aligned_cols=68 Identities=13% Similarity=0.294 Sum_probs=56.0
Q ss_pred CCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceE
Q psy13107 80 FKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIF 158 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~ 158 (170)
..|+++.|.|..+.+.|+|+.++.. ++|++.+++.+.+. .. | +..+..|+.+..||.+++-+.+++.
T Consensus 1161 k~g~iv~G~V~nv~~~glfi~ls~~v~a~v~is~~~ds~~-----k~--w-----~k~~~~gklv~~rv~~ve~~s~rie 1228 (1710)
T KOG1070|consen 1161 KIGDIVRGFVKNVETKGLFIALSRKVEAFVPISGLSDSFE-----KE--W-----EKHLPVGKLVTGRVLSVEEDSKRIE 1228 (1710)
T ss_pred ccCceeEEEEEEecCCcEEEEEccceEEEEEccccccchh-----hh--h-----hccCCccceeeeEEEEeeccCceEE
Confidence 5899999999999999999999985 99999999864432 11 1 2378999999999999988777765
Q ss_pred E
Q psy13107 159 A 159 (170)
Q Consensus 159 ~ 159 (170)
.
T Consensus 1229 l 1229 (1710)
T KOG1070|consen 1229 L 1229 (1710)
T ss_pred E
Confidence 4
No 112
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=95.04 E-value=0.018 Score=50.85 Aligned_cols=61 Identities=23% Similarity=0.357 Sum_probs=50.1
Q ss_pred cCCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
-..|+.+.|+|+++.++|+|+++..- .|++|.+++..+ ..+..||++-|++.++..+.+++
T Consensus 120 ve~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~------------------~~~~vgdeiiV~v~~vr~~~gei 181 (715)
T COG1107 120 VEAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD------------------PDYAVGDEIIVQVSDVRPEKGEI 181 (715)
T ss_pred cccceeeeccccchhhhcceeecChhhhccccccccCCC------------------CCCCCCCeEEEEeeccCCCCCcc
Confidence 36899999999999999999999875 999999988742 15578888888888887765554
No 113
>KOG3409|consensus
Probab=94.01 E-value=0.36 Score=36.36 Aligned_cols=64 Identities=17% Similarity=0.214 Sum_probs=46.1
Q ss_pred ecCCCCEEEEEEEEEecccEEEEe---cC------eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEE
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEI---GP------LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIV 148 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~l---g~------~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~ 148 (170)
-|+.|.++.++|+.++..-+-|.+ +. |.|+|+..++-.- +-|..+ --..|++||.|+.+|.
T Consensus 65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~t-Ekdrv~---------v~ksFrPgDiVlAkVi 134 (193)
T KOG3409|consen 65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRAT-EKDRVK---------VYKSFRPGDIVLAKVI 134 (193)
T ss_pred CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhcccc-ccchhh---------hhhccCCCcEEEEEEe
Confidence 599999999999999998888776 22 4688888777421 111100 0137899999999999
Q ss_pred EEE
Q psy13107 149 GTR 151 (170)
Q Consensus 149 ~v~ 151 (170)
+..
T Consensus 135 s~~ 137 (193)
T KOG3409|consen 135 SLG 137 (193)
T ss_pred ecC
Confidence 943
No 114
>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=93.71 E-value=0.71 Score=28.70 Aligned_cols=56 Identities=14% Similarity=0.240 Sum_probs=37.8
Q ss_pred EEEEEEEEec---ccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEE
Q psy13107 85 LDAVVTQVNK---VGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFA 159 (170)
Q Consensus 85 ~~g~V~~i~~---~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ 159 (170)
..|+|+..++ +|+...-+.- +.|+|.+++..+. + ..++.|+.|+|.+.. ..++..|
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~-~---------------~~l~~G~~V~F~~~~---~~~g~~A 60 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNG-F---------------RSLKEGDRVEFEVEE---GKKGPQA 60 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSS-S---------------TS--TTSEEEEEEEE---CTTSEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccc-c---------------ccCCCCCEEEEEEEE---CCCCCEE
Confidence 4689999887 4544443443 8999999987441 0 267899999999988 5566554
No 115
>KOG1004|consensus
Probab=93.61 E-value=1.1 Score=34.84 Aligned_cols=93 Identities=22% Similarity=0.181 Sum_probs=68.6
Q ss_pred CceEEeEEEEEEEeecCCCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCe
Q psy13107 64 GFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDE 142 (170)
Q Consensus 64 g~~~~~v~f~~i~f~p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~ 142 (170)
+.-.+.+..+..-|-|..|+.+-|+|++.+.....|.+|.- -+.++.-.++ .. .+++.-.++.||.
T Consensus 48 ~~~v~~vds~~kRYiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L~~laFe------~A-------tkrNrPnl~vGdl 114 (230)
T KOG1004|consen 48 GGGVYWVDSQQKRYIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASLSYLAFE------GA-------TKRNRPNLQVGDL 114 (230)
T ss_pred cceeEEEecccceecCCCCCEEEEEEEeccCceEEEecCCCCeeeeeecccc------Cc-------cccCCCccccccE
Confidence 34467888888999999999999999999999999999864 5555544433 11 1233448999999
Q ss_pred EEEEEEEEEecC-CceEEEEEec-CCCCC
Q psy13107 143 IRLKIVGTRVDA-SGIFAIGTLM-DDYLG 169 (170)
Q Consensus 143 VrvrV~~v~~~~-~~i~~ig~~~-~~~LG 169 (170)
|-.||...+.+. -.+.|+.+.. ..|.|
T Consensus 115 iyakv~~a~~~~Epel~Cids~graaGfG 143 (230)
T KOG1004|consen 115 IYAKVVDANKDMEPELTCIDSTGRAAGFG 143 (230)
T ss_pred EEEEEEecCCCcCcceEEEcccCcccCcc
Confidence 999999886533 3566777754 45555
No 116
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=93.44 E-value=0.27 Score=39.66 Aligned_cols=53 Identities=21% Similarity=0.260 Sum_probs=45.4
Q ss_pred CCCEEEEEEEEEecccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEec
Q psy13107 81 KGEVLDAVVTQVNKVGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVD 153 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~ 153 (170)
.++.++|+|-+..+.|.|+.+... -||||.|..- ...+.|+.+.+||.+++.+
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr~--------------------~~prlG~~l~~rVi~~reD 208 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSERF--------------------AEPRLGERLTARVIGVRED 208 (287)
T ss_pred hcCeeeeEEEEEeccceEEEEcCCeEEEEcchhhc--------------------ccccCCceEEEEEEEEccC
Confidence 489999999999999999999665 8999988641 1568999999999999873
No 117
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=93.43 E-value=0.098 Score=34.68 Aligned_cols=67 Identities=13% Similarity=0.089 Sum_probs=49.8
Q ss_pred EeecCCCCEEEEEEEEEecccEEEEecC--eeEEEE-cCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEe
Q psy13107 76 VFRPFKGEVLDAVVTQVNKVGMFAEIGP--LSCFIS-HHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRV 152 (170)
Q Consensus 76 ~f~p~~gev~~g~V~~i~~~Gifv~lg~--~~~~i~-~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 152 (170)
+--|.+|++.. .|..+.+.|++|.|-. ++|+|. .+++..+ .+ +.-.+.+ .|-.+.|+|..+|.
T Consensus 11 y~~P~v~dvv~-~Vv~i~d~~~YV~LleY~iegmIl~~selsr~-ri-----------rsi~kll-VGk~e~v~ViRVDk 76 (86)
T PHA02858 11 YVFPNINEVTK-GIVFVKDNIFYVKLIDYGLEALIVNYVNVNAD-RA-----------EKLKKKL-VGKTINVQVIRTDK 76 (86)
T ss_pred EecCCCCeEEE-EEEEEeccEEEEEEecCccceEEecHHHHhHH-HH-----------Hhhhhhh-cCCeeEEEEEEECC
Confidence 34699999999 8999999999999954 488887 7776533 00 1112255 99999999999987
Q ss_pred cCCc
Q psy13107 153 DASG 156 (170)
Q Consensus 153 ~~~~ 156 (170)
+.+-
T Consensus 77 ~KGY 80 (86)
T PHA02858 77 LKGY 80 (86)
T ss_pred CCCE
Confidence 7653
No 118
>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=93.24 E-value=0.61 Score=32.09 Aligned_cols=57 Identities=11% Similarity=0.295 Sum_probs=44.4
Q ss_pred eecCCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEe
Q psy13107 77 FRPFKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRV 152 (170)
Q Consensus 77 f~p~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 152 (170)
.-+..|.++.|+|..+...-+|+.+|. |.+..+.... +...|..|+.||+|+.+...
T Consensus 19 lG~~~gk~V~G~I~hvv~ddLYIDfG~KFhcVc~rp~~-------------------~~~~y~~G~rV~lrLkdlEL 76 (104)
T PF10246_consen 19 LGDPEGKIVIGKIFHVVDDDLYIDFGGKFHCVCKRPAV-------------------NGEKYVRGSRVRLRLKDLEL 76 (104)
T ss_pred cCCccCCEEEEEEEEEecCceEEEeCCceeEEEecccc-------------------cccccccCCEEEEEECCHhh
Confidence 456789999999999999999999987 5777653221 11267889999999988764
No 119
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=92.49 E-value=0.062 Score=46.34 Aligned_cols=77 Identities=17% Similarity=0.256 Sum_probs=57.4
Q ss_pred ecCCCCEEEEEEEEEecccEEEEe-cCe-eEEEEcCCCCCC---ceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEe
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEI-GPL-SCFISHHSIPTD---MQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRV 152 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~l-g~~-~~~i~~~~l~~~---~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~ 152 (170)
++.....+.+.|..++..|+.|.+ ... ..|||...|-+. ...+.++. +..- ++..+|+.||.|.|++.+|+.
T Consensus 558 k~~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~~reei~~n~e~g--tv~I-~ge~~Yk~~D~i~V~l~eVr~ 634 (645)
T COG4776 558 KAGTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHANREELVCNQENG--TVQI-KGETVYKVGDVIDVTLAEVRM 634 (645)
T ss_pred ccccCchhhhhhhhhccCceEEEeccCCcceecchhhhccchhheEecCCCc--eEEE-ccEEEEeeccEEEEEeHHHHH
Confidence 445667799999999999999998 345 899998888544 44554443 2222 234699999999999999987
Q ss_pred cCCce
Q psy13107 153 DASGI 157 (170)
Q Consensus 153 ~~~~i 157 (170)
+++.+
T Consensus 635 etRsi 639 (645)
T COG4776 635 ETRSI 639 (645)
T ss_pred hhhhh
Confidence 76654
No 120
>PRK15463 cold shock-like protein CspF; Provisional
Probab=90.17 E-value=1.1 Score=28.71 Aligned_cols=49 Identities=4% Similarity=0.076 Sum_probs=34.5
Q ss_pred EEEEEEEEec-ccE-EEEecC-e-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEE
Q psy13107 85 LDAVVTQVNK-VGM-FAEIGP-L-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVG 149 (170)
Q Consensus 85 ~~g~V~~i~~-~Gi-fv~lg~-~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 149 (170)
+.|+|+.-+. .|. |++-.. . |+|+|.+.|... . ...++.|+.|.+.+..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~------g----------~~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLR------D----------AEELTTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhc------C----------CCCCCCCCEEEEEEEE
Confidence 4789999888 344 444433 3 999999999622 1 1267899999998765
No 121
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=89.87 E-value=2.6 Score=36.99 Aligned_cols=85 Identities=15% Similarity=0.152 Sum_probs=61.3
Q ss_pred CCceEEeEEEEEEEeecCCCCEEEEEEEEEecc--cEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcC
Q psy13107 63 QGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKV--GMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQE 139 (170)
Q Consensus 63 ~g~~~~~v~f~~i~f~p~~gev~~g~V~~i~~~--Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~ 139 (170)
++....++.++.-.-+-.+|-+|.|+|+++.|. .+||.+|.- .||+|.+++.+. |.... ...-...++.
T Consensus 19 ~~~~l~el~ie~~~~~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~~--~~~~~------~~~i~~~lr~ 90 (487)
T COG1530 19 DGGALQELDIERGAKEQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVPY--FRAVL------EEKIKVRLRG 90 (487)
T ss_pred eCCEEEEEEEecCCcEeeecCceEEEecccCccchhheeeccCCccceEEecccchh--hhhcc------cccceeeecC
Confidence 445555666665556667899999999999995 899999986 999999999752 11100 0011348999
Q ss_pred CCeEEEEEEEEEecCC
Q psy13107 140 DDEIRLKIVGTRVDAS 155 (170)
Q Consensus 140 Gd~VrvrV~~v~~~~~ 155 (170)
|+.+-|.|........
T Consensus 91 ~~~~~Vqv~ke~~G~K 106 (487)
T COG1530 91 GQATLVQVVKEPRGTK 106 (487)
T ss_pred CceEEEEEEeecCccc
Confidence 9999999988765443
No 122
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=89.69 E-value=1.5 Score=27.29 Aligned_cols=50 Identities=6% Similarity=0.166 Sum_probs=36.4
Q ss_pred CEEEEEEEEEecccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEE
Q psy13107 83 EVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTR 151 (170)
Q Consensus 83 ev~~g~V~~i~~~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 151 (170)
...+|+|+++++....+.|....-+ .||.++.++ -+++|.+|+|--..++
T Consensus 3 ~~veG~I~~id~~~~titLdDGksy----~lp~ef~~~---------------~L~~G~kV~V~yd~~~ 52 (61)
T PF07076_consen 3 ADVEGTIKSIDPETMTITLDDGKSY----KLPEEFDFD---------------GLKPGMKVVVFYDEVD 52 (61)
T ss_pred ccceEEEEEEcCCceEEEecCCCEE----ECCCccccc---------------ccCCCCEEEEEEEccC
Confidence 3579999999999999999765444 455444332 6788999888776653
No 123
>PRK15464 cold shock-like protein CspH; Provisional
Probab=89.45 E-value=1.4 Score=28.23 Aligned_cols=49 Identities=10% Similarity=0.142 Sum_probs=35.0
Q ss_pred EEEEEEEEec-ccE-EEEecC-e-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEE
Q psy13107 85 LDAVVTQVNK-VGM-FAEIGP-L-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVG 149 (170)
Q Consensus 85 ~~g~V~~i~~-~Gi-fv~lg~-~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 149 (170)
+.|+|+.-+. .|. |+.-.. . |+|+|.+.|... . ...+..|+.|.+.+..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~------g----------~~~l~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPR------D----------AEVLIPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhc------C----------CCCCCCCCEEEEEEEE
Confidence 4789998888 354 455533 3 999999998522 1 1267899999999876
No 124
>PRK09890 cold shock protein CspG; Provisional
Probab=87.62 E-value=2.6 Score=26.83 Aligned_cols=49 Identities=16% Similarity=0.320 Sum_probs=33.4
Q ss_pred EEEEEEEEec-ccE-EEEec-C-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEE
Q psy13107 85 LDAVVTQVNK-VGM-FAEIG-P-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVG 149 (170)
Q Consensus 85 ~~g~V~~i~~-~Gi-fv~lg-~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 149 (170)
+.|+|+.-++ .|. |++-. . -+.|+|.+.|..+ . -..++.|+.|+|.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~------~----------~~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN------E----------FRTLNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccC------C----------CCCCCCCCEEEEEEEE
Confidence 4799988776 333 34443 3 3899999998632 1 0267889999998765
No 125
>PRK10943 cold shock-like protein CspC; Provisional
Probab=86.84 E-value=2.6 Score=26.76 Aligned_cols=51 Identities=16% Similarity=0.264 Sum_probs=34.6
Q ss_pred EEEEEEEEEec-ccE-EEEe-cCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEE
Q psy13107 84 VLDAVVTQVNK-VGM-FAEI-GPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGT 150 (170)
Q Consensus 84 v~~g~V~~i~~-~Gi-fv~l-g~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 150 (170)
.+.|+|+.-+. .|. |++- +.- +.|+|.+.+... . -..+..|+.|.+.+..-
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~------g----------~~~l~~G~~V~f~~~~~ 57 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN------G----------FKTLAEGQNVEFEIQDG 57 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHcccc------C----------CCCCCCCCEEEEEEEEC
Confidence 35788888777 343 3443 333 999999998622 1 12678999999988763
No 126
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=86.43 E-value=3.2 Score=26.35 Aligned_cols=50 Identities=18% Similarity=0.308 Sum_probs=33.9
Q ss_pred EEEEEEEEec-ccE-EEEe-cCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEE
Q psy13107 85 LDAVVTQVNK-VGM-FAEI-GPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGT 150 (170)
Q Consensus 85 ~~g~V~~i~~-~Gi-fv~l-g~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 150 (170)
+.|+|+.-+. .|. |+.- +.- |.|+|.+.|..+ . -..+..|+.|.+.+..-
T Consensus 4 ~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~------g----------~~~l~~G~~V~f~~~~~ 57 (69)
T PRK09507 4 IKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN------G----------FKTLAEGQRVEFEITNG 57 (69)
T ss_pred cceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc------C----------CCCCCCCCEEEEEEEEC
Confidence 5688888776 333 3444 333 899999998622 1 12678999999988764
No 127
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=84.61 E-value=4.2 Score=25.79 Aligned_cols=49 Identities=18% Similarity=0.337 Sum_probs=33.3
Q ss_pred EEEEEEEEec-ccE-EEEe-cC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEE
Q psy13107 85 LDAVVTQVNK-VGM-FAEI-GP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVG 149 (170)
Q Consensus 85 ~~g~V~~i~~-~Gi-fv~l-g~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 149 (170)
..|+|+.-++ .|. |++- +. -+.|+|.+.|..+ . -..++.|+.|.|.+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~------g----------~~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND------G----------YKSLDEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc------C----------CCCCCCCCEEEEEEEE
Confidence 3788988775 333 3444 33 3899999998622 1 1267899999998766
No 128
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=84.58 E-value=5.2 Score=32.44 Aligned_cols=71 Identities=14% Similarity=0.171 Sum_probs=45.3
Q ss_pred cCCCCEEEEEEEEEecccEEEEecCe--eEEEEcCCCCCC----------ceecCCCCCeEEEecCceeEEcCCCeEEEE
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEIGPL--SCFISHHSIPTD----------MQFCPNSNPVCYKSVHGEVVIQEDDEIRLK 146 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~lg~~--~~~i~~~~l~~~----------~~~d~~~~~~~~~~~~~~~~~~~Gd~Vrvr 146 (170)
-.+|+.....|.+.+++|.|+.-+.. +.+.|.+...++ +.|...++ +....-..-....|+.=..+
T Consensus 3 ~~iG~~~~l~V~~~~~~g~fL~~~~~~~~ilL~k~~~~~~e~evGdev~vFiY~D~~~--rl~aTt~~p~~tvg~~g~~~ 80 (287)
T COG2996 3 IKIGQINSLEVVEFSDFGYFLDAGEDGTTILLPKSEPEEDELEVGDEVTVFIYVDSED--RLIATTREPKATVGEYGWLK 80 (287)
T ss_pred ccccceEEEEEEEeeceeEEEecCCCceEEeccccCCcCCccccCcEEEEEEEECCCC--ceeheeecceEeecceeEEE
Confidence 45799999999999999999999876 788888755322 12211111 01111112356777777777
Q ss_pred EEEEE
Q psy13107 147 IVGTR 151 (170)
Q Consensus 147 V~~v~ 151 (170)
|.+++
T Consensus 81 Vv~v~ 85 (287)
T COG2996 81 VVEVN 85 (287)
T ss_pred EEEEc
Confidence 77775
No 129
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=84.58 E-value=9.3 Score=25.53 Aligned_cols=58 Identities=16% Similarity=0.129 Sum_probs=39.5
Q ss_pred EEEEEEEEEecccEE-EEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 84 VLDAVVTQVNKVGMF-AEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 84 v~~g~V~~i~~~Gif-v~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
.++|+|+.+-+.+.| |.|... +.+-|.+- . -+.+.-.+.+||.|.|.+..-|..+++|
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isG----------K------mR~~rIrIl~GD~V~VE~spYDltkGRI 67 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASG----------R------MRKHRIRILAGDRVTLELSPYDLTKGRI 67 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEecc----------c------eeeeeEEecCCCEEEEEECcccCCceeE
Confidence 478999999999888 577543 44443321 1 1122247889999999999887766665
No 130
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=83.74 E-value=4.1 Score=26.29 Aligned_cols=49 Identities=14% Similarity=0.193 Sum_probs=32.9
Q ss_pred EEEEEEEec-ccE-EEEec-C-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEE
Q psy13107 86 DAVVTQVNK-VGM-FAEIG-P-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGT 150 (170)
Q Consensus 86 ~g~V~~i~~-~Gi-fv~lg-~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 150 (170)
.|+|+.-+. .|. |+.-. . -++|+|.+.|..+ . -..+..|+.|.+.+..-
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~------g----------~~~l~~G~~V~f~~~~~ 55 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD------G----------YRTLKAGQSVQFDVHQG 55 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeecccc------C----------CCCCCCCCEEEEEEEEC
Confidence 477887776 344 44443 3 3999999998622 1 12678899999988763
No 131
>PRK14998 cold shock-like protein CspD; Provisional
Probab=80.02 E-value=6.4 Score=25.28 Aligned_cols=49 Identities=18% Similarity=0.251 Sum_probs=32.9
Q ss_pred EEEEEEEec-ccE-EEEe-cCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEE
Q psy13107 86 DAVVTQVNK-VGM-FAEI-GPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGT 150 (170)
Q Consensus 86 ~g~V~~i~~-~Gi-fv~l-g~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 150 (170)
.|+|+.-+. .|. |+.- +.. |+|+|.|.|..+ . -..+..|+.|.|.+..-
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~------g----------~~~l~~G~~V~f~~~~~ 55 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD------G----------YRTLKAGQSVRFDVHQG 55 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeeccc------C----------CCCCCCCCEEEEEEEEC
Confidence 477877766 343 3444 333 999999998622 1 12678999999998764
No 132
>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=79.74 E-value=4.4 Score=25.56 Aligned_cols=49 Identities=18% Similarity=0.271 Sum_probs=32.5
Q ss_pred EEEEEEEec-ccE-EEEe-cC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEE
Q psy13107 86 DAVVTQVNK-VGM-FAEI-GP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGT 150 (170)
Q Consensus 86 ~g~V~~i~~-~Gi-fv~l-g~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 150 (170)
.|+|+.-+. .|. |++- +. -+.|+|.|.+..+ . -..++.|+.|++.+..-
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~------g----------~~~l~~G~~V~f~~~~~ 55 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMD------G----------YRTLKAGQKVQFEVVQG 55 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhc------C----------CCCCCCCCEEEEEEEEC
Confidence 478887765 344 4444 32 3899999998622 1 12678999999987663
No 133
>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=79.44 E-value=6.6 Score=24.13 Aligned_cols=49 Identities=12% Similarity=0.215 Sum_probs=32.2
Q ss_pred EEEEEEEec---ccEEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEE
Q psy13107 86 DAVVTQVNK---VGMFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGT 150 (170)
Q Consensus 86 ~g~V~~i~~---~Gifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 150 (170)
.|+|+..++ +|+...-+.- +.|+|.+.+... . ...++.|+.|.|.+..-
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~------~----------~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGD------G----------FRSLEEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhcc------C----------CCcCCCCCEEEEEEEEC
Confidence 477877777 3433333323 889988888522 0 12678999999988774
No 134
>KOG2916|consensus
Probab=79.38 E-value=0.89 Score=36.60 Aligned_cols=65 Identities=9% Similarity=0.181 Sum_probs=47.4
Q ss_pred cCCCCEEEEEEEEEecccEEEEe---cCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCC
Q psy13107 79 PFKGEVLDAVVTQVNKVGMFAEI---GPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDAS 155 (170)
Q Consensus 79 p~~gev~~g~V~~i~~~Gifv~l---g~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~ 155 (170)
|.++|++-+.|.+|.+.|++|.| +.++|+|-.|.|+.- +-+.-...+++|-.=-|-|..||-+++
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrR------------RIRSI~klirVGr~E~vvVlrVDkekG 81 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRR------------RIRSIQKLIRVGRNEPVVVLRVDKEKG 81 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHH------------HHHHHHHHHhcCCcceEEEEEEcCCCC
Confidence 89999999999999999999998 456999999988622 011112356777655566777765544
No 135
>KOG1856|consensus
Probab=77.17 E-value=6 Score=38.08 Aligned_cols=63 Identities=13% Similarity=0.213 Sum_probs=47.6
Q ss_pred CCCCEEEEEEEEEeccc---EEEEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecC
Q psy13107 80 FKGEVLDAVVTQVNKVG---MFAEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDA 154 (170)
Q Consensus 80 ~~gev~~g~V~~i~~~G---ifv~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 154 (170)
+.|-++.++|++++..- +.|.+... +||++.+++++- .+..- ...+++|+.|-+||..++.++
T Consensus 984 ~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~-~v~~p-----------~~~v~vgq~v~~kvi~id~e~ 1050 (1299)
T KOG1856|consen 984 YEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDR-DVRRP-----------ENRVKVGQTVYCKVIKIDKER 1050 (1299)
T ss_pred ccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChh-hccCH-----------HHhhccCceEEEEeeeeeHhh
Confidence 47889999999999876 55677765 999999999741 11111 126679999999999998653
No 136
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=74.38 E-value=19 Score=23.42 Aligned_cols=59 Identities=14% Similarity=0.168 Sum_probs=39.5
Q ss_pred EEEEEEEEEecccEE-EEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 84 VLDAVVTQVNKVGMF-AEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 84 v~~g~V~~i~~~Gif-v~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
.+.|+|...-+.+.| |.+. +|..-...+|.- .+.+.-.+.+||.|.|.....+.++.+|
T Consensus 8 e~~g~V~e~L~~~~f~v~~e--dg~~~~ahI~GK-------------mr~~~i~I~~GD~V~Ve~~~~d~~kg~I 67 (75)
T COG0361 8 EMEGTVIEMLPNGRFRVELE--NGHERLAHISGK-------------MRKNRIRILPGDVVLVELSPYDLTKGRI 67 (75)
T ss_pred EEEEEEEEecCCCEEEEEec--CCcEEEEEccCc-------------chheeEEeCCCCEEEEEecccccccccE
Confidence 478999999998887 6664 344444444422 1122347899999999998887665554
No 137
>KOG4078|consensus
Probab=74.13 E-value=7.2 Score=28.49 Aligned_cols=64 Identities=11% Similarity=0.341 Sum_probs=46.9
Q ss_pred EEEEEeecCCCCEEEEEEEEEecccEEEEecC-eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEE
Q psy13107 72 YRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGT 150 (170)
Q Consensus 72 f~~i~f~p~~gev~~g~V~~i~~~Gifv~lg~-~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v 150 (170)
-+++-+-+..|..+.|+|-.+...-+|+..|. |......-.+ ++..|+.|..||.|+.+.
T Consensus 73 Skl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~rP~~-------------------n~e~Y~~GaRVrlRl~Dl 133 (173)
T KOG4078|consen 73 SKLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCKRPAL-------------------NGEAYQKGARVRLRLIDL 133 (173)
T ss_pred CccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEcCcCc-------------------CHHHhhcCceEEEEEcCh
Confidence 45556778999999999999999999999975 3444322211 123788999999999887
Q ss_pred EecC
Q psy13107 151 RVDA 154 (170)
Q Consensus 151 ~~~~ 154 (170)
...+
T Consensus 134 ELs~ 137 (173)
T KOG4078|consen 134 ELSE 137 (173)
T ss_pred hHhh
Confidence 6543
No 138
>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=72.58 E-value=15 Score=25.72 Aligned_cols=45 Identities=16% Similarity=0.110 Sum_probs=33.9
Q ss_pred CeEEEecCceeEEcCCCeEEEEEEEEEecCCceEEEEEecCCCCC
Q psy13107 125 PVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLG 169 (170)
Q Consensus 125 ~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ig~~~~~~LG 169 (170)
.|...-.+++..++.|+..+++|..+.+..+.+......+.--||
T Consensus 37 ~wepiIAdEdvevk~Ge~~~IkIk~I~iP~~tIv~p~~~~rha~G 81 (112)
T PF01629_consen 37 KWEPIIADEDVEVKKGEVKIIKIKKIEIPPNTIVMPCAYMRHALG 81 (112)
T ss_pred eEEEEEEcCeeEEecCCEEEEEEEEEecCCCCEEEEchHhhccCc
Confidence 366555666789999999999999999999987655555544443
No 139
>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=66.30 E-value=31 Score=21.93 Aligned_cols=58 Identities=14% Similarity=0.145 Sum_probs=37.0
Q ss_pred EEEEEEEEEecccEE-EEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEEecCCce
Q psy13107 84 VLDAVVTQVNKVGMF-AEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGI 157 (170)
Q Consensus 84 v~~g~V~~i~~~Gif-v~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i 157 (170)
.++|+|+..-+.+.| |.|... +.+-|.+- .. +...-.+.+||.|.|.+..-+.++++|
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~G----------Km------r~~rI~I~~GD~V~Ve~spyd~tkgrI 65 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISG----------KI------RMHYIRILPGDKVKVELSPYDLTRGRI 65 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecC----------cc------hhccEEECCCCEEEEEECcccCCcEeE
Confidence 378999999999888 576543 43333221 10 111236889999999988776555543
No 140
>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=61.27 E-value=31 Score=20.82 Aligned_cols=42 Identities=14% Similarity=0.095 Sum_probs=21.8
Q ss_pred EEEEEEecccEEEEecC--eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEE
Q psy13107 87 AVVTQVNKVGMFAEIGP--LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVG 149 (170)
Q Consensus 87 g~V~~i~~~Gifv~lg~--~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 149 (170)
|++....+---|+.... -|.|||..+|. .--.||+|+|++..
T Consensus 1 G~~~~~~~GfGFv~~~~~~~DifIp~~~l~---------------------~A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 1 GTLKIHPKGFGFVIPDDGGEDIFIPPRNLN---------------------GAMDGDKVLVRITP 44 (58)
T ss_dssp EEEEE-SSS-EEEEECT-TEEEEE-HHHHT---------------------TS-TT-EEEEEEEE
T ss_pred CEEEEEcCCCEEEEECCCCCCEEECHHHHC---------------------CCCCCCEEEEEEec
Confidence 34444433333444433 27787777664 22568899999988
No 141
>COG1278 CspC Cold shock proteins [Transcription]
Probab=59.51 E-value=28 Score=22.10 Aligned_cols=48 Identities=17% Similarity=0.252 Sum_probs=31.4
Q ss_pred EEEEEEEecccEEEEecC----eeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEE
Q psy13107 86 DAVVTQVNKVGMFAEIGP----LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVG 149 (170)
Q Consensus 86 ~g~V~~i~~~Gifv~lg~----~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 149 (170)
.|+|+--++..=|--+-| -|.|+|.|.+... . -..+..|++|.|.+..
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~G~~DvFVH~Sai~~~------g----------~~~L~eGQ~V~f~~~~ 54 (67)
T COG1278 3 TGTVKWFNATKGFGFITPEDGGKDVFVHISAIQRA------G----------FRTLREGQKVEFEVEQ 54 (67)
T ss_pred cceEEEeeCCCcceEcCCCCCCcCEEEEeeeeccC------C----------CcccCCCCEEEEEEec
Confidence 466776666544433422 3899999988522 1 1277889999998876
No 142
>KOG3013|consensus
Probab=54.98 E-value=23 Score=28.58 Aligned_cols=68 Identities=16% Similarity=0.238 Sum_probs=46.9
Q ss_pred EeecCCCCEEEEEEEEEecccEEEEecCe-eEEEEcC--CCCCCceecCCCCCeEEEecCc---eeEEcCCCeEEEEEEE
Q psy13107 76 VFRPFKGEVLDAVVTQVNKVGMFAEIGPL-SCFISHH--SIPTDMQFCPNSNPVCYKSVHG---EVVIQEDDEIRLKIVG 149 (170)
Q Consensus 76 ~f~p~~gev~~g~V~~i~~~Gifv~lg~~-~~~i~~~--~l~~~~~~d~~~~~~~~~~~~~---~~~~~~Gd~VrvrV~~ 149 (170)
-|.|.+|+++.|+|..+.+.-..++++.- ++.+..+ +||....= ... ..|+ ..+++.||-|-..|.+
T Consensus 80 rY~pEvGDvVVgRV~eVq~KRWkvd~nsk~d~vL~LsSvNLPGg~~R-Rk~------~~DEl~MR~fl~egDLi~AEVQ~ 152 (301)
T KOG3013|consen 80 RYAPEVGDVVVGRVIEVQQKRWKVDLNSKQDAVLMLSSVNLPGGIQR-RKS------EEDELQMRSFLKEGDLIVAEVQN 152 (301)
T ss_pred hcCCccCCEEEEEeeeeecceeEEecccccceEEEeecccCCchhhh-ccc------hhhHHHHHHHhhccCeehHHHHH
Confidence 37899999999999999999999999885 6665555 45644110 000 0111 2378888888777766
Q ss_pred E
Q psy13107 150 T 150 (170)
Q Consensus 150 v 150 (170)
+
T Consensus 153 v 153 (301)
T KOG3013|consen 153 V 153 (301)
T ss_pred h
Confidence 5
No 143
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=54.08 E-value=44 Score=20.30 Aligned_cols=29 Identities=14% Similarity=0.304 Sum_probs=24.4
Q ss_pred EEEEEEEEecccEEEEecCe--eEEEEcCCC
Q psy13107 85 LDAVVTQVNKVGMFAEIGPL--SCFISHHSI 113 (170)
Q Consensus 85 ~~g~V~~i~~~Gifv~lg~~--~~~i~~~~l 113 (170)
+.|+|..+++..+.++.+++ +.++|.+.+
T Consensus 5 l~G~v~~~~~~~vvi~~~GvGy~v~v~~~~~ 35 (61)
T PF01330_consen 5 LKGKVVEKNPDYVVIDVNGVGYEVFVPSNTL 35 (61)
T ss_dssp EEEEEEEEESSEEEEEETTEEEEEEE-HHHH
T ss_pred EEEEEEEEcCCEEEEEECCEEEEEEeCCchH
Confidence 78999999999999999875 899987643
No 144
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=51.63 E-value=23 Score=21.29 Aligned_cols=47 Identities=21% Similarity=0.319 Sum_probs=26.3
Q ss_pred EEEEEEEEEeccc----EEEEecCe---eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEE
Q psy13107 84 VLDAVVTQVNKVG----MFAEIGPL---SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVG 149 (170)
Q Consensus 84 v~~g~V~~i~~~G----ifv~lg~~---~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 149 (170)
.+.|+|..+.+.| +.+.++.. ...++..+. .++.+++||+|.+.+..
T Consensus 6 ~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~-------------------~~L~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 6 QLPGTVESIENLGSEVEVTLDLGGGETLTARITPESA-------------------EELGLKPGDEVYASIKA 59 (64)
T ss_dssp EEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHH-------------------HHCT-STT-EEEEEE-G
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHH-------------------HHcCCCCCCEEEEEEeh
Confidence 4789999999999 44444432 222222111 12457789999888754
No 145
>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=49.10 E-value=70 Score=20.57 Aligned_cols=49 Identities=18% Similarity=0.204 Sum_probs=26.1
Q ss_pred EEEEEEEEec----ccEEEEecCeeEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEE
Q psy13107 85 LDAVVTQVNK----VGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLK 146 (170)
Q Consensus 85 ~~g~V~~i~~----~Gifv~lg~~~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~Vrvr 146 (170)
++|.|+...+ .|+|+.=. ..| .++......|.+......+++||.|++.
T Consensus 2 v~GvVTa~~~~~~~~GffiQd~-----------~~d--~~~~ts~gifV~~~~~~~~~~Gd~V~vt 54 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQDE-----------DGD--GDPATSEGIFVYTGSGADVAVGDLVRVT 54 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEcC-----------CCC--CCCcccceEEEecCCCCCCCCCCEEEEE
Confidence 6788998887 45554321 111 1111111233332223477999999886
No 146
>COG1417 Uncharacterized conserved protein [Function unknown]
Probab=48.85 E-value=54 Score=26.57 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=33.5
Q ss_pred CeEEEecCceeEEcCCCeEEEEEEEEEecCCceEEEEEecCCCCC
Q psy13107 125 PVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLG 169 (170)
Q Consensus 125 ~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ig~~~~~~LG 169 (170)
.|.-.-.+++..++.||..++||..++...+.+....++...-||
T Consensus 66 ~~ePlVAdEdV~V~~Gev~~IkIk~V~lPpnTVv~p~~~arna~G 110 (288)
T COG1417 66 VWEPLVADEDVEVEKGEVKRIKIKEVELPPNTVVVPLPYARNALG 110 (288)
T ss_pred EEEEEEecceeEEecCceEEEEEEEeccCCCcEEEEchhhcCcCc
Confidence 355555566779999999999999999999887765555543333
No 147
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=48.04 E-value=56 Score=19.12 Aligned_cols=15 Identities=33% Similarity=0.689 Sum_probs=12.0
Q ss_pred EEcCCCeEEEEEEEE
Q psy13107 136 VIQEDDEIRLKIVGT 150 (170)
Q Consensus 136 ~~~~Gd~VrvrV~~v 150 (170)
....||.|.|++..-
T Consensus 36 ~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 36 SLREGDEVEFKVVSP 50 (64)
T ss_pred cCCCCCEEEEEEEEc
Confidence 467799999998763
No 148
>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=46.03 E-value=67 Score=20.42 Aligned_cols=35 Identities=14% Similarity=0.158 Sum_probs=26.8
Q ss_pred EeEEEEEEEeecCCCCEEEEEEEEEecccEEEEec
Q psy13107 68 YPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIG 102 (170)
Q Consensus 68 ~~v~f~~i~f~p~~gev~~g~V~~i~~~Gifv~lg 102 (170)
+.+...+.......+..+.|++..++..|+.+.+.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~diS~~G~~~~~~ 42 (102)
T PF07238_consen 8 VPVNLPIRVILDPGGSSFQGTIVDISEGGCAFRSP 42 (102)
T ss_dssp EEEEEEEE-EEEETTEEEEEEEEEETTSEEEEEEC
T ss_pred EeccceEEEEEecCCcEEEEEEEEECccceEEEEC
Confidence 34444554466778888999999999999999884
No 149
>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=43.70 E-value=40 Score=20.23 Aligned_cols=24 Identities=29% Similarity=0.524 Sum_probs=17.6
Q ss_pred ecCCCCEEEEEEEEEecccEEEEe
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEI 101 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~l 101 (170)
.|.+|+.++.+|++..++-++.++
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 466799999999999999887654
No 150
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=41.40 E-value=81 Score=25.64 Aligned_cols=25 Identities=32% Similarity=0.550 Sum_probs=23.0
Q ss_pred ecCCCCEEEEEEEEEecccEEEEec
Q psy13107 78 RPFKGEVLDAVVTQVNKVGMFAEIG 102 (170)
Q Consensus 78 ~p~~gev~~g~V~~i~~~Gifv~lg 102 (170)
+|..||.-+|.|.+..+.|.++.+|
T Consensus 102 ~~~~Ge~ReG~v~~~~~~~~~v~iG 126 (272)
T COG2106 102 SPKEGEYREGLVIRRGKKGNLVDIG 126 (272)
T ss_pred CccceeecceEEEEecCCceEEEec
Confidence 5789999999999999999999887
No 151
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=39.04 E-value=98 Score=24.07 Aligned_cols=20 Identities=10% Similarity=0.155 Sum_probs=16.9
Q ss_pred CEEEEEEEEEecccEEEEec
Q psy13107 83 EVLDAVVTQVNKVGMFAEIG 102 (170)
Q Consensus 83 ev~~g~V~~i~~~Gifv~lg 102 (170)
..++|+|..+++.-|+++.-
T Consensus 40 ~tiEGrVvEV~~~~i~iesk 59 (213)
T PRK06763 40 STIEGRVVEVDNGVIVIKSK 59 (213)
T ss_pred ceeeeEEEEEeCCEEEEEec
Confidence 57899999999888888773
No 152
>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=38.23 E-value=39 Score=21.31 Aligned_cols=16 Identities=19% Similarity=0.358 Sum_probs=12.1
Q ss_pred eEEcCCCeEEEEEEEE
Q psy13107 135 VVIQEDDEIRLKIVGT 150 (170)
Q Consensus 135 ~~~~~Gd~VrvrV~~v 150 (170)
..++.||.|+|.+...
T Consensus 41 ~~l~~Gd~V~F~~~~~ 56 (70)
T PF11604_consen 41 AGLKPGDKVRFTFERT 56 (70)
T ss_dssp SS-STT-EEEEEEEEE
T ss_pred hcCCCCCEEEEEEEEC
Confidence 3789999999999875
No 153
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.57 E-value=1.5e+02 Score=22.54 Aligned_cols=30 Identities=17% Similarity=0.365 Sum_probs=24.7
Q ss_pred EEEEEEEEEecccEEEEecCe--eEEEEcCCC
Q psy13107 84 VLDAVVTQVNKVGMFAEIGPL--SCFISHHSI 113 (170)
Q Consensus 84 v~~g~V~~i~~~Gifv~lg~~--~~~i~~~~l 113 (170)
-+.|+|..+++..+-++++++ +.++|.+.+
T Consensus 4 ~l~G~v~~~~~~~~ii~~~GvGY~v~v~~~~~ 35 (186)
T PRK14600 4 SLSGIVEEVRSDYIILNVGNVGYIVYLSAKVL 35 (186)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHH
Confidence 378999999999999999874 888876554
No 154
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=34.50 E-value=74 Score=22.31 Aligned_cols=54 Identities=13% Similarity=0.215 Sum_probs=33.5
Q ss_pred EEEEEEEEeccc--EEEEecCeeEE-EEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEE
Q psy13107 85 LDAVVTQVNKVG--MFAEIGPLSCF-ISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVG 149 (170)
Q Consensus 85 ~~g~V~~i~~~G--ifv~lg~~~~~-i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~ 149 (170)
.+|+|.+++... +.++-+|+..+ .|.-.+ .|.-... ..-..++.||.|+|.+..
T Consensus 45 ~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM----~F~v~~~-------~~l~~lk~G~~V~F~~~~ 101 (115)
T PRK09838 45 GTGVVKGIDLESKKITIHHEPIPAVNWPEMTM----RFTITPQ-------TKMSEIKTGDKVAFNFVQ 101 (115)
T ss_pred EEEEEEEEeCCCCEEEEeecccccCCCCCccc----cccCCCh-------hhhccCCCCCEEEEEEEE
Confidence 489999998877 77777765332 232222 2332221 011268999999999875
No 155
>TIGR02866 CoxB cytochrome c oxidase, subunit II. Cytochrome c oxidase is the terminal electron acceptor of mitochondria (and one of several possible acceptors in prokaryotes) in the electron transport chain of aerobic respiration. The enzyme couples the oxidation of reduced cytochrome c with the reduction of molecular oxygen to water. This process results in the pumping of four protons across the membrane which are used in the proton gradient powered synthesis of ATP. The oxidase contains two heme a cofactors and three copper atoms as well as other bound ions.
Probab=33.16 E-value=70 Score=24.41 Aligned_cols=21 Identities=24% Similarity=0.444 Sum_probs=18.0
Q ss_pred ceeEEcCCCeEEEEEEEEEec
Q psy13107 133 GEVVIQEDDEIRLKIVGTRVD 153 (170)
Q Consensus 133 ~~~~~~~Gd~VrvrV~~v~~~ 153 (170)
+...+..|+.|++++.+.|..
T Consensus 117 ~~l~vp~g~~v~~~~ts~DV~ 137 (201)
T TIGR02866 117 NELVVPAGTPVRLQVTSKDVI 137 (201)
T ss_pred CEEEEEcCCEEEEEEEeCchh
Confidence 357899999999999998864
No 156
>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=32.69 E-value=90 Score=17.91 Aligned_cols=19 Identities=5% Similarity=0.247 Sum_probs=16.9
Q ss_pred CCCEEEEEEEEEecccEEE
Q psy13107 81 KGEVLDAVVTQVNKVGMFA 99 (170)
Q Consensus 81 ~gev~~g~V~~i~~~Gifv 99 (170)
.++.++|++..+++.|..+
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 5788999999999999875
No 157
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=31.22 E-value=1.7e+02 Score=22.34 Aligned_cols=30 Identities=17% Similarity=0.166 Sum_probs=25.1
Q ss_pred EEEEEEEEEecccEEEEecCe--eEEEEcCCC
Q psy13107 84 VLDAVVTQVNKVGMFAEIGPL--SCFISHHSI 113 (170)
Q Consensus 84 v~~g~V~~i~~~Gifv~lg~~--~~~i~~~~l 113 (170)
-+.|+|..+.+..+-++++.+ +.++|.+.+
T Consensus 4 ~l~G~v~~~~~~~vvi~v~GvGY~v~v~~~~~ 35 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNGVGYELQVPMTCA 35 (191)
T ss_pred eEEEEEEEEcCCEEEEEECCEEEEEEecHHHH
Confidence 378999999999999999875 888876554
No 158
>COG3175 COX11 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=30.80 E-value=2.4e+02 Score=21.64 Aligned_cols=42 Identities=14% Similarity=0.153 Sum_probs=32.6
Q ss_pred CCCeEEEecCceeEEcCCCeEEEEEEEEEecCCceEEEEEec
Q psy13107 123 SNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLM 164 (170)
Q Consensus 123 ~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~i~~ig~~~ 164 (170)
..+|.|........+.+|+...+.-.+.+.....+...++-|
T Consensus 75 ~lpW~F~p~q~~v~v~pGet~~~~y~a~N~sd~~itg~A~~n 116 (195)
T COG3175 75 GLPWRFRPVQREVYVRPGETNLIFYEAENLSDKPITGQATYN 116 (195)
T ss_pred CCceeeEecCceeEeccCceEEEEEEEecCCCCCceeEEecc
Confidence 347888888778899999999999888887766666555444
No 159
>PF07177 Neuralized: Neuralized; InterPro: IPR006573 NEUZ is a domain of unknown function found in neuralized proteins, i.e. proteins involved in the specification of the neuroblast during cellular differentiation. ; PDB: 2YUE_A 2E63_A.
Probab=30.77 E-value=96 Score=19.50 Aligned_cols=30 Identities=17% Similarity=0.222 Sum_probs=16.9
Q ss_pred eEEcCCCeEEEEEEEEEecCCceEEEEEec
Q psy13107 135 VVIQEDDEIRLKIVGTRVDASGIFAIGTLM 164 (170)
Q Consensus 135 ~~~~~Gd~VrvrV~~v~~~~~~i~~ig~~~ 164 (170)
+.++.|+.+.+||..++..=..-..+|-+.
T Consensus 37 rPl~~~E~~~v~I~~~~~~wsG~L~~GvT~ 66 (69)
T PF07177_consen 37 RPLRIGEKFEVRIDEVEPSWSGSLRIGVTS 66 (69)
T ss_dssp S-B-TT-EEEEEEEEE-SSSSS--EEEEES
T ss_pred CCccCCCEEEEEEEecCCCceeEEEEeeEc
Confidence 489999999999999864333333555544
No 160
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=29.84 E-value=1.8e+02 Score=19.79 Aligned_cols=57 Identities=21% Similarity=0.142 Sum_probs=36.5
Q ss_pred eecCCCCEEEEEEEEEecccEE-EEecCe-eEEEEcCCCCCCceecCCCCCeEEEecCceeEEcCCCeEEEEEEEEE
Q psy13107 77 FRPFKGEVLDAVVTQVNKVGMF-AEIGPL-SCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQEDDEIRLKIVGTR 151 (170)
Q Consensus 77 f~p~~gev~~g~V~~i~~~Gif-v~lg~~-~~~i~~~~l~~~~~~d~~~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 151 (170)
..|..|| +.|+|+.....+.| |.+... ..+.+ ||.-+. . ...++.||.|.|.....+
T Consensus 16 ~~p~e~e-~~g~V~~~lG~~~~~V~~~dG~~~la~---i~GK~R-------------k-~IwI~~GD~VlVe~~~~~ 74 (100)
T PRK04012 16 PMPEEGE-VFGVVEQMLGANRVRVRCMDGVERMGR---IPGKMK-------------K-RMWIREGDVVIVAPWDFQ 74 (100)
T ss_pred cCCCCCE-EEEEEEEEcCCCEEEEEeCCCCEEEEE---Echhhc-------------c-cEEecCCCEEEEEecccC
Confidence 4555555 78999999999988 566543 44443 332211 1 236788999988876655
No 161
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.01 E-value=1.4e+02 Score=22.82 Aligned_cols=29 Identities=14% Similarity=0.070 Sum_probs=23.8
Q ss_pred EEEEEEEEEecccEEEEecCe--eEEEEcCC
Q psy13107 84 VLDAVVTQVNKVGMFAEIGPL--SCFISHHS 112 (170)
Q Consensus 84 v~~g~V~~i~~~Gifv~lg~~--~~~i~~~~ 112 (170)
-+.|+|..+.+..+-++++.+ +.++|.+.
T Consensus 4 ~l~G~i~~~~~~~vvi~~~GvGY~V~vs~~~ 34 (197)
T PRK14603 4 YLSGVVLEKREGSAVLLAGGVGLEVQCPAPT 34 (197)
T ss_pred eEEEEEEEecCCEEEEEECCEEEEEEcCHHH
Confidence 368999999999999999774 88887654
No 162
>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=26.43 E-value=1e+02 Score=20.08 Aligned_cols=18 Identities=6% Similarity=0.362 Sum_probs=14.9
Q ss_pred EEcCCCeEEEEEEEEEec
Q psy13107 136 VIQEDDEIRLKIVGTRVD 153 (170)
Q Consensus 136 ~~~~Gd~VrvrV~~v~~~ 153 (170)
.|++||.|.+|+.-.+.+
T Consensus 10 iYrPGetV~~~~~~~~~~ 27 (99)
T PF01835_consen 10 IYRPGETVHFRAIVRDLD 27 (99)
T ss_dssp EE-TTSEEEEEEEEEEEC
T ss_pred CcCCCCEEEEEEEEeccc
Confidence 899999999999966665
No 163
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=21.83 E-value=85 Score=20.17 Aligned_cols=14 Identities=14% Similarity=0.513 Sum_probs=12.2
Q ss_pred EEcCCCeEEEEEEE
Q psy13107 136 VIQEDDEIRLKIVG 149 (170)
Q Consensus 136 ~~~~Gd~VrvrV~~ 149 (170)
.|+.||.++|++..
T Consensus 2 ~~~~Ge~v~~~~~~ 15 (83)
T PF14326_consen 2 VYRVGERVRFRVTS 15 (83)
T ss_pred cccCCCEEEEEEEe
Confidence 57899999999987
No 164
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.44 E-value=2.1e+02 Score=22.00 Aligned_cols=30 Identities=7% Similarity=0.192 Sum_probs=24.6
Q ss_pred EEEEEEEEEecccEEEEecCe--eEEEEcCCC
Q psy13107 84 VLDAVVTQVNKVGMFAEIGPL--SCFISHHSI 113 (170)
Q Consensus 84 v~~g~V~~i~~~Gifv~lg~~--~~~i~~~~l 113 (170)
-+.|+|..+.+..+-++++.+ +.++|.+.+
T Consensus 4 ~l~G~v~~~~~~~vvidv~GVGY~v~vs~~~~ 35 (196)
T PRK13901 4 KIYGKIIEKKESSIVIMATPFEFELLVSSFCL 35 (196)
T ss_pred EEEEEEEEEeCCEEEEEeCCEEEEEEecHHHH
Confidence 378999999999999999875 888876543
No 165
>TIGR01433 CyoA cytochrome o ubiquinol oxidase subunit II. This enzyme catalyzes the oxidation of ubiquinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. Subunit II is responsible for binding and oxidation of the ubiquinone substrate. This sequence is closely related to QoxA, which oxidizes quinol in gram positive bacteria but which is in complex with subunits which utilize cytochromes a in the reduction of molecular oxygen. Slightly more distantly related is subunit II of cytochrome c oxidase which uses cyt. c as the oxidant.
Probab=20.15 E-value=1.6e+02 Score=23.09 Aligned_cols=21 Identities=24% Similarity=0.357 Sum_probs=18.5
Q ss_pred ceeEEcCCCeEEEEEEEEEec
Q psy13107 133 GEVVIQEDDEIRLKIVGTRVD 153 (170)
Q Consensus 133 ~~~~~~~Gd~VrvrV~~v~~~ 153 (170)
++.++-.|..||+++.+.|..
T Consensus 139 nel~lP~g~pV~~~ltS~DVi 159 (226)
T TIGR01433 139 NEIAFPVNTPINFKITSNSVM 159 (226)
T ss_pred ceEEEECCCEEEEEEEECchh
Confidence 467999999999999999864
Done!