Query psy18072
Match_columns 174
No_of_seqs 280 out of 1421
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 21:55:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy18072.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/18072hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00248 eukaryotic translatio 100.0 2.9E-32 6.3E-37 233.2 17.2 153 1-154 3-303 (319)
2 KOG2916|consensus 100.0 1.8E-28 3.8E-33 202.9 12.6 148 1-148 1-296 (304)
3 COG2996 Predicted RNA-bindinin 99.9 2.7E-21 5.8E-26 161.2 10.6 115 15-141 155-274 (287)
4 COG1093 SUI2 Translation initi 99.9 5.3E-21 1.1E-25 158.6 12.0 75 5-79 1-75 (269)
5 COG1098 VacB Predicted RNA bin 99.8 6E-19 1.3E-23 131.8 6.6 73 14-88 4-76 (129)
6 PRK03987 translation initiatio 99.7 2.8E-16 6.1E-21 132.1 12.8 71 9-79 2-72 (262)
7 PHA02945 interferon resistance 99.6 1.4E-15 3.1E-20 107.4 8.3 73 10-85 6-81 (88)
8 cd05686 S1_pNO40 S1_pNO40: pNO 99.6 2.7E-15 5.9E-20 102.7 9.0 72 13-85 1-72 (73)
9 cd05704 S1_Rrp5_repeat_hs13 S1 99.6 2.8E-15 6.1E-20 102.6 7.7 69 14-85 2-71 (72)
10 cd05705 S1_Rrp5_repeat_hs14 S1 99.6 4.1E-15 8.9E-20 102.5 7.9 64 14-79 2-68 (74)
11 cd04452 S1_IF2_alpha S1_IF2_al 99.6 1.4E-14 3E-19 98.9 9.2 73 13-85 1-74 (76)
12 PRK08582 hypothetical protein; 99.6 1.7E-14 3.8E-19 110.8 9.3 73 14-88 4-76 (139)
13 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.6 2.2E-14 4.8E-19 100.6 8.8 78 12-91 3-84 (86)
14 PRK08059 general stress protei 99.5 7.8E-15 1.7E-19 110.3 5.7 99 14-115 6-105 (123)
15 cd05706 S1_Rrp5_repeat_sc10 S1 99.5 8.1E-14 1.7E-18 94.7 9.1 70 14-85 2-72 (73)
16 cd05698 S1_Rrp5_repeat_hs6_sc5 99.5 6.3E-14 1.4E-18 94.4 8.2 68 16-85 1-69 (70)
17 cd05707 S1_Rrp5_repeat_sc11 S1 99.5 6.2E-14 1.3E-18 94.2 8.0 62 16-79 1-62 (68)
18 cd04454 S1_Rrp4_like S1_Rrp4_l 99.5 1E-13 2.3E-18 96.5 9.1 79 11-91 2-80 (82)
19 cd05703 S1_Rrp5_repeat_hs12_sc 99.5 8E-14 1.7E-18 95.7 8.3 68 16-85 1-71 (73)
20 cd05692 S1_RPS1_repeat_hs4 S1_ 99.5 8.6E-14 1.9E-18 92.2 8.2 68 16-85 1-68 (69)
21 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.5 8.8E-14 1.9E-18 93.7 8.2 67 16-84 1-68 (69)
22 PF00575 S1: S1 RNA binding do 99.5 1.3E-13 2.9E-18 93.6 8.9 70 14-85 3-73 (74)
23 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.5 1.2E-13 2.5E-18 94.3 8.2 67 16-84 1-70 (71)
24 PRK05807 hypothetical protein; 99.5 1.3E-13 2.7E-18 105.7 9.0 72 14-88 4-75 (136)
25 cd04461 S1_Rrp5_repeat_hs8_sc7 99.5 1.2E-13 2.6E-18 96.5 8.1 69 14-84 13-82 (83)
26 cd05691 S1_RPS1_repeat_ec6 S1_ 99.5 2.4E-13 5.1E-18 91.8 8.2 69 16-86 1-70 (73)
27 cd05689 S1_RPS1_repeat_ec4 S1_ 99.5 3.2E-13 6.9E-18 91.5 8.6 65 12-79 1-66 (72)
28 cd05690 S1_RPS1_repeat_ec5 S1_ 99.5 2.4E-13 5.2E-18 91.1 7.4 62 16-79 1-63 (69)
29 PRK07252 hypothetical protein; 99.5 3.1E-13 6.7E-18 101.5 8.7 71 14-86 2-73 (120)
30 COG0539 RpsA Ribosomal protein 99.5 2E-13 4.4E-18 124.1 8.8 74 10-87 188-262 (541)
31 cd05708 S1_Rrp5_repeat_sc12 S1 99.4 5.2E-13 1.1E-17 90.9 8.5 72 14-86 1-73 (77)
32 cd05684 S1_DHX8_helicase S1_DH 99.4 9.1E-13 2E-17 91.1 8.4 70 16-86 1-72 (79)
33 cd05687 S1_RPS1_repeat_ec1_hs1 99.4 1E-12 2.2E-17 88.5 8.3 67 16-84 1-68 (70)
34 COG0539 RpsA Ribosomal protein 99.4 3E-13 6.6E-18 123.0 7.1 79 7-88 270-349 (541)
35 cd05685 S1_Tex S1_Tex: The C-t 99.4 1E-12 2.2E-17 86.9 7.4 61 16-78 1-61 (68)
36 cd04472 S1_PNPase S1_PNPase: P 99.4 1.6E-12 3.4E-17 86.3 8.1 67 16-84 1-67 (68)
37 PRK09521 exosome complex RNA-b 99.4 1.6E-13 3.4E-18 110.1 3.2 96 11-110 60-163 (189)
38 cd05693 S1_Rrp5_repeat_hs1_sc1 99.4 1.7E-12 3.7E-17 94.5 7.4 72 14-87 2-96 (100)
39 cd05702 S1_Rrp5_repeat_hs11_sc 99.4 3.1E-12 6.8E-17 86.6 7.5 64 16-81 1-66 (70)
40 cd05791 S1_CSL4 S1_CSL4: CSL4, 99.4 2.7E-12 5.9E-17 92.1 7.6 80 11-92 2-91 (92)
41 cd04453 S1_RNase_E S1_RNase_E: 99.4 3.3E-12 7.1E-17 90.9 7.9 64 14-79 6-74 (88)
42 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.4 4E-12 8.8E-17 85.5 7.7 60 16-79 1-60 (66)
43 TIGR02696 pppGpp_PNP guanosine 99.4 2E-12 4.4E-17 120.9 8.4 71 12-84 644-718 (719)
44 PRK04163 exosome complex RNA-b 99.4 3.1E-12 6.8E-17 106.0 8.6 80 10-91 58-141 (235)
45 cd05694 S1_Rrp5_repeat_hs2_sc2 99.3 8.3E-12 1.8E-16 86.1 8.9 66 14-86 3-69 (74)
46 PHA02858 EIF2a-like PKR inhibi 99.3 4.3E-12 9.3E-17 89.0 7.3 67 11-80 12-79 (86)
47 smart00316 S1 Ribosomal protei 99.3 8.6E-12 1.9E-16 82.3 8.3 69 15-85 2-71 (72)
48 cd05688 S1_RPS1_repeat_ec3 S1_ 99.3 9.2E-12 2E-16 82.5 7.8 61 15-78 1-61 (68)
49 PLN00207 polyribonucleotide nu 99.3 5.6E-12 1.2E-16 120.2 7.9 73 13-87 751-824 (891)
50 PRK07400 30S ribosomal protein 99.3 1.9E-11 4E-16 105.5 10.1 73 10-86 192-265 (318)
51 COG1096 Predicted RNA-binding 99.3 1.8E-12 3.8E-17 103.4 3.0 113 10-126 59-180 (188)
52 PRK13806 rpsA 30S ribosomal pr 99.3 1E-11 2.2E-16 112.6 8.4 74 10-86 375-449 (491)
53 cd04465 S1_RPS1_repeat_ec2_hs2 99.3 3.8E-11 8.2E-16 80.4 8.3 65 16-85 1-66 (67)
54 PRK11824 polynucleotide phosph 99.2 2.2E-11 4.8E-16 114.4 9.2 72 13-86 619-690 (693)
55 cd04473 S1_RecJ_like S1_RecJ_l 99.2 8E-11 1.7E-15 81.4 9.4 62 14-85 15-76 (77)
56 cd04471 S1_RNase_R S1_RNase_R: 99.2 8.1E-11 1.7E-15 81.2 9.0 69 15-84 1-81 (83)
57 PRK07899 rpsA 30S ribosomal pr 99.2 3.6E-11 7.9E-16 108.9 8.8 73 10-86 204-277 (486)
58 TIGR03591 polynuc_phos polyrib 99.2 3.6E-11 7.9E-16 112.9 7.8 68 12-81 615-682 (684)
59 PRK12269 bifunctional cytidyla 99.2 4.4E-11 9.5E-16 114.5 8.2 75 10-87 574-650 (863)
60 PRK13806 rpsA 30S ribosomal pr 99.2 6.7E-11 1.4E-15 107.3 8.8 75 10-87 288-364 (491)
61 PRK07899 rpsA 30S ribosomal pr 99.2 6.1E-11 1.3E-15 107.5 8.5 81 9-92 288-369 (486)
62 cd00164 S1_like S1_like: Ribos 99.1 1.4E-10 3E-15 75.1 6.5 58 19-78 1-58 (65)
63 cd04460 S1_RpoE S1_RpoE: RpoE, 99.1 3.7E-10 8E-15 81.4 8.9 73 17-92 1-90 (99)
64 TIGR00717 rpsA ribosomal prote 99.1 2.7E-10 5.8E-15 103.2 8.7 73 10-85 442-515 (516)
65 PRK12269 bifunctional cytidyla 99.1 3.1E-10 6.8E-15 108.7 8.8 76 8-86 659-736 (863)
66 COG1185 Pnp Polyribonucleotide 99.1 2.9E-10 6.3E-15 105.2 7.2 72 13-86 617-688 (692)
67 PRK06676 rpsA 30S ribosomal pr 99.1 6.2E-10 1.3E-14 97.8 8.6 75 11-88 274-349 (390)
68 PRK07400 30S ribosomal protein 99.1 9.1E-10 2E-14 95.0 9.4 73 13-87 29-102 (318)
69 PRK06299 rpsA 30S ribosomal pr 99.0 5.7E-10 1.2E-14 102.3 8.3 75 10-87 369-445 (565)
70 PRK06676 rpsA 30S ribosomal pr 99.0 1.3E-09 2.8E-14 95.7 8.5 71 14-87 191-262 (390)
71 PRK06299 rpsA 30S ribosomal pr 99.0 1.2E-09 2.7E-14 100.1 8.5 73 14-88 459-532 (565)
72 COG2183 Tex Transcriptional ac 99.0 7.4E-10 1.6E-14 103.9 6.9 76 12-89 655-731 (780)
73 PRK00087 4-hydroxy-3-methylbut 99.0 1.7E-09 3.7E-14 101.1 8.8 76 10-88 558-634 (647)
74 TIGR02063 RNase_R ribonuclease 98.9 3.1E-09 6.7E-14 100.2 8.7 78 3-84 618-707 (709)
75 PRK08563 DNA-directed RNA poly 98.9 1.5E-08 3.2E-13 81.0 9.9 87 13-108 79-182 (187)
76 TIGR00717 rpsA ribosomal prote 98.9 4.9E-09 1.1E-13 95.0 8.0 73 11-86 269-343 (516)
77 PRK00087 4-hydroxy-3-methylbut 98.9 5.6E-09 1.2E-13 97.6 8.4 71 14-87 476-547 (647)
78 cd04455 S1_NusA S1_NusA: N-uti 98.9 1.4E-08 3E-13 68.3 7.5 57 14-79 2-58 (67)
79 COG1097 RRP4 RNA-binding prote 98.8 1.4E-08 3E-13 84.1 7.8 85 5-91 54-142 (239)
80 COG1107 Archaea-specific RecJ- 98.8 1.2E-09 2.5E-14 99.8 1.2 110 14-131 121-243 (715)
81 PRK11642 exoribonuclease R; Pr 98.8 1.4E-08 3E-13 97.2 7.9 73 3-79 634-717 (813)
82 TIGR00448 rpoE DNA-directed RN 98.8 2.9E-08 6.3E-13 79.0 8.5 75 14-91 80-171 (179)
83 COG1095 RPB7 DNA-directed RNA 98.8 1.1E-08 2.4E-13 81.6 5.9 76 13-91 79-171 (183)
84 cd05790 S1_Rrp40 S1_Rrp40: Rrp 98.7 5.3E-08 1.1E-12 69.2 7.7 75 11-88 2-76 (86)
85 TIGR00358 3_prime_RNase VacB a 98.7 2.8E-08 6.1E-13 93.1 8.0 73 3-79 563-646 (654)
86 PF10447 EXOSC1: Exosome compo 98.7 7E-08 1.5E-12 68.0 6.1 64 12-75 1-82 (82)
87 KOG1067|consensus 98.5 9.5E-08 2.1E-12 87.2 5.0 68 15-84 668-735 (760)
88 PRK09202 nusA transcription el 98.5 6.6E-07 1.4E-11 81.0 9.0 94 8-116 127-223 (470)
89 TIGR00757 RNaseEG ribonuclease 98.4 6.9E-06 1.5E-10 73.4 13.0 61 11-74 22-96 (414)
90 PRK05054 exoribonuclease II; P 98.3 1.3E-06 2.8E-11 81.9 7.7 75 3-79 550-636 (644)
91 KOG1070|consensus 98.3 1.2E-06 2.7E-11 86.4 6.7 75 8-86 594-669 (1710)
92 cd04462 S1_RNAPII_Rpb7 S1_RNAP 98.3 6.6E-06 1.4E-10 58.5 7.9 61 15-78 1-72 (88)
93 PRK12327 nusA transcription el 98.2 8.2E-06 1.8E-10 71.8 8.8 92 10-116 129-223 (362)
94 TIGR01953 NusA transcription t 98.2 9.7E-06 2.1E-10 70.8 9.2 88 14-116 130-221 (341)
95 TIGR02062 RNase_B exoribonucle 98.1 8.1E-06 1.8E-10 76.6 7.1 75 3-79 546-632 (639)
96 COG0557 VacB Exoribonuclease R 98.1 8.1E-06 1.8E-10 77.3 6.5 72 3-78 613-695 (706)
97 PTZ00162 DNA-directed RNA poly 98.0 3.2E-05 7E-10 61.6 8.2 62 14-78 80-153 (176)
98 KOG1070|consensus 97.8 7.6E-05 1.7E-09 74.2 8.4 72 14-87 1161-1233(1710)
99 KOG3409|consensus 97.8 8.2E-05 1.8E-09 59.1 6.8 85 8-92 61-153 (193)
100 cd05699 S1_Rrp5_repeat_hs7 S1_ 97.7 0.00026 5.7E-09 48.7 7.0 56 16-73 1-60 (72)
101 PF13509 S1_2: S1 domain; PDB: 97.5 0.00058 1.3E-08 45.1 7.2 60 15-85 1-60 (61)
102 PRK12328 nusA transcription el 97.5 0.00043 9.4E-09 61.1 8.4 94 8-116 131-229 (374)
103 KOG1856|consensus 97.5 0.00016 3.4E-09 70.8 5.9 63 15-79 985-1050(1299)
104 PRK11712 ribonuclease G; Provi 97.5 0.002 4.3E-08 59.0 12.1 59 15-75 38-110 (489)
105 PRK12329 nusA transcription el 97.4 0.00095 2.1E-08 60.1 9.2 97 8-116 145-248 (449)
106 PRK10811 rne ribonuclease E; R 97.2 0.00067 1.4E-08 66.0 6.4 61 13-75 36-107 (1068)
107 KOG3013|consensus 96.6 0.0029 6.3E-08 53.3 4.2 81 9-91 79-169 (301)
108 COG1530 CafA Ribonucleases G a 96.4 0.035 7.6E-07 50.8 10.7 62 15-79 37-105 (487)
109 KOG3298|consensus 95.7 0.058 1.3E-06 42.6 7.2 61 15-78 81-152 (170)
110 PF08292 RNA_pol_Rbc25: RNA po 94.0 0.37 7.9E-06 36.3 7.5 61 15-77 3-76 (122)
111 KOG1004|consensus 92.9 0.55 1.2E-05 38.7 7.3 65 12-79 62-126 (230)
112 PF10246 MRP-S35: Mitochondria 92.3 0.96 2.1E-05 33.2 7.2 51 15-74 23-73 (104)
113 PRK15464 cold shock-like prote 89.9 1.2 2.7E-05 30.2 5.6 51 19-74 5-57 (70)
114 PRK15463 cold shock-like prote 89.1 1.5 3.3E-05 29.6 5.5 51 19-74 5-57 (70)
115 TIGR00008 infA translation ini 88.8 2.1 4.6E-05 29.0 6.0 54 18-78 6-61 (68)
116 PRK12442 translation initiatio 88.2 2 4.3E-05 30.6 5.7 55 18-79 8-64 (87)
117 PRK09890 cold shock protein Cs 87.3 2.8 6.1E-05 28.2 6.0 51 19-74 5-57 (70)
118 PF00313 CSD: 'Cold-shock' DNA 87.3 5.5 0.00012 25.9 7.3 51 19-74 1-53 (66)
119 cd04322 LysRS_N LysRS_N: N-ter 86.6 3.5 7.5E-05 29.6 6.5 53 18-70 3-58 (108)
120 PF04871 Uso1_p115_C: Uso1 / p 86.5 1.2 2.7E-05 34.0 4.2 20 131-150 101-120 (136)
121 TIGR00638 Mop molybdenum-pteri 85.6 2.6 5.6E-05 27.3 5.0 55 16-74 6-61 (69)
122 PTZ00248 eukaryotic translatio 84.6 0.034 7.4E-07 48.3 -5.8 47 9-58 100-153 (319)
123 COG2996 Predicted RNA-bindinin 84.5 5.2 0.00011 34.3 7.4 51 14-72 4-54 (287)
124 PRK10354 RNA chaperone/anti-te 84.2 4.8 0.0001 27.0 5.9 51 19-74 5-57 (70)
125 PRK09507 cspE cold shock prote 82.3 6.3 0.00014 26.4 5.9 53 18-75 3-57 (69)
126 PRK10943 cold shock-like prote 82.1 5.3 0.00012 26.8 5.4 53 18-75 3-57 (69)
127 PRK09937 stationary phase/star 80.6 6.9 0.00015 26.7 5.6 52 20-76 3-56 (74)
128 COG2106 Uncharacterized conser 79.1 5.7 0.00012 33.9 5.8 58 3-75 92-150 (272)
129 PF03459 TOBE: TOBE domain; I 76.0 4.1 9E-05 26.1 3.3 51 16-73 4-58 (64)
130 TIGR02381 cspD cold shock doma 75.9 7.5 0.00016 25.9 4.6 50 20-74 3-54 (68)
131 cd05701 S1_Rrp5_repeat_hs10 S1 75.9 3.9 8.4E-05 27.6 3.1 59 18-77 3-61 (69)
132 KOG1832|consensus 74.9 1.9 4.1E-05 42.7 2.0 6 134-139 1397-1402(1516)
133 COG4776 Rnb Exoribonuclease II 74.7 1.1 2.5E-05 41.1 0.5 74 3-78 550-635 (645)
134 PRK14998 cold shock-like prote 74.2 13 0.00027 25.3 5.5 52 20-76 3-56 (73)
135 COG1278 CspC Cold shock protei 73.4 7.6 0.00016 26.3 4.1 50 20-74 3-54 (67)
136 cd05700 S1_Rrp5_repeat_hs9 S1_ 72.1 13 0.00028 24.8 4.8 56 16-77 1-56 (65)
137 COG1915 Uncharacterized conser 71.3 73 0.0016 28.1 11.2 103 29-132 109-222 (415)
138 PF04931 DNA_pol_phi: DNA poly 70.2 2.7 5.8E-05 40.7 1.8 15 124-138 619-633 (784)
139 cd04458 CSP_CDS Cold-Shock Pro 68.6 18 0.00039 23.3 5.1 51 20-75 2-54 (65)
140 cd04482 RPA2_OBF_like RPA2_OBF 67.4 15 0.00033 25.8 4.8 51 18-71 2-57 (91)
141 PRK04012 translation initiatio 67.2 30 0.00066 25.1 6.4 59 12-78 17-76 (100)
142 smart00357 CSP Cold shock prot 67.2 17 0.00037 22.5 4.7 48 21-75 2-50 (64)
143 cd04320 AspRS_cyto_N AspRS_cyt 67.0 36 0.00078 23.9 6.8 52 18-70 3-60 (102)
144 PRK00484 lysS lysyl-tRNA synth 66.8 21 0.00046 32.8 6.9 52 18-70 58-112 (491)
145 KOG4078|consensus 66.6 20 0.00044 27.9 5.6 53 14-75 81-133 (173)
146 KOG4134|consensus 66.5 4 8.7E-05 34.0 1.9 65 5-79 98-164 (253)
147 COG0361 InfA Translation initi 64.8 37 0.00081 23.4 6.2 56 16-77 6-62 (75)
148 COG1545 Predicted nucleic-acid 64.2 43 0.00092 25.5 7.1 59 12-79 60-127 (140)
149 TIGR00499 lysS_bact lysyl-tRNA 63.4 28 0.0006 32.1 7.0 54 18-71 57-113 (496)
150 cd04319 PhAsnRS_like_N PhAsnRS 61.7 52 0.0011 23.2 6.8 52 18-71 3-57 (103)
151 TIGR00237 xseA exodeoxyribonuc 61.0 86 0.0019 28.3 9.6 118 16-140 19-153 (432)
152 COG3269 Predicted RNA-binding 60.9 47 0.001 22.9 6.0 49 14-78 14-62 (73)
153 PF01336 tRNA_anti-codon: OB-f 59.0 44 0.00096 21.2 6.1 50 18-71 2-54 (75)
154 PRK06763 F0F1 ATP synthase sub 58.9 36 0.00077 28.0 6.0 46 16-71 39-84 (213)
155 PF07076 DUF1344: Protein of u 58.5 48 0.001 22.0 5.6 51 17-77 3-53 (61)
156 TIGR00458 aspS_arch aspartyl-t 58.4 35 0.00076 30.7 6.6 52 18-70 16-70 (428)
157 PF12857 TOBE_3: TOBE-like dom 58.1 31 0.00066 22.0 4.6 53 16-71 4-56 (58)
158 cd04487 RecJ_OBF2_like RecJ_OB 57.5 39 0.00085 22.7 5.3 50 18-71 2-53 (73)
159 PRK08572 rps17p 30S ribosomal 57.2 29 0.00062 25.7 4.8 64 4-70 18-86 (108)
160 PF08206 OB_RNB: Ribonuclease 56.8 45 0.00097 21.3 5.3 44 21-74 1-44 (58)
161 PRK12445 lysyl-tRNA synthetase 56.5 38 0.00083 31.3 6.6 54 18-71 69-125 (505)
162 cd04318 EcAsnRS_like_N EcAsnRS 54.2 63 0.0014 21.6 7.0 50 18-71 3-57 (82)
163 cd04316 ND_PkAspRS_like_N ND_P 53.9 77 0.0017 22.5 6.7 52 19-71 17-71 (108)
164 KOG0943|consensus 53.5 8.2 0.00018 39.8 1.8 6 101-106 1682-1687(3015)
165 KOG3130|consensus 52.6 8 0.00017 35.0 1.5 7 117-123 204-210 (514)
166 TIGR03630 arch_S17P archaeal r 51.6 41 0.00088 24.6 4.8 64 4-70 16-84 (102)
167 KOG1991|consensus 50.7 16 0.00034 36.4 3.3 20 128-147 872-891 (1010)
168 KOG3297|consensus 50.4 56 0.0012 26.6 5.8 61 15-77 81-158 (202)
169 cd04489 ExoVII_LU_OBF ExoVII_L 50.0 62 0.0014 21.0 5.3 51 18-73 3-57 (78)
170 cd05793 S1_IF1A S1_IF1A: Trans 50.0 64 0.0014 22.1 5.4 52 19-77 2-54 (77)
171 PRK10334 mechanosensitive chan 49.0 39 0.00085 28.8 5.1 49 8-59 126-179 (286)
172 PTZ00417 lysine-tRNA ligase; P 48.2 60 0.0013 30.7 6.6 54 18-71 136-195 (585)
173 cd04323 AsnRS_cyto_like_N AsnR 48.0 84 0.0018 21.2 6.2 51 18-71 3-56 (84)
174 PF03066 Nucleoplasmin: Nucleo 47.6 6.2 0.00013 30.6 0.0 7 117-123 96-102 (149)
175 cd04317 EcAspRS_like_N EcAspRS 47.6 69 0.0015 23.6 5.8 51 18-71 18-71 (135)
176 smart00652 eIF1a eukaryotic tr 47.5 94 0.002 21.6 6.0 54 16-76 4-58 (83)
177 PLN02502 lysyl-tRNA synthetase 47.2 68 0.0015 30.1 6.8 54 18-71 112-170 (553)
178 PF01938 TRAM: TRAM domain; I 46.4 74 0.0016 20.1 6.1 50 15-77 4-53 (61)
179 cd00210 PTS_IIA_glc PTS_IIA, P 46.1 48 0.001 24.9 4.7 56 19-76 42-102 (124)
180 COG1190 LysU Lysyl-tRNA synthe 45.6 54 0.0012 30.5 5.7 56 17-72 64-122 (502)
181 PF12869 tRNA_anti-like: tRNA_ 44.6 77 0.0017 23.3 5.6 53 17-73 70-128 (144)
182 cd04508 TUDOR Tudor domains ar 44.3 43 0.00094 19.8 3.5 35 15-50 11-46 (48)
183 PRK09439 PTS system glucose-sp 43.0 70 0.0015 25.3 5.3 57 19-77 64-125 (169)
184 cd04486 YhcR_OBF_like YhcR_OBF 42.0 40 0.00086 23.0 3.4 45 19-71 2-54 (78)
185 PRK02983 lysS lysyl-tRNA synth 41.9 77 0.0017 32.2 6.6 54 18-71 655-711 (1094)
186 PRK13901 ruvA Holliday junctio 41.8 1.8E+02 0.0038 23.6 7.6 52 18-79 4-56 (196)
187 COG1096 Predicted RNA-binding 41.3 47 0.001 26.9 4.2 38 5-46 112-149 (188)
188 PF07238 PilZ: PilZ domain; I 41.2 96 0.0021 20.5 5.3 23 15-37 21-43 (102)
189 KOG1832|consensus 41.1 15 0.00033 36.7 1.5 32 136-167 1393-1424(1516)
190 PRK14600 ruvA Holliday junctio 40.5 1.9E+02 0.0041 23.1 7.6 47 18-74 4-50 (186)
191 KOG3241|consensus 40.4 19 0.00042 29.1 1.8 6 98-103 95-100 (227)
192 cd05791 S1_CSL4 S1_CSL4: CSL4, 39.2 33 0.00072 24.1 2.7 25 13-37 61-86 (92)
193 smart00333 TUDOR Tudor domain. 39.0 75 0.0016 19.4 4.1 35 15-50 15-50 (57)
194 TIGR00830 PTBA PTS system, glu 38.8 76 0.0016 23.7 4.7 56 19-76 42-102 (121)
195 PRK05159 aspC aspartyl-tRNA sy 38.0 1.1E+02 0.0024 27.5 6.5 51 19-71 21-74 (437)
196 PF11213 DUF3006: Protein of u 35.6 1.3E+02 0.0029 19.9 6.5 41 20-70 1-42 (71)
197 PRK14604 ruvA Holliday junctio 35.5 2.4E+02 0.0051 22.7 7.6 51 18-77 4-54 (195)
198 PTZ00241 40S ribosomal protein 35.0 84 0.0018 24.8 4.6 33 4-37 57-90 (158)
199 PRK09521 exosome complex RNA-b 35.0 68 0.0015 25.4 4.2 52 28-79 23-79 (189)
200 PRK10676 DNA-binding transcrip 35.0 79 0.0017 26.5 4.8 55 16-74 199-254 (263)
201 PRK00286 xseA exodeoxyribonucl 34.9 3.3E+02 0.0071 24.3 12.1 120 15-140 24-159 (438)
202 PF15243 ANAPC15: Anaphase-pro 34.9 43 0.00094 24.0 2.7 22 94-115 32-54 (92)
203 PF02724 CDC45: CDC45-like pro 34.8 42 0.00091 31.8 3.4 15 60-74 68-82 (622)
204 PTZ00329 eukaryotic translatio 34.3 1.8E+02 0.004 22.8 6.4 57 12-76 28-85 (155)
205 PF01176 eIF-1a: Translation i 34.2 1.3E+02 0.0029 19.5 5.8 50 17-73 3-53 (65)
206 COG2100 Predicted Fe-S oxidore 34.2 1.7E+02 0.0037 26.2 6.7 58 6-75 346-404 (414)
207 PF00358 PTS_EIIA_1: phosphoen 34.2 68 0.0015 24.3 3.9 57 19-77 46-107 (132)
208 PF03066 Nucleoplasmin: Nucleo 34.2 13 0.00029 28.7 0.0 10 42-51 29-38 (149)
209 PF02237 BPL_C: Biotin protein 34.0 75 0.0016 19.4 3.4 23 15-37 11-34 (48)
210 PTZ00385 lysyl-tRNA synthetase 33.9 1.3E+02 0.0028 29.0 6.5 55 17-71 110-168 (659)
211 PLN02850 aspartate-tRNA ligase 33.4 1.5E+02 0.0033 27.6 6.7 54 16-70 81-141 (530)
212 PRK03932 asnC asparaginyl-tRNA 33.0 1.7E+02 0.0037 26.5 6.9 52 18-71 20-74 (450)
213 PF01106 NifU: NifU-like domai 33.0 1.3E+02 0.0028 19.9 4.7 46 96-141 2-58 (68)
214 TIGR00523 eIF-1A eukaryotic/ar 32.7 1.9E+02 0.0041 20.8 6.2 50 16-72 18-68 (99)
215 PF02598 Methyltrn_RNA_3: Puta 32.5 1.4E+02 0.003 25.6 6.0 58 3-74 102-162 (291)
216 PF13742 tRNA_anti_2: OB-fold 32.5 1.8E+02 0.0039 20.5 6.3 53 15-72 22-79 (99)
217 PLN00208 translation initiatio 31.6 1.9E+02 0.004 22.5 5.9 58 12-77 28-86 (145)
218 cd04456 S1_IF1A_like S1_IF1A_l 31.5 1.7E+02 0.0038 20.0 5.6 50 19-75 2-52 (78)
219 KOG1189|consensus 30.8 28 0.00061 34.1 1.5 12 27-38 765-776 (960)
220 PRK00276 infA translation init 30.2 1.7E+02 0.0037 19.5 6.5 53 18-76 8-61 (72)
221 PF04871 Uso1_p115_C: Uso1 / p 30.0 42 0.00092 25.5 2.1 8 146-153 111-118 (136)
222 PTZ00415 transmission-blocking 29.8 29 0.00062 37.2 1.4 11 60-70 73-83 (2849)
223 PF01330 RuvA_N: RuvA N termin 29.7 1.5E+02 0.0033 18.8 6.9 46 18-73 4-49 (61)
224 TIGR00084 ruvA Holliday juncti 29.7 2.6E+02 0.0056 22.3 6.8 49 18-76 4-52 (191)
225 PF06347 SH3_4: Bacterial SH3 29.3 71 0.0015 19.7 2.8 24 27-51 31-54 (55)
226 PHA02608 67 prohead core prote 28.1 95 0.0021 21.6 3.4 14 136-149 42-55 (80)
227 PF00924 MS_channel: Mechanose 27.2 2.9E+02 0.0064 21.3 9.7 50 8-60 57-111 (206)
228 PF10844 DUF2577: Protein of u 26.9 1.6E+02 0.0034 20.9 4.6 21 15-37 16-36 (100)
229 PRK10929 putative mechanosensi 26.6 7.3E+02 0.016 25.6 10.8 47 8-57 932-983 (1109)
230 PTZ00415 transmission-blocking 26.6 42 0.00091 36.1 2.0 8 5-12 17-24 (2849)
231 PF14444 S1-like: S1-like 26.1 2E+02 0.0043 18.9 5.5 43 18-74 3-46 (58)
232 COG1551 CsrA RNA-binding globa 26.0 54 0.0012 22.5 1.9 21 59-79 9-29 (73)
233 PRK14605 ruvA Holliday junctio 25.7 3.4E+02 0.0074 21.7 6.8 50 18-76 4-53 (194)
234 PRK11281 hypothetical protein; 25.6 7.5E+02 0.016 25.5 10.5 48 8-58 935-987 (1113)
235 PRK12820 bifunctional aspartyl 25.2 2.5E+02 0.0054 27.3 6.8 52 18-70 22-76 (706)
236 TIGR00457 asnS asparaginyl-tRN 24.9 2.9E+02 0.0062 25.1 6.9 54 15-70 15-75 (453)
237 PRK14603 ruvA Holliday junctio 24.4 3.6E+02 0.0077 21.7 6.7 49 18-76 4-52 (197)
238 PF02599 CsrA: Global regulato 24.0 51 0.0011 21.2 1.4 22 58-79 8-29 (54)
239 COG2190 NagE Phosphotransferas 23.5 2.1E+02 0.0045 22.5 5.0 54 19-77 49-110 (156)
240 PF09883 DUF2110: Uncharacteri 23.5 3.1E+02 0.0068 22.8 6.2 60 16-78 75-139 (225)
241 KOG1885|consensus 23.3 1.9E+02 0.004 27.1 5.3 54 18-71 108-166 (560)
242 KOG1999|consensus 23.2 4.6E+02 0.0099 26.7 8.2 57 12-71 408-469 (1024)
243 COG0632 RuvA Holliday junction 23.1 3.9E+02 0.0085 21.7 6.7 53 18-79 4-56 (201)
244 PRK00124 hypothetical protein; 22.8 81 0.0018 24.6 2.6 76 60-141 63-147 (151)
245 TIGR00300 conserved hypothetic 22.7 5.9E+02 0.013 23.2 10.3 75 60-134 139-225 (407)
246 PF05086 Dicty_REP: Dictyostel 22.3 44 0.00095 32.8 1.2 6 62-67 787-792 (911)
247 PF05678 VQ: VQ motif; InterP 22.2 1.4E+02 0.0029 17.0 2.8 22 117-139 3-24 (31)
248 PRK00568 carbon storage regula 22.1 65 0.0014 22.3 1.7 22 58-79 8-29 (76)
249 PF11813 DUF3334: Protein of u 21.7 80 0.0017 26.2 2.4 19 28-48 49-67 (229)
250 COG4148 ModC ABC-type molybdat 21.2 1.7E+02 0.0037 25.8 4.4 56 16-77 293-350 (352)
251 KOG2140|consensus 21.1 53 0.0012 31.1 1.4 8 43-50 323-330 (739)
252 TIGR02062 RNase_B exoribonucle 21.1 1.9E+02 0.0041 27.6 5.1 48 15-74 15-63 (639)
253 PF01835 A2M_N: MG2 domain; I 21.1 1E+02 0.0022 21.1 2.6 19 60-78 9-27 (99)
254 PRK01712 carbon storage regula 21.0 85 0.0018 21.0 2.0 22 58-79 8-29 (64)
255 PTZ00401 aspartyl-tRNA synthet 20.9 3.4E+02 0.0074 25.5 6.7 55 15-70 77-137 (550)
256 PRK14601 ruvA Holliday junctio 20.4 4.5E+02 0.0097 21.0 6.5 52 18-79 4-57 (183)
257 KOG0127|consensus 20.2 1.2E+02 0.0027 28.7 3.5 10 41-50 72-81 (678)
No 1
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=100.00 E-value=2.9e-32 Score=233.22 Aligned_cols=153 Identities=53% Similarity=0.853 Sum_probs=143.0
Q ss_pred CCcccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-
Q psy18072 1 MPLSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK- 79 (174)
Q Consensus 1 ~~~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~- 79 (174)
|.+.||||.++||++|++|.|+|++|.+|||||.|.+|++++||||+|++||++++++++.+++||.|.|+|++||+.+
T Consensus 3 ~~~~cr~~~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg 82 (319)
T PTZ00248 3 DLLDCRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKG 82 (319)
T ss_pred CcccccchhhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCC
Confidence 3589999999999999999999999999999999998878999999999999999999999999999999999999877
Q ss_pred --------------------------------------------------------------------------------
Q psy18072 80 -------------------------------------------------------------------------------- 79 (174)
Q Consensus 80 -------------------------------------------------------------------------------- 79 (174)
T Consensus 83 ~IdLS~K~v~~~pw~~~~e~~~~g~~v~~~V~~ia~~~g~~~eely~~i~~pl~~~~gh~y~af~~~v~~~~evl~~l~i 162 (319)
T PTZ00248 83 YIDLSKKRVSPEDIEACEEKFSKSKKVHSIMRHIAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTNPDNVFEGLDI 162 (319)
T ss_pred EEEEEeeecccchHHHHHHhCcCCCEEEEEEEEchhhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHhcCchhhhccCCC
Confidence
Q ss_pred -------------------------------------------------------------------ceeeecccccchH
Q psy18072 80 -------------------------------------------------------------------VMTTVTPEKADGL 92 (174)
Q Consensus 80 -------------------------------------------------------------------~l~ls~~~k~~g~ 92 (174)
.+++++.++..|.
T Consensus 163 ~~ev~~~l~~~i~~~l~~~~vkI~a~iel~c~~~dGIe~IK~aL~~~~~~~~~~~~i~i~~igaP~Y~i~~~~~d~k~g~ 242 (319)
T PTZ00248 163 PEEVKESLLQDIQRRLKPQPLKLRADIEVSCFDYEGIDAVKEALIAGQEVATDECKITIKLIAPPQYVIVTTCSDKDKGM 242 (319)
T ss_pred CHHHHHHHHHHHHHhCCCCcEEEEEEEEEEeCCCchHHHHHHHHHHHHhcCCCcCcEEEEEEcCCeEEEEEEeCCHHHHH
Confidence 5788999999999
Q ss_pred HHHHHHHHHHHHHHhhhCCeeEEeeCceeEeccCHHHHHHHHHHHHHhcccccCCCCccccc
Q psy18072 93 KALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADDDEDEED 154 (174)
Q Consensus 93 ~~i~~~~~~i~~~l~~~~g~l~~k~~P~~i~~~~~~~~k~~~~~l~k~~~e~~gd~~~~~~~ 154 (174)
..|.++++.|.+.|+++||.+.|+..|++++..++.. .++|+++.++++++++++++++++
T Consensus 243 ~~l~~a~~~i~~~i~~~gG~~~~~~~p~~v~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 303 (319)
T PTZ00248 243 EIIGAALEAIKEVIKKKGGDFKVKGEPEVVGGDEEDL-EELLEKAEEEEEEDDYSESEDEDE 303 (319)
T ss_pred HHHHHHHHHHHHHHHHcCCeEEEEECCEEecchhHHH-HHHHHHHhhhhccccccccccccc
Confidence 9999999999999999999999999999999998888 999999999999999876554444
No 2
>KOG2916|consensus
Probab=99.96 E-value=1.8e-28 Score=202.89 Aligned_cols=148 Identities=73% Similarity=1.081 Sum_probs=143.3
Q ss_pred CC-cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 1 MP-LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 1 ~~-~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
|+ +.||||+.+||+++++|.+.|.+|...||||.|.+|++++|||..|+||++|++++++.+++|..-.|.|++||+++
T Consensus 1 m~~~~cR~ye~kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrVDkek 80 (304)
T KOG2916|consen 1 MSTLECRFYENKYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEK 80 (304)
T ss_pred CCcceeehhhccCCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEEcCCC
Confidence 44 89999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred --------------------------------------------------------------------------------
Q psy18072 80 -------------------------------------------------------------------------------- 79 (174)
Q Consensus 80 -------------------------------------------------------------------------------- 79 (174)
T Consensus 81 GYIDLSkrrVs~ed~~kC~Er~~ksK~v~sIlrhvAe~~g~~LeeLY~~igW~~~rk~g~aYdaFK~~vtd~tV~d~l~~ 160 (304)
T KOG2916|consen 81 GYIDLSKRRVSPEDKEKCEERFAKSKLVYSILRHVAEKLGYELEELYQRIGWPLERKYGHAYDAFKIAVTDPTVLDELDL 160 (304)
T ss_pred CceechhccCCHHHHHHHHHHHHHhHHHHHHHHHHHHHhCCcHHHHHHHhCCchhhhhchHHHHHHHhccCcccccccCC
Confidence
Q ss_pred -------------------------------------------------------------------ceeeecccccchH
Q psy18072 80 -------------------------------------------------------------------VMTTVTPEKADGL 92 (174)
Q Consensus 80 -------------------------------------------------------------------~l~ls~~~k~~g~ 92 (174)
++++++++|..|+
T Consensus 161 ~~~vk~~Llk~Irrrltpq~vKIRADIEv~Cf~yeGI~aIK~alk~a~~~~te~~piki~LIApPlYVlTT~tldK~~g~ 240 (304)
T KOG2916|consen 161 SEEVKEVLLKNIRRRLTPQTVKIRADIEVSCFGYEGIDAIKAALKAALNLSTEECPIKIKLIAPPLYVLTTQTLDKTKGL 240 (304)
T ss_pred CHHHHHHHHHHHHHhcCCcceEEEeeeEEEeccccCHHHHHHHHHHHHhCCcccCceEEEEecCceEEEEEeeccccccH
Confidence 6799999999999
Q ss_pred HHHHHHHHHHHHHHhhhCCeeEEeeCceeEeccCHHHHHHHHHHHHHhcccccCCC
Q psy18072 93 KALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELARQMERAEAENAEVAADD 148 (174)
Q Consensus 93 ~~i~~~~~~i~~~l~~~~g~l~~k~~P~~i~~~~~~~~k~~~~~l~k~~~e~~gd~ 148 (174)
.++..+|..|...|.+.+|.+.+++.|++++.+|+..+++.|++...+|+|++|||
T Consensus 241 e~l~~Ai~~i~~~I~~~~G~~~V~~~pk~vte~d~~~l~~~~e~~E~e~~e~~~dd 296 (304)
T KOG2916|consen 241 EVLEEAIEVIISKIEEYGGTFTVIMEPKLVTETDEAELARRMEREEEENAEVSGDD 296 (304)
T ss_pred HHHHHHHHHHHHHHHhhCCEEEEEeCCeecccccHHHHHHHHHhhhhhcccccCcc
Confidence 99999999999999999999999999999999999999999999999999999985
No 3
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=99.85 E-value=2.7e-21 Score=161.19 Aligned_cols=115 Identities=20% Similarity=0.237 Sum_probs=110.3
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccccchHHH
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKADGLKA 94 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k~~g~~~ 94 (174)
.++.|.|+||++...|.||-+.+ ++.||||.||.. ..+++|+.+++||+.++.+++|++|++.+ +.++
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e~--~~~GfIh~sEr~--------~~prlG~~l~~rVi~~reDg~lnLSl~p~--~~E~ 222 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITEN--GYLGFIHKSERF--------AEPRLGERLTARVIGVREDGKLNLSLRPR--AHEM 222 (287)
T ss_pred hcCeeeeEEEEEeccceEEEEcC--CeEEEEcchhhc--------ccccCCceEEEEEEEEccCCeeecccccc--cHHh
Confidence 48999999999999999999988 899999999987 67999999999999999999999999888 9999
Q ss_pred HHHHHHHHHHHHhhhCCeeEE--eeCceeEe---ccCHHHHHHHHHHHHHhc
Q psy18072 95 LQEAIDTIKAKIEQLGGVFQV--QMAPKVVT---ASDEAELARQMERAEAEN 141 (174)
Q Consensus 95 i~~~~~~i~~~l~~~~g~l~~--k~~P~~i~---~~~~~~~k~~~~~l~k~~ 141 (174)
+..+++.|.++|+.+||+||+ ||+|+.|+ ++||.+||||+|+|+|++
T Consensus 223 l~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g 274 (287)
T COG2996 223 LDEDAQMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAG 274 (287)
T ss_pred hhhhHHHHHHHHHHcCCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence 999999999999999999999 89999999 999999999999999986
No 4
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=5.3e-21 Score=158.61 Aligned_cols=75 Identities=35% Similarity=0.590 Sum_probs=73.8
Q ss_pred cchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 5 CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 5 ~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
||++...||+.|++|.|+|.+|.+|||||.|.+|++.+||||+|+++..|+++++++++.||.+.|+|++||+.+
T Consensus 1 m~~~~~~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~r 75 (269)
T COG1093 1 MRMKRREYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKR 75 (269)
T ss_pred CcccccCCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999999988
No 5
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.77 E-value=6e-19 Score=131.78 Aligned_cols=73 Identities=21% Similarity=0.368 Sum_probs=69.1
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccc
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEK 88 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k 88 (174)
++|++++|+|++|++|||||+|++ +-.||||||+++..|++++.+++++||.|.|+|+++|.+++++||.+.-
T Consensus 4 kvG~~l~GkItgI~~yGAFV~l~~--g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKisLSIr~~ 76 (129)
T COG1098 4 KVGSKLKGKITGITPYGAFVELEG--GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKISLSIRKL 76 (129)
T ss_pred cccceEEEEEEeeEecceEEEecC--CCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeeccCCCcceehHHh
Confidence 599999999999999999999988 8999999999999999999999999999999999999999998887543
No 6
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.69 E-value=2.8e-16 Score=132.07 Aligned_cols=71 Identities=34% Similarity=0.563 Sum_probs=66.8
Q ss_pred hccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 9 ~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
.+++|++|++|.|+|++|.++|+||.|.+|++++||||+|++++++++++++.|++||.|.|+|++++..+
T Consensus 2 ~~~~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k 72 (262)
T PRK03987 2 RKEWPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRK 72 (262)
T ss_pred CCCCCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEeccc
Confidence 46789999999999999999999999998767999999999999999999999999999999999999865
No 7
>PHA02945 interferon resistance protein; Provisional
Probab=99.63 E-value=1.4e-15 Score=107.42 Aligned_cols=73 Identities=30% Similarity=0.383 Sum_probs=65.9
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceec--chhhhhccccccCCCCEEEEEEEEEeCCC-ceeeec
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSEL--SRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVT 85 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSel--s~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~ 85 (174)
-.+|++|++|.|+|+. .+|||||.|.+|++.+||||+|++ +..++++ ++++ .||.|.|+|++||+.+ -+.+|+
T Consensus 6 y~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~-rd~l-~GqkvV~KVirVd~~kg~IDlSl 81 (88)
T PHA02945 6 YSLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKY-RDKL-VGKTVKVKVIRVDYTKGYIDVNY 81 (88)
T ss_pred ecCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEee-eeEe-cCCEEEEEEEEECCCCCEEEeEe
Confidence 3688999999999999 999999999999999999999955 9999999 9999 9999999999999976 345554
No 8
>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=99.62 E-value=2.7e-15 Score=102.67 Aligned_cols=72 Identities=24% Similarity=0.342 Sum_probs=64.3
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVT 85 (174)
Q Consensus 13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~ 85 (174)
|+.|+++.|+|++|.+||+||+|.++ +.+||+|+|++++.++.++.+.|++||.|+|+|++++..+.+.+|+
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~-~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~ki~ls~ 72 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGC-RKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCC-CeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCCcEEEEe
Confidence 35899999999999999999999653 2799999999999999999999999999999999999877666654
No 9
>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=99.61 E-value=2.8e-15 Score=102.59 Aligned_cols=69 Identities=16% Similarity=0.116 Sum_probs=63.8
Q ss_pred CCCCEEEEEEEEEec-ceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072 14 EVEDVVMVTVISIAE-MGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVT 85 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~-~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~ 85 (174)
++|++|.|+|+++.+ +|+||+|.+ +..|++|+|+++++++.++.+.|++||.|+|+|++++. +++.+|+
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~--~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~-~~i~LSl 71 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPF--GKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD-GKYQLSL 71 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCC--CCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC-CEEEEEe
Confidence 489999999999985 899999988 89999999999999999999999999999999999986 6777775
No 10
>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=99.60 E-value=4.1e-15 Score=102.53 Aligned_cols=64 Identities=23% Similarity=0.365 Sum_probs=58.9
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhc---cccccCCCCEEEEEEEEEeCCC
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRS---INKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~---~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
++|++|.|+|.+++++|+||.|.+ +++|+||++++++.++.+ +.+.|++||.|+|+|+++|+++
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~~--~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~ 68 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSS--SIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEK 68 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeCC--CCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCC
Confidence 489999999999999999999988 899999999999998666 4589999999999999999854
No 11
>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=99.58 E-value=1.4e-14 Score=98.86 Aligned_cols=73 Identities=68% Similarity=0.961 Sum_probs=64.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVT 85 (174)
Q Consensus 13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~ 85 (174)
|++|++|.|+|+++.++|+||.|.++++++||||+|+++++++.++.+.|++||.|+|+|++++.. +.+.+++
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~ 74 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSK 74 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEE
Confidence 468999999999999999999998654699999999999999999999999999999999999975 3466654
No 12
>PRK08582 hypothetical protein; Provisional
Probab=99.56 E-value=1.7e-14 Score=110.82 Aligned_cols=73 Identities=26% Similarity=0.431 Sum_probs=67.4
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccc
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEK 88 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k 88 (174)
++|++|.|+|++|++|||||.|.+ +++||||+|++++.++.++.+.|++||.|+|+|++++.++.+.+++...
T Consensus 4 kvG~iv~G~V~~I~~fG~fV~L~~--~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~~gkI~LSlk~~ 76 (139)
T PRK08582 4 EVGSKLQGKVTGITNFGAFVELPE--GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKA 76 (139)
T ss_pred cCCCEEEEEEEEEECCeEEEEECC--CCEEEEEeeccCcccccccccccCCCCEEEEEEEEECCCCcEEEEEEec
Confidence 489999999999999999999988 8999999999999999999999999999999999999877788777544
No 13
>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=99.56 E-value=2.2e-14 Score=100.62 Aligned_cols=78 Identities=22% Similarity=0.207 Sum_probs=69.4
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch----hhhhccccccCCCCEEEEEEEEEeCCCceeeeccc
Q psy18072 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR----RRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPE 87 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~----~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~ 87 (174)
.|++|++|.|+|+++.++|+||.|.. +++|+||+|++++ .+..++.+.+++||.|.|+|+++++++.+.+|++.
T Consensus 3 ~p~~GdiV~g~V~~i~~~g~~v~i~~--~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~~~i~LS~~~ 80 (86)
T cd05789 3 IPEVGDVVIGRVTEVGFKRWKVDINS--PYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRS 80 (86)
T ss_pred cCCCCCEEEEEEEEECCCEEEEECCC--CeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCCCCEEEEeCc
Confidence 45799999999999999999999987 8999999999985 45677888999999999999999988889999877
Q ss_pred ccch
Q psy18072 88 KADG 91 (174)
Q Consensus 88 k~~g 91 (174)
..+|
T Consensus 81 ~~~g 84 (86)
T cd05789 81 LKYG 84 (86)
T ss_pred cccc
Confidence 7554
No 14
>PRK08059 general stress protein 13; Validated
Probab=99.54 E-value=7.8e-15 Score=110.32 Aligned_cols=99 Identities=23% Similarity=0.331 Sum_probs=82.4
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC-CCceeeecccccchH
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK-EKVMTTVTPEKADGL 92 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~-~~~l~ls~~~k~~g~ 92 (174)
++|++|.|+|+++.++|+||.|.+ ++.||||++++++.++.++.+.|++||.|.|+|++++. .+.+.++.+......
T Consensus 6 k~G~iv~G~V~~i~~~G~fV~i~~--~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk~~~~~~ 83 (123)
T PRK08059 6 EVGSVVTGKVTGIQPYGAFVALDE--ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEAP 83 (123)
T ss_pred CCCCEEEEEEEEEecceEEEEECC--CCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEEEcccCc
Confidence 489999999999999999999987 79999999999999988888999999999999999986 456776765443221
Q ss_pred HHHHHHHHHHHHHHhhhCCeeEE
Q psy18072 93 KALQEAIDTIKAKIEQLGGVFQV 115 (174)
Q Consensus 93 ~~i~~~~~~i~~~l~~~~g~l~~ 115 (174)
. .......++..++..||++++
T Consensus 84 ~-~~~~~~~~l~~~~~~~g~~~l 105 (123)
T PRK08059 84 E-AKRKKGKILIPNPSEQGFNTL 105 (123)
T ss_pred c-cccccccccccccccCCchhH
Confidence 0 334456778888889999987
No 15
>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=99.53 E-value=8.1e-14 Score=94.70 Aligned_cols=70 Identities=14% Similarity=0.168 Sum_probs=63.2
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVT 85 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~ 85 (174)
++|++|.|+|+++.++|+||+|.+ +++|++|++++++++..++.+.|++||.|+|+|++++.. +.+.+|+
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~--~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~ 72 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGN--KVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSL 72 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCC--CcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 489999999999999999999998 899999999999988888889999999999999999985 4566554
No 16
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=99.52 E-value=6.3e-14 Score=94.39 Aligned_cols=68 Identities=25% Similarity=0.328 Sum_probs=61.6
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVT 85 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~ 85 (174)
|++|.|+|+++.++|+||+|.+ +++||||+|++++.++.++.+.|++||.++|+|+++++. +.+.+|.
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~--~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~ 69 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYN--NVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSC 69 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECC--CCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEe
Confidence 7899999999999999999987 799999999999988889999999999999999999984 4555553
No 17
>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=99.52 E-value=6.2e-14 Score=94.24 Aligned_cols=62 Identities=27% Similarity=0.389 Sum_probs=58.7
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
|++|.|+|+++.++|+||+|.+ +++||||++++++.++.++.+.|++||.|+|+|+++++.+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~--~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~ 62 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGR--GVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDN 62 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCC--CCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCC
Confidence 7899999999999999999987 7999999999999999999999999999999999999843
No 18
>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=99.51 E-value=1e-13 Score=96.55 Aligned_cols=79 Identities=19% Similarity=0.193 Sum_probs=72.0
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccccc
Q psy18072 11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEKAD 90 (174)
Q Consensus 11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k~~ 90 (174)
++|++|++|.|+|+++.+.+|+|.+.. .++|+||.++++..+..++...|++||.|.|+|++++..+.+.||+....+
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~--~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~~~i~LS~~~~~~ 79 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILS--RGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDDMNVLLTTADNEL 79 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCC--CceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCCCCEEEEECCCCC
Confidence 356799999999999999999999977 799999999999888888889999999999999999987789999888766
Q ss_pred h
Q psy18072 91 G 91 (174)
Q Consensus 91 g 91 (174)
|
T Consensus 80 G 80 (82)
T cd04454 80 G 80 (82)
T ss_pred c
Confidence 5
No 19
>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=99.51 E-value=8e-14 Score=95.72 Aligned_cols=68 Identities=21% Similarity=0.273 Sum_probs=61.7
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh--hhccccccCCCCEEEEEEEEEeCCC-ceeeec
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR--IRSINKLIRVGKTEPVVVIRVDKEK-VMTTVT 85 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~--v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~ 85 (174)
|++|.|+|+++.++|+||+|.+ +++|+||.+++++.+ ..++.+.|++||.|+|+|+++|+++ .+.+|.
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~--~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~ 71 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISP--DVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSA 71 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCC--CcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEe
Confidence 7899999999999999999988 899999999999764 7889999999999999999999864 667665
No 20
>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=99.51 E-value=8.6e-14 Score=92.19 Aligned_cols=68 Identities=24% Similarity=0.465 Sum_probs=62.1
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVT 85 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~ 85 (174)
|++|.|+|+++.++|+||.|.+ ++.||||.++++++++.++.+.|++||.|+|+|++++..+.+.+++
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~--~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~~~~i~ls~ 68 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGG--GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSI 68 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECC--CCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECCCCcEEEEE
Confidence 7899999999999999999987 7999999999999888888899999999999999999855666664
No 21
>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=99.51 E-value=8.8e-14 Score=93.73 Aligned_cols=67 Identities=24% Similarity=0.353 Sum_probs=60.7
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeee
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTV 84 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls 84 (174)
|++|.|+|++|.++|+||+|.+ +++||||++++++.++.++.+.|++||.++|+|+++|.. +.+.++
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~--~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls 68 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSD--HIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecC--CcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence 7899999999999999999988 899999999999998888889999999999999999985 344443
No 22
>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=99.51 E-value=1.3e-13 Score=93.61 Aligned_cols=70 Identities=39% Similarity=0.541 Sum_probs=64.3
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCc-eeeec
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKV-MTTVT 85 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~-l~ls~ 85 (174)
++|++|.|+|+++.++|+||.|.+ +++||||.+++++.+...+...+++||.|.|+|++++..+. +.+|.
T Consensus 3 ~~G~iv~g~V~~v~~~g~~V~l~~--~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~ 73 (74)
T PF00575_consen 3 KEGDIVEGKVTSVEDFGVFVDLGN--GIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSL 73 (74)
T ss_dssp STTSEEEEEEEEEETTEEEEEEST--SSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEES
T ss_pred CCCCEEEEEEEEEECCEEEEEECC--cEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEE
Confidence 589999999999999999999986 79999999999999888999999999999999999999763 66654
No 23
>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=99.50 E-value=1.2e-13 Score=94.29 Aligned_cols=67 Identities=22% Similarity=0.344 Sum_probs=60.9
Q ss_pred CCEEE-EEEEEE-ecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeee
Q psy18072 16 EDVVM-VTVISI-AEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTV 84 (174)
Q Consensus 16 GdiV~-G~V~~i-~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls 84 (174)
|++|. |+|+++ .++|+||+|.+ +++||||+|++++.++.++.+.|++||.+.|+|+++++.. .+.+|
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~--gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS 70 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKD--GLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLS 70 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCC--CCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence 78899 999999 79999999988 8999999999999999999999999999999999999754 56665
No 24
>PRK05807 hypothetical protein; Provisional
Probab=99.50 E-value=1.3e-13 Score=105.66 Aligned_cols=72 Identities=21% Similarity=0.402 Sum_probs=66.2
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccc
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEK 88 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k 88 (174)
++|++|.|+|++|+++||||.| + +..||||+|++++.++.++...|++||.|+|+|++++.++.+.+|++..
T Consensus 4 ~vG~vv~G~Vt~i~~~GafV~L-~--~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~~gkI~LSlk~~ 75 (136)
T PRK05807 4 KAGSILEGTVVNITNFGAFVEV-E--GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQA 75 (136)
T ss_pred cCCCEEEEEEEEEECCeEEEEE-C--CEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECCCCcEEEEEEec
Confidence 3899999999999999999999 5 5899999999999999999999999999999999999877888887553
No 25
>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=99.49 E-value=1.2e-13 Score=96.47 Aligned_cols=69 Identities=22% Similarity=0.226 Sum_probs=63.0
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeee
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTV 84 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls 84 (174)
++|++|.|+|.++.++|+||.|.+ +.+||+|+++++++++.++.+.|++||.|+|+|++++.. +.+.+|
T Consensus 13 ~~G~i~~g~V~~v~~~G~fv~l~~--~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~ls 82 (83)
T cd04461 13 KPGMVVHGYVRNITPYGVFVEFLG--GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82 (83)
T ss_pred CCCCEEEEEEEEEeeceEEEEcCC--CCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEe
Confidence 489999999999999999999987 899999999999999999999999999999999999974 345544
No 26
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=99.47 E-value=2.4e-13 Score=91.81 Aligned_cols=69 Identities=25% Similarity=0.407 Sum_probs=62.9
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP 86 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~ 86 (174)
|++|.|+|+++.++|+||+|.+ +++|+||++++++.++.++.+.|++||.++|+|++++.. +.+.++.+
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~--~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k 70 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGD--GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCC--CCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence 7899999999999999999987 799999999999999989999999999999999999986 45666654
No 27
>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=99.47 E-value=3.2e-13 Score=91.50 Aligned_cols=65 Identities=26% Similarity=0.535 Sum_probs=57.9
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchh-hhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~-~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
|| +|+++.|+|++|+++|+||+|.+ +.+||+|++++++. +..++.+.|++||.|+|+|++++..+
T Consensus 1 ~~-~g~~~~g~V~~i~~~G~fv~l~~--~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~ 66 (72)
T cd05689 1 YP-EGTRLFGKVTNLTDYGCFVELEE--GVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEER 66 (72)
T ss_pred Cc-CCCEEEEEEEEEEeeEEEEEcCC--CCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCc
Confidence 45 89999999999999999999988 79999999999864 44467788999999999999999754
No 28
>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=99.46 E-value=2.4e-13 Score=91.07 Aligned_cols=62 Identities=29% Similarity=0.532 Sum_probs=57.0
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch-hhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR-RRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~-~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
|++|.|+|++++++|+||+|.+ +.+||+|++++++ .+..++.+.|++||.|+|+|+++|..+
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~--~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~ 63 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDG--GIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVER 63 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCC--CCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCc
Confidence 7899999999999999999988 8999999999996 567788899999999999999999753
No 29
>PRK07252 hypothetical protein; Provisional
Probab=99.46 E-value=3.1e-13 Score=101.52 Aligned_cols=71 Identities=27% Similarity=0.384 Sum_probs=63.5
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP 86 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~ 86 (174)
++|++|.|+|++|.++|+||+|.+ ++.||||+|++++.++.++.+.|++||.|+|+|++++.. +.+.+++.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~--~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk 73 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALEN--GTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR 73 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECC--CCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence 479999999999999999999987 799999999999999999999999999999999999984 45555543
No 30
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.46 E-value=2e-13 Score=124.09 Aligned_cols=74 Identities=28% Similarity=0.495 Sum_probs=66.0
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeeccc
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTPE 87 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~~ 87 (174)
+.+. +|++|.|+|++|++|||||.|.+ +.||||+|++||.|+.+|.+.|++||.|+|+|+++|..+ .+++|++.
T Consensus 188 ~~l~-~G~vV~G~V~~It~~GafVdigG---vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSlK~ 262 (541)
T COG0539 188 NKLE-VGEVVEGVVKNITDYGAFVDIGG---VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSLKQ 262 (541)
T ss_pred hcCC-CCceEEEEEEEeecCcEEEEecC---eeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEehh
Confidence 4444 99999999999999999999964 999999999999999999999999999999999999765 56666543
No 31
>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=99.45 E-value=5.2e-13 Score=90.88 Aligned_cols=72 Identities=26% Similarity=0.408 Sum_probs=63.2
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP 86 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~ 86 (174)
++|++|.|+|+++.++|+||+|.+. +++|++|++++++.+..++.+.|++||.|+|+|++++.. +.+.++.+
T Consensus 1 ~~g~~v~g~V~~i~~~g~~v~l~~~-~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k 73 (77)
T cd05708 1 KVGQKIDGTVRRVEDYGVFIDIDGT-NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73 (77)
T ss_pred CCCCEEEEEEEEEEcceEEEEECCC-CeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEE
Confidence 3699999999999999999999742 599999999999988888889999999999999999984 46666653
No 32
>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=99.42 E-value=9.1e-13 Score=91.08 Aligned_cols=70 Identities=21% Similarity=0.327 Sum_probs=61.8
Q ss_pred CCEEEEEEEEEecceEEEEECCC-CCeEEEEEceecchhhh-hccccccCCCCEEEEEEEEEeCCCceeeecc
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEY-NNIEGMILLSELSRRRI-RSINKLIRVGKTEPVVVIRVDKEKVMTTVTP 86 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~-~~~~GlI~iSels~~~v-~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~ 86 (174)
|+++.|+|+++.+||+||+|.++ .+..||+|++++++.++ .++.+.|++||.|+|+|++++ .+.+.++.+
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd-~~~i~~s~k 72 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ-NGKISLSMK 72 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe-CCEEEEEEE
Confidence 68999999999999999999853 25899999999999886 888999999999999999999 666666653
No 33
>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=99.42 E-value=1e-12 Score=88.52 Aligned_cols=67 Identities=30% Similarity=0.377 Sum_probs=60.5
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeee
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTV 84 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls 84 (174)
|++|.|+|.++.++|+||.|.. +.+|+||.+++++.+..++.+.|++||.++|+|+++++. +.+.+|
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~--~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS 68 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGY--KSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLS 68 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCC--CceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEE
Confidence 7899999999999999999976 799999999999999999999999999999999999854 345554
No 34
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.42 E-value=3e-13 Score=122.96 Aligned_cols=79 Identities=28% Similarity=0.463 Sum_probs=71.3
Q ss_pred hhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeec
Q psy18072 7 FYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVT 85 (174)
Q Consensus 7 ~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~ 85 (174)
....+|| +|+.+.|+|+++++|||||++.+ +++||+|+|+++|.+...|++++++||.|.|+|+.||+++ ++++++
T Consensus 270 ~i~~~~~-~g~~v~G~Vt~i~~~GafVei~~--GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~i 346 (541)
T COG0539 270 GIEKKYP-VGDKVEGKVTNLTDYGAFVEIEE--GVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGL 346 (541)
T ss_pred HHhhhcC-CCCEEEEEEEEeecCcEEEEecC--CccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeee
Confidence 3467787 99999999999999999999988 9999999999999998889999999999999999999965 677776
Q ss_pred ccc
Q psy18072 86 PEK 88 (174)
Q Consensus 86 ~~k 88 (174)
+..
T Consensus 347 Kq~ 349 (541)
T COG0539 347 KQL 349 (541)
T ss_pred hhh
Confidence 543
No 35
>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=99.41 E-value=1e-12 Score=86.92 Aligned_cols=61 Identities=26% Similarity=0.448 Sum_probs=57.3
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE 78 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~ 78 (174)
|++|.|+|++++++|+||.|.+ +..||+|.+++++.++.++...|++||.|+|+|++++..
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~--~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~ 61 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGV--KQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEE 61 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCC--CCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECC
Confidence 6899999999999999999987 799999999999888888889999999999999999974
No 36
>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=99.40 E-value=1.6e-12 Score=86.34 Aligned_cols=67 Identities=28% Similarity=0.532 Sum_probs=60.3
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeee
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTV 84 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls 84 (174)
|+++.|+|+++.++|+||.|.. +..||+|++++++.++.++.+.|++||.|+|+|+++++.+.+.+|
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~--~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~~~~i~ls 67 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILP--GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLS 67 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCC--CCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECCCCcEEee
Confidence 6899999999999999999987 799999999999998888889999999999999999974455444
No 37
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.39 E-value=1.6e-13 Score=110.14 Aligned_cols=96 Identities=18% Similarity=0.242 Sum_probs=83.6
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCC--------CeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCcee
Q psy18072 11 KYPEVEDVVMVTVISIAEMGAYVHLLEYN--------NIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMT 82 (174)
Q Consensus 11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~--------~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ 82 (174)
..|++|++|.|+|+++.++||||.|..+. ++.|+||.+++++.+..++.+.|++||.|.|+|++++ +.+.
T Consensus 60 ~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~--~~i~ 137 (189)
T PRK09521 60 PLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT--DPLQ 137 (189)
T ss_pred CCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC--CcEE
Confidence 45569999999999999999999995321 5899999999999888889999999999999999998 6799
Q ss_pred eecccccchHHHHHHHHHHHHHHHhhhC
Q psy18072 83 TVTPEKADGLKALQEAIDTIKAKIEQLG 110 (174)
Q Consensus 83 ls~~~k~~g~~~i~~~~~~i~~~l~~~~ 110 (174)
+|++...+| ++.+.|..|+..|...+
T Consensus 138 LS~k~~~lG--vv~a~~~~~g~~~~~~~ 163 (189)
T PRK09521 138 LSTKGKDLG--VIYAMCSRCRTPLVKKG 163 (189)
T ss_pred EEEecCCce--EEEEEccccCCceEECC
Confidence 999877665 78889999998887655
No 38
>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=99.37 E-value=1.7e-12 Score=94.46 Aligned_cols=72 Identities=18% Similarity=0.282 Sum_probs=63.2
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-------------------ccccccCCCCEEEEEEEE
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-------------------SINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-------------------~~~~~l~vGd~V~vrVi~ 74 (174)
++|++|.|+|++|.++|+||.|++ ++.|++|++++++.+.. ++.+.|++||.|+|+|++
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~--g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~ 79 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPN--GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVS 79 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCC--CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEE
Confidence 489999999999999999999988 89999999999987632 367899999999999999
Q ss_pred EeCC----Cceeeeccc
Q psy18072 75 VDKE----KVMTTVTPE 87 (174)
Q Consensus 75 Vd~~----~~l~ls~~~ 87 (174)
+++. +.+.+|.+.
T Consensus 80 ~d~~~~~~~~i~LSlr~ 96 (100)
T cd05693 80 LDKSKSGKKRIELSLEP 96 (100)
T ss_pred ccCCcCCCcEEEEEecH
Confidence 9985 477777654
No 39
>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=99.36 E-value=3.1e-12 Score=86.60 Aligned_cols=64 Identities=23% Similarity=0.242 Sum_probs=58.9
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh--hhccccccCCCCEEEEEEEEEeCCCce
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR--IRSINKLIRVGKTEPVVVIRVDKEKVM 81 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~--v~~~~~~l~vGd~V~vrVi~Vd~~~~l 81 (174)
|++|.|+|+++.++|+||.|.. +++|+||++++++.+ ..++.+.|++||.|.|+|++++..+.+
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~--~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~~ 66 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLAD--NVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTH 66 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCC--CcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCcccc
Confidence 7899999999999999999987 899999999999885 778889999999999999999987644
No 40
>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=99.36 E-value=2.7e-12 Score=92.08 Aligned_cols=80 Identities=23% Similarity=0.269 Sum_probs=70.1
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEE--------CCCCCeEEEEEceecchhhhh--ccccccCCCCEEEEEEEEEeCCCc
Q psy18072 11 KYPEVEDVVMVTVISIAEMGAYVHL--------LEYNNIEGMILLSELSRRRIR--SINKLIRVGKTEPVVVIRVDKEKV 80 (174)
Q Consensus 11 ~~p~~GdiV~G~V~~i~~~GafV~L--------~~~~~~~GlI~iSels~~~v~--~~~~~l~vGd~V~vrVi~Vd~~~~ 80 (174)
..|++|++|.|+|++++...|+|.| .. .+.|+||++++...+.. .+.+.|++||.|+|||+++.....
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~--~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~~~ 79 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKE--SFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDASS 79 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCC--CcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCCCC
Confidence 3578999999999999999999999 55 68999999999876655 688999999999999999987677
Q ss_pred eeeecccccchH
Q psy18072 81 MTTVTPEKADGL 92 (174)
Q Consensus 81 l~ls~~~k~~g~ 92 (174)
+.+|+.++++|.
T Consensus 80 ~~Lst~~~~lGV 91 (92)
T cd05791 80 YYLSTAENELGV 91 (92)
T ss_pred cEEEecCCCCcc
Confidence 999999887773
No 41
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=99.36 E-value=3.3e-12 Score=90.92 Aligned_cols=64 Identities=22% Similarity=0.306 Sum_probs=58.0
Q ss_pred CCCCEEEEEEEEEecc--eEEEEECCCCCeEEEEEceecch---hhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 14 EVEDVVMVTVISIAEM--GAYVHLLEYNNIEGMILLSELSR---RRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~--GafV~L~~~~~~~GlI~iSels~---~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
++|++|.|+|++|.++ ||||+|.+ +.+||||+|++++ .++.++.+.+++||.|.|+|++.....
T Consensus 6 ~~G~iy~g~V~~i~~~~~GaFV~l~~--g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~ 74 (88)
T cd04453 6 IVGNIYLGRVKKIVPGLQAAFVDIGL--GKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGT 74 (88)
T ss_pred CCCCEEEEEEEEeccCCcEEEEEeCC--CCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCC
Confidence 4899999999999996 99999988 7999999999998 567788899999999999999976554
No 42
>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=99.35 E-value=4e-12 Score=85.54 Aligned_cols=60 Identities=15% Similarity=0.227 Sum_probs=53.9
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
|++|.|+|+++.++|+||.|.+ +++|++|.++++..+.. .+.|++|+.|+|+|+.+++.+
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~--~v~g~v~~~~l~~~~~~--~~~~~~G~~i~~kVi~id~~~ 60 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLS--SFTGTVDFLHLDPEKSS--KSTYKEGQKVRARILYVDPST 60 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcC--CceEEEEHHHcCCccCc--ccCcCCCCEEEEEEEEEeCCC
Confidence 7899999999999999999987 79999999999765444 678999999999999999854
No 43
>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=99.35 E-value=2e-12 Score=120.89 Aligned_cols=71 Identities=25% Similarity=0.537 Sum_probs=64.6
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecc----hhhhhccccccCCCCEEEEEEEEEeCCCceeee
Q psy18072 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS----RRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTV 84 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels----~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls 84 (174)
.|++|++|.|+|++|++||+||+|.+ +.+||||+|+++ +.++.++.+.|++||.|+|+|+++|..++++++
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~--G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~~gKI~L~ 718 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLP--GKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDDRGKLSLV 718 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecC--CceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECCCCCeeec
Confidence 36699999999999999999999987 899999999996 468999999999999999999999987777765
No 44
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=99.35 E-value=3.1e-12 Score=106.00 Aligned_cols=80 Identities=21% Similarity=0.270 Sum_probs=72.3
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh----hccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI----RSINKLIRVGKTEPVVVIRVDKEKVMTTVT 85 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v----~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~ 85 (174)
.+.|++||+|.|+|+++.++||||.|.. .+.|+||++++++.++ .+++..|++||.|+|||++++.++.+.+|+
T Consensus 58 ~y~P~vGDiViG~V~~i~~~~~~vdI~~--~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~~~LS~ 135 (235)
T PRK04163 58 KYIPKVGDLVIGKVTDVTFSGWEVDINS--PYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRDVVLTL 135 (235)
T ss_pred cccCCCCCEEEEEEEEEeCceEEEEeCC--CceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCcEEEEE
Confidence 3667899999999999999999999987 7899999999999887 788999999999999999999888888888
Q ss_pred ccccch
Q psy18072 86 PEKADG 91 (174)
Q Consensus 86 ~~k~~g 91 (174)
+.+.+|
T Consensus 136 k~~~lG 141 (235)
T PRK04163 136 KGKGLG 141 (235)
T ss_pred cCCCCC
Confidence 877554
No 45
>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=99.34 E-value=8.3e-12 Score=86.06 Aligned_cols=66 Identities=17% Similarity=0.175 Sum_probs=56.7
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeecc
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTP 86 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~ 86 (174)
+.|++|.|+|.+|.++|+||.+. +.++.||||.+++++. ..+++||.+.|+|+++++.+ .+.+|++
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g-~~gv~Gfl~~~~~~~~------~~~~~Gq~v~~~V~~vd~~~~~v~ls~k 69 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIG-IPGTTGFLPKKDAGNF------SKLKVGQLLLCVVEKVKDDGRVVSLSAD 69 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeC-CCCcEEEEEHHHCCcc------cccCCCCEEEEEEEEEECCCCEEEEEEe
Confidence 48999999999999999999995 2279999999999975 67999999999999999865 4566553
No 46
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=99.34 E-value=4.3e-12 Score=89.02 Aligned_cols=67 Identities=31% Similarity=0.543 Sum_probs=62.6
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEE-ceecchhhhhccccccCCCCEEEEEEEEEeCCCc
Q psy18072 11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMIL-LSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKV 80 (174)
Q Consensus 11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~-iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~ 80 (174)
.||++|+++. .|..+++.|+||.|.+|+ ++|||. .++++.++++++++.+ +|..+.|+|+++|+.+.
T Consensus 12 ~~P~v~dvv~-~Vv~i~d~~~YV~LleY~-iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KG 79 (86)
T PHA02858 12 VFPNINEVTK-GIVFVKDNIFYVKLIDYG-LEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKG 79 (86)
T ss_pred ecCCCCeEEE-EEEEEeccEEEEEEecCc-cceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCC
Confidence 5889999999 677899999999999996 999999 9999999999999999 99999999999999764
No 47
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.33 E-value=8.6e-12 Score=82.27 Aligned_cols=69 Identities=38% Similarity=0.558 Sum_probs=61.7
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVT 85 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~ 85 (174)
+|++|.|+|+++.++|+||.+.+ ++.|++|.++++..+..++...|++||.|.|+|++++.. +.+.+++
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~--~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~ 71 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGN--GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCC--CCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEe
Confidence 79999999999999999999987 799999999999887777778899999999999999986 5565554
No 48
>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=99.32 E-value=9.2e-12 Score=82.49 Aligned_cols=61 Identities=36% Similarity=0.605 Sum_probs=56.6
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE 78 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~ 78 (174)
+|++|.|+|+++.++|+||.|. +++|+||.+++++.++.++.+.|++||.|+|+|++++..
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~---~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~ 61 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLG---GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKE 61 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEEC---CeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECC
Confidence 4899999999999999999995 489999999999888888889999999999999999975
No 49
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.29 E-value=5.6e-12 Score=120.22 Aligned_cols=73 Identities=27% Similarity=0.396 Sum_probs=66.9
Q ss_pred CCCCCEEE-EEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeeccc
Q psy18072 13 PEVEDVVM-VTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPE 87 (174)
Q Consensus 13 p~~GdiV~-G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~ 87 (174)
|++|++|. |+|++|.+||+||+|.+ +.+||||+|++++.++.++.+.|++||.|+|+|+++|..+.+.++.+.
T Consensus 751 ~~vG~iy~~g~V~~I~~FGaFVeL~~--g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~~grI~LSlK~ 824 (891)
T PLN00207 751 PTVGDIYRNCEIKSIAPYGAFVEIAP--GREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRA 824 (891)
T ss_pred cCCCcEEECcEEEEEeccEEEEEeCC--CCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECCCCcEEEEEec
Confidence 56999995 69999999999999987 899999999999999999999999999999999999987777777643
No 50
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.29 E-value=1.9e-11 Score=105.48 Aligned_cols=73 Identities=27% Similarity=0.462 Sum_probs=64.0
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP 86 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~ 86 (174)
+.+ ++|++|.|+|++|++||+||.+. ++.||||+|++++.++.++.+.|++||.|+|+|++++.. +.+.++++
T Consensus 192 ~~~-k~G~vv~G~V~~I~~~G~fV~i~---gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K 265 (318)
T PRK07400 192 NRL-EVGEVVVGTVRGIKPYGAFIDIG---GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTK 265 (318)
T ss_pred ccC-CCCCEEEEEEEEEECCeEEEEEC---CEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence 344 48999999999999999999984 599999999999999999999999999999999999974 45555553
No 51
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=99.28 E-value=1.8e-12 Score=103.38 Aligned_cols=113 Identities=15% Similarity=0.194 Sum_probs=94.6
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCC--------CeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCce
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYN--------NIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVM 81 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~--------~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l 81 (174)
..+|+.|++|.|+|+++....|.|++.... ...|-||+|+++..+++++++.|++||.|+|+|++.- ..+
T Consensus 59 ~~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~--~~~ 136 (188)
T COG1096 59 PPLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG--DPI 136 (188)
T ss_pred CCCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC--CCe
Confidence 578889999999999999999999886421 2678999999999999999999999999999999985 469
Q ss_pred eeecccccchHHHHHHHHHHHHHHHhhhCCeeEE-eeCceeEeccC
Q psy18072 82 TTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQV-QMAPKVVTASD 126 (174)
Q Consensus 82 ~ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~-k~~P~~i~~~~ 126 (174)
.||+..+.+| ++.+.|++|+..|...+..|.- +.+-+....++
T Consensus 137 ~Lst~~~dlG--VI~A~CsrC~~~L~~~~~~l~Cp~Cg~tEkRKia 180 (188)
T COG1096 137 QLSTKGNDLG--VIYARCSRCRAPLVKKGNMLKCPNCGNTEKRKIA 180 (188)
T ss_pred EEEecCCcce--EEEEEccCCCcceEEcCcEEECCCCCCEEeeeec
Confidence 9999999888 7899999999999986666654 45554444333
No 52
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.28 E-value=1e-11 Score=112.56 Aligned_cols=74 Identities=23% Similarity=0.351 Sum_probs=67.4
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeecc
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTP 86 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~ 86 (174)
..|+ +|++|.|+|+++++||+||.|.+ ++.||||+|++++.+..++.+.|++||.|+|+|+.+++++ .++++.+
T Consensus 375 ~~~~-vG~~v~G~V~~i~~~G~FV~l~~--gv~Gli~~se~s~~~~~~~~~~~~~Gd~v~~~V~~id~e~~ri~Ls~~ 449 (491)
T PRK13806 375 ERFA-PGTTVTGTVEKRAQFGLFVNLAP--GVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLAPA 449 (491)
T ss_pred hhCC-CCCEEEEEEEEEecCceEEEcCC--CcEEEEEHHHcCcccccchhhcCCCCCEEEEEEEEEeCCCCEEEEEee
Confidence 4666 89999999999999999999987 8999999999999999889999999999999999999854 6777765
No 53
>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=99.26 E-value=3.8e-11 Score=80.42 Aligned_cols=65 Identities=18% Similarity=0.327 Sum_probs=55.9
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC-CCceeeec
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK-EKVMTTVT 85 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~-~~~l~ls~ 85 (174)
|++|.|+|+++.++|+||.+ + +++||||.|++++.+..++.. .+||.+.|+|++++. .+.+.+|.
T Consensus 1 G~iv~g~V~~v~~~G~~v~l-~--g~~gfip~s~~~~~~~~~~~~--~vG~~i~~~i~~vd~~~~~i~lS~ 66 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI-E--GVRAFLPASQVDLRPVEDLDE--YVGKELKFKIIEIDRERNNIVLSR 66 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE-C--CEEEEEEHHHCCCcccCChHH--hCCCEEEEEEEEEeCCCCEEEEEc
Confidence 78999999999999999999 6 799999999999887766655 389999999999997 44566553
No 54
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.25 E-value=2.2e-11 Score=114.44 Aligned_cols=72 Identities=25% Similarity=0.533 Sum_probs=66.9
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecc
Q psy18072 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTP 86 (174)
Q Consensus 13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~ 86 (174)
+++|++|.|+|++|.+||+||+|.+ +.+||||+|++++.+++++.+.|++||.|+|+|+++|..+.+.+|.+
T Consensus 619 ~~vG~v~~G~V~~I~~fGafVei~~--~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~grI~LS~k 690 (693)
T PRK11824 619 PEVGEIYEGKVVRIVDFGAFVEILP--GKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRK 690 (693)
T ss_pred CcCCeEEEEEEEEEECCeEEEEECC--CCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCCCcEEEEEE
Confidence 4699999999999999999999987 89999999999999999999999999999999999998777877763
No 55
>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=99.24 E-value=8e-11 Score=81.37 Aligned_cols=62 Identities=24% Similarity=0.340 Sum_probs=54.6
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVT 85 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~ 85 (174)
++|+.+.|+|++++++|+||.+.+ ++.||+|.|++. +.+++||.++|+|+++...+.+.++.
T Consensus 15 ~~G~~~~g~V~~i~~~G~fV~l~~--~~~Glv~~se~~--------~~~~iGd~v~v~I~~i~e~~~i~l~~ 76 (77)
T cd04473 15 EVGKLYKGKVNGVAKYGVFVDLND--HVRGLIHRSNLL--------RDYEVGDEVIVQVTDIPENGNIDLIP 76 (77)
T ss_pred CCCCEEEEEEEeEecceEEEEECC--CcEEEEEchhcc--------CcCCCCCEEEEEEEEECCCCcEEEEE
Confidence 489999999999999999999988 799999999975 67999999999999995555666553
No 56
>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=99.23 E-value=8.1e-11 Score=81.20 Aligned_cols=69 Identities=23% Similarity=0.390 Sum_probs=57.0
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-----------ccccccCCCCEEEEEEEEEeCC-Ccee
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-----------SINKLIRVGKTEPVVVIRVDKE-KVMT 82 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-----------~~~~~l~vGd~V~vrVi~Vd~~-~~l~ 82 (174)
+|+++.|+|++|+++|+||+|.+| +.+|++|.+++++.++. .....|++||.|+|+|++++.. +.+.
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~-~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~ 79 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNL-TVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKID 79 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCC-CEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEE
Confidence 389999999999999999999876 49999999999865432 3457899999999999999974 3444
Q ss_pred ee
Q psy18072 83 TV 84 (174)
Q Consensus 83 ls 84 (174)
++
T Consensus 80 ~~ 81 (83)
T cd04471 80 FE 81 (83)
T ss_pred EE
Confidence 43
No 57
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.22 E-value=3.6e-11 Score=108.90 Aligned_cols=73 Identities=27% Similarity=0.430 Sum_probs=65.4
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP 86 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~ 86 (174)
..+. +|++|.|+|+++++||+||.| . ++.||||+|+++|.++.++.+.|++||.|+|+|+++++. +.+.+|.+
T Consensus 204 ~~lk-~G~iv~G~V~~i~~~G~FVdl-g--gv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSlK 277 (486)
T PRK07899 204 NQLQ-KGQVRKGVVSSIVNFGAFVDL-G--GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLK 277 (486)
T ss_pred Hhcc-CCCEEEEEEEEEECCeEEEEE-C--CEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEEe
Confidence 3454 999999999999999999999 3 599999999999999999999999999999999999985 56666665
No 58
>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=99.20 E-value=3.6e-11 Score=112.85 Aligned_cols=68 Identities=26% Similarity=0.561 Sum_probs=62.6
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCce
Q psy18072 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVM 81 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l 81 (174)
.|++|++|.|+|++|.+||+||+|.+ +.+||||+|++++.++.++.+.|++||.|+|+|++++..+.+
T Consensus 615 ~~~~G~i~~G~V~~I~~~GafVei~~--g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~~gki 682 (684)
T TIGR03591 615 EPEVGKIYEGKVVRIMDFGAFVEILP--GKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQGRI 682 (684)
T ss_pred ccccCcEEEEEEEEEeCCEEEEEECC--CcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECCCCCc
Confidence 35699999999999999999999987 899999999999999999999999999999999999974443
No 59
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.19 E-value=4.4e-11 Score=114.53 Aligned_cols=75 Identities=27% Similarity=0.478 Sum_probs=66.4
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch-hhhhccccccCCCCEEEEEEEEEeCCC-ceeeeccc
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR-RRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTPE 87 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~-~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~~ 87 (174)
++|+ +|++|.|+|+++.+||+||.|.+ +++||||+|+++| .++.++.+.|++||.|+|+|+++|..+ .+++|.+.
T Consensus 574 ~~~~-vG~iV~G~V~~I~~fG~fVeL~~--gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~iD~e~~rIsLS~K~ 650 (863)
T PRK12269 574 NKFG-VNDVVKGRVTKIADFGAFIELAE--GIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQ 650 (863)
T ss_pred ccCC-CCCEEEEEEEEEeCCeEEEEecC--CceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEEecccCceEEEehh
Confidence 4566 99999999999999999999987 8999999999999 578899999999999999999999754 56666643
No 60
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.19 E-value=6.7e-11 Score=107.27 Aligned_cols=75 Identities=25% Similarity=0.472 Sum_probs=65.7
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch-hhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR-RRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE 87 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~-~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~ 87 (174)
..++ +|++|.|+|+++++||+||.|.+ +++||||+|+++| .++.++.+.+++||.|+|+|+++|+. +.+.+|.+.
T Consensus 288 ~~~~-~G~~v~G~V~~v~~~G~fV~l~~--gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K~ 364 (491)
T PRK13806 288 DRLK-AGDKVTGKVVRLAPFGAFVEILP--GIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRD 364 (491)
T ss_pred ccCC-CCCEEEEEEEEEeCceEEEEeCC--CcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEee
Confidence 3565 89999999999999999999987 8999999999998 56788889999999999999999985 466666543
No 61
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.19 E-value=6.1e-11 Score=107.46 Aligned_cols=81 Identities=27% Similarity=0.473 Sum_probs=69.7
Q ss_pred hccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072 9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE 87 (174)
Q Consensus 9 ~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~ 87 (174)
...++ +|++|.|+|+++.+||+||+|.+ ++.||||+|++++.++..+.+.|++||.|+|+|+++|.. +.+.++.+.
T Consensus 288 ~~~~~-vG~vv~G~V~~I~~fGvFVeL~~--gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK~ 364 (486)
T PRK07899 288 ARTHA-IGQIVPGKVTKLVPFGAFVRVEE--GIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQ 364 (486)
T ss_pred HHhcC-CCCEEEEEEEEEeccEEEEEeCC--CcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEEE
Confidence 34454 89999999999999999999987 899999999999999988999999999999999999974 467777665
Q ss_pred ccchH
Q psy18072 88 KADGL 92 (174)
Q Consensus 88 k~~g~ 92 (174)
...+.
T Consensus 365 ~~~~~ 369 (486)
T PRK07899 365 ANEGV 369 (486)
T ss_pred cccCC
Confidence 54443
No 62
>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=99.15 E-value=1.4e-10 Score=75.12 Aligned_cols=58 Identities=34% Similarity=0.607 Sum_probs=53.5
Q ss_pred EEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072 19 VMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE 78 (174)
Q Consensus 19 V~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~ 78 (174)
|.|+|+++.++|+||.+.. +..|++|.+++++.++.++...|++||.|+|+|++++..
T Consensus 1 v~g~V~~v~~~g~~v~l~~--~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~d~~ 58 (65)
T cd00164 1 VTGKVVSITKFGVFVELED--GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPE 58 (65)
T ss_pred CEEEEEEEEeeeEEEEecC--CCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEEcCC
Confidence 5799999999999999987 799999999999888778888999999999999999874
No 63
>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=99.13 E-value=3.7e-10 Score=81.44 Aligned_cols=73 Identities=18% Similarity=0.360 Sum_probs=62.0
Q ss_pred CEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhcc-----------ccccCCCCEEEEEEEEEeCC------C
Q psy18072 17 DVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSI-----------NKLIRVGKTEPVVVIRVDKE------K 79 (174)
Q Consensus 17 diV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~-----------~~~l~vGd~V~vrVi~Vd~~------~ 79 (174)
++|.|+|++|.++|+||+|.. ++||+|+++++..++... ...|++||.|+|+|++++.. +
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~---v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~ 77 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGP---VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRES 77 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcC---eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCc
Confidence 479999999999999999963 899999999987765432 47899999999999999975 4
Q ss_pred ceeeecccccchH
Q psy18072 80 VMTTVTPEKADGL 92 (174)
Q Consensus 80 ~l~ls~~~k~~g~ 92 (174)
.+.+|.....+|.
T Consensus 78 ~i~ls~k~~~~g~ 90 (99)
T cd04460 78 KIGLTMRQPGLGK 90 (99)
T ss_pred eEEEEEecCCCCc
Confidence 6888888887773
No 64
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=99.10 E-value=2.7e-10 Score=103.24 Aligned_cols=73 Identities=34% Similarity=0.479 Sum_probs=65.8
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVT 85 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~ 85 (174)
+.++ +|+++.|+|++++++|+||.|.+ ++.||||.|++++.++.++.+.|++||.|+|+|++++.. +.+.++.
T Consensus 442 ~~~~-~G~~v~g~V~~v~~~G~fV~l~~--~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~ 515 (516)
T TIGR00717 442 AKYK-VGSVVKGKVTEIKDFGAFVELPG--GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSV 515 (516)
T ss_pred hccC-cceEEEEEEEEEecceEEEEcCC--CeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 3455 89999999999999999999988 899999999999999999999999999999999999874 5666664
No 65
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.09 E-value=3.1e-10 Score=108.74 Aligned_cols=76 Identities=22% Similarity=0.444 Sum_probs=65.6
Q ss_pred hhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-hccccccCCCCEEEEEEEEEeCC-Cceeeec
Q psy18072 8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-RSINKLIRVGKTEPVVVIRVDKE-KVMTTVT 85 (174)
Q Consensus 8 ~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~ 85 (174)
+...|+ +|++|.|+|+++++||+||.|.+ +++||||+|+++|.+. .++...|++||.|+|+|+.+|+. +.+.+|.
T Consensus 659 ~~~~~~-vG~~v~G~V~~i~~~G~fV~l~~--gV~GlIh~sels~~~~~~~~~~~~kvGq~VkvkVl~ID~e~rrI~LS~ 735 (863)
T PRK12269 659 IEARYP-VGARFTRRIVKVTNAGAFIEMEE--GIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIECDPQARRIRLGV 735 (863)
T ss_pred HHHhCC-CCCEEEEEEEEEecceEEEEeCC--CcEEEEEhHHhhccccccchhhccCCCCEEEEEEEEEeccCCEEEEEe
Confidence 456676 99999999999999999999987 8999999999998654 44556899999999999999986 4677776
Q ss_pred c
Q psy18072 86 P 86 (174)
Q Consensus 86 ~ 86 (174)
+
T Consensus 736 K 736 (863)
T PRK12269 736 K 736 (863)
T ss_pred c
Confidence 4
No 66
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.06 E-value=2.9e-10 Score=105.20 Aligned_cols=72 Identities=29% Similarity=0.528 Sum_probs=67.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecc
Q psy18072 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTP 86 (174)
Q Consensus 13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~ 86 (174)
+++|.+|.|+|+++.+|||||.|.+ +.+||+|+|++++.|+....+.+++||.|+|||+.+|..+++.++..
T Consensus 617 ~evg~iy~G~V~ri~~fGaFv~l~~--gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~ls~~ 688 (692)
T COG1185 617 VEVGEVYEGTVVRIVDFGAFVELLP--GKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRLSIK 688 (692)
T ss_pred cccccEEEEEEEEEeecceEEEecC--CcceeEEehhhhhhhhhcccceeecCceEEEEEeeecccCCccceeh
Confidence 3599999999999999999999988 88999999999999999999999999999999999999888877753
No 67
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.05 E-value=6.2e-10 Score=97.77 Aligned_cols=75 Identities=28% Similarity=0.504 Sum_probs=66.2
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecccc
Q psy18072 11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPEK 88 (174)
Q Consensus 11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~k 88 (174)
.+. +|+++.|+|+++.++|+||+|.+ ++.||+|+|++++.++.++...|++||.|+|+|+++|.. +.+.++.+..
T Consensus 274 ~~~-~G~~v~g~V~~i~~~G~fV~l~~--gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k~~ 349 (390)
T PRK06676 274 KLP-EGDVIEGTVKRLTDFGAFVEVLP--GVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKAL 349 (390)
T ss_pred hhc-CCcEEEEEEEEEeCceEEEEECC--CCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEEEec
Confidence 354 89999999999999999999987 899999999999988888889999999999999999964 5677776543
No 68
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.05 E-value=9.1e-10 Score=95.03 Aligned_cols=73 Identities=18% Similarity=0.271 Sum_probs=65.4
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE 87 (174)
Q Consensus 13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~ 87 (174)
.++|++|.|+|.++.++|+||.|.. +..|+||.+++++.++.++...|++||.|.|+|++++.. +.+.+|.+.
T Consensus 29 ~~~G~iv~G~V~~i~~~g~~Vdig~--k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS~k~ 102 (318)
T PRK07400 29 FKPGDIVNGTVFSLEPRGALIDIGA--KTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRR 102 (318)
T ss_pred cCCCCEEEEEEEEEECCEEEEEECC--CeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEehhh
Confidence 3599999999999999999999965 799999999999999999999999999999999999875 456777654
No 69
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.04 E-value=5.7e-10 Score=102.31 Aligned_cols=75 Identities=35% Similarity=0.526 Sum_probs=65.6
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-hccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-RSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE 87 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~ 87 (174)
..++ +|++|.|+|++++++|+||+|.+ +++||||+|++++.+. .++...|++||.|+|+|+++|+. +.+.+|.+.
T Consensus 369 ~~~~-~G~~v~g~V~~v~~~G~fV~l~~--~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~k~ 445 (565)
T PRK06299 369 EKYP-VGDVVEGKVKNITDFGAFVGLEG--GIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGIKQ 445 (565)
T ss_pred HhCC-CCCEEEEEEEEEecceEEEECCC--CCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEEeh
Confidence 3454 89999999999999999999987 7999999999998876 78889999999999999999974 467666543
No 70
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.00 E-value=1.3e-09 Score=95.71 Aligned_cols=71 Identities=28% Similarity=0.494 Sum_probs=63.7
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE 87 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~ 87 (174)
++|++|.|+|+++.++|+||.+. +++|+||+|++++.++.++.+.|++||.|+|+|+++++. +.+.+|.+.
T Consensus 191 ~~G~~v~g~V~~v~~~G~fV~l~---~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~k~ 262 (390)
T PRK06676 191 KEGDVVEGTVARLTDFGAFVDIG---GVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKD 262 (390)
T ss_pred CCCCEEEEEEEEEecceEEEEeC---CeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEEee
Confidence 48999999999999999999994 599999999999999999999999999999999999874 566666653
No 71
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.00 E-value=1.2e-09 Score=100.14 Aligned_cols=73 Identities=29% Similarity=0.496 Sum_probs=66.8
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecccc
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPEK 88 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~k 88 (174)
++|++|.|+|+++.++|+||.+.+ ++.||||.|+++..++.++.+.|++||.|+|+|++++.+ +.+++|....
T Consensus 459 ~~G~vV~G~V~~v~~~G~fV~l~~--gi~g~i~~se~s~~~~~~~~~~~~~Gd~v~~~V~~vd~~~~~i~LS~k~~ 532 (565)
T PRK06299 459 KKGSIVTGTVTEVKDKGAFVELED--GVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKAL 532 (565)
T ss_pred CCCCEEEEEEEEEecCceEEecCC--CcEEEEEHHHhcchhccCccccCCCCCEEEEEEEEEccccCEEEEEeeeh
Confidence 389999999999999999999987 899999999999999999999999999999999999974 5788887544
No 72
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=98.99 E-value=7.4e-10 Score=103.90 Aligned_cols=76 Identities=22% Similarity=0.353 Sum_probs=68.0
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeeccccc
Q psy18072 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTPEKA 89 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~~k~ 89 (174)
..++|.++.|+|.++.+||+||.|.- +..|+||+|+++.+++.+|.+++++||.|+|+|+.||..+ .+.+|.+..+
T Consensus 655 dLk~Gm~leg~Vrnv~~fgafVdIgv--~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr~~~ 731 (780)
T COG2183 655 DLKPGMILEGTVRNVVDFGAFVDIGV--HQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMRLDE 731 (780)
T ss_pred hccCCCEEEEEEEEeeeccceEEecc--ccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEeeccC
Confidence 44599999999999999999999987 7899999999999999999999999999999999999865 5666665543
No 73
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.98 E-value=1.7e-09 Score=101.07 Aligned_cols=76 Identities=32% Similarity=0.554 Sum_probs=67.2
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeecccc
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPEK 88 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~k 88 (174)
..++ +|++|.|+|++++++|+||.|.+ ++.||+|++++++.++.++...|++||.|+|+|++++.+ +.+.++.+..
T Consensus 558 ~~~~-~G~~v~g~V~~i~~~G~fV~l~~--~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk~~ 634 (647)
T PRK00087 558 EKYP-VGSIVLGKVVRIAPFGAFVELEP--GVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEV 634 (647)
T ss_pred hhcc-CCeEEEEEEEEEECCeEEEEECC--CCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEeec
Confidence 3454 89999999999999999999987 899999999999999999999999999999999999974 5666666544
No 74
>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=98.93 E-value=3.1e-09 Score=100.18 Aligned_cols=78 Identities=21% Similarity=0.364 Sum_probs=63.5
Q ss_pred cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-----------hccccccCCCCEEEEE
Q psy18072 3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-----------RSINKLIRVGKTEPVV 71 (174)
Q Consensus 3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-----------~~~~~~l~vGd~V~vr 71 (174)
+.|+|+... +|.++.|+|++|++||+||+|.++ +++||||+|++++.++ ++..+.|++||.|+|+
T Consensus 618 ~~~~yl~~~---iG~~~~g~V~~v~~fGifV~L~~~-~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vk 693 (709)
T TIGR02063 618 KKAEYMSEK---IGEEFEGVISGVTSFGLFVELENN-TIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVR 693 (709)
T ss_pred HHHHhhhcc---CCcEEEEEEEEEEeCCEEEEecCC-ceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEE
Confidence 368876653 699999999999999999999875 4999999999986653 2345689999999999
Q ss_pred EEEEeCC-Cceeee
Q psy18072 72 VIRVDKE-KVMTTV 84 (174)
Q Consensus 72 Vi~Vd~~-~~l~ls 84 (174)
|++||.. +.+.++
T Consensus 694 v~~vd~~~~~I~~~ 707 (709)
T TIGR02063 694 VVKADLDTGKIDFE 707 (709)
T ss_pred EEEEecccCeEEEE
Confidence 9999974 445443
No 75
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.89 E-value=1.5e-08 Score=80.97 Aligned_cols=87 Identities=20% Similarity=0.423 Sum_probs=69.7
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-----------ccccccCCCCEEEEEEEEEeCCC--
Q psy18072 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-----------SINKLIRVGKTEPVVVIRVDKEK-- 79 (174)
Q Consensus 13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-----------~~~~~l~vGd~V~vrVi~Vd~~~-- 79 (174)
|.+|+++.|+|+++.++|+||+|.. ++|++|.+++..+++. +....+++||.|++||++++...
T Consensus 79 P~~GEVv~g~V~~v~~~Gi~V~lg~---~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~ 155 (187)
T PRK08563 79 PELQEVVEGEVVEVVEFGAFVRIGP---VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERR 155 (187)
T ss_pred ccCCCEEEEEEEEEEccEEEEEEeC---ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCC
Confidence 4589999999999999999999964 8999999999866432 34568999999999999998752
Q ss_pred ----ceeeecccccchHHHHHHHHHHHHHHHhh
Q psy18072 80 ----VMTTVTPEKADGLKALQEAIDTIKAKIEQ 108 (174)
Q Consensus 80 ----~l~ls~~~k~~g~~~i~~~~~~i~~~l~~ 108 (174)
.+.+|...+-+| .++|+.+..++
T Consensus 156 ~~~~~I~ls~~~~~LG------~~~w~~~~~~~ 182 (187)
T PRK08563 156 PRGSKIGLTMRQPGLG------KLEWIEEEKKK 182 (187)
T ss_pred CCCCEEEEEecCCCCC------cHHHHHHHHhh
Confidence 577788777666 45777665554
No 76
>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=98.88 E-value=4.9e-09 Score=95.00 Aligned_cols=73 Identities=26% Similarity=0.495 Sum_probs=63.1
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchh-hhhccccccCCCCEEEEEEEEEeCC-Cceeeecc
Q psy18072 11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTP 86 (174)
Q Consensus 11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~-~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~ 86 (174)
.++ +|+++.|+|+++.++|+||.|.+ ++.||||+|++++. ...++.+.+++||.|+|+|+++|+. +.+.+|++
T Consensus 269 ~~~-~G~i~~g~V~~v~~~G~fV~l~~--~v~g~v~~sels~~~~~~~~~~~~~vG~~v~v~V~~id~~~~~i~lS~k 343 (516)
T TIGR00717 269 KFP-VGDKITGRVTNLTDYGVFVEIEE--GIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343 (516)
T ss_pred hcc-CCCEEEEEEEEeeCCcEEEEeCC--CCEEEEEHHHcCCccccCCHHHhccCCCEEEEEEEEEcCCCCEEEEEeh
Confidence 454 89999999999999999999987 89999999999975 3556677899999999999999985 46777654
No 77
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=98.88 E-value=5.6e-09 Score=97.60 Aligned_cols=71 Identities=28% Similarity=0.513 Sum_probs=64.1
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC-Cceeeeccc
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE-KVMTTVTPE 87 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~-~~l~ls~~~ 87 (174)
++|++|.|+|+++.++|+||.| + +++||||+|++++.++.++.+.|++||.|+|+|+++++. +.+.+|++.
T Consensus 476 ~~G~iV~g~V~~v~~~G~fV~l-~--gv~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~id~~~~~I~lS~K~ 547 (647)
T PRK00087 476 EEGDVVEGEVKRLTDFGAFVDI-G--GVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK 547 (647)
T ss_pred CCCCEEEEEEEEEeCCcEEEEE-C--CEEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEeec
Confidence 4899999999999999999999 6 799999999999999999999999999999999999874 567777643
No 78
>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=98.86 E-value=1.4e-08 Score=68.28 Aligned_cols=57 Identities=19% Similarity=0.188 Sum_probs=50.1
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
+.|++|.|+|.++.++|+||.+. +.+|+||.++++. .+.+++||.|+|.|++++..+
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig---~~eg~lp~~e~~~------~~~~~~Gd~v~v~v~~v~~~~ 58 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLG---KVEAILPKKEQIP------GESYRPGDRIKAYVLEVRKTS 58 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcC---CeEEEeeHHHCCC------CCcCCCCCEEEEEEEEEecCC
Confidence 37999999999999999999994 4899999999872 367899999999999998653
No 79
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=98.82 E-value=1.4e-08 Score=84.06 Aligned_cols=85 Identities=22% Similarity=0.360 Sum_probs=73.2
Q ss_pred cchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh----hccccccCCCCEEEEEEEEEeCCCc
Q psy18072 5 CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI----RSINKLIRVGKTEPVVVIRVDKEKV 80 (174)
Q Consensus 5 ~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v----~~~~~~l~vGd~V~vrVi~Vd~~~~ 80 (174)
+++...+.|++||+|.|+|..+...+|.|.|.. .+.|++|+|++.++.+ ++++..|++||.|.|||.+++....
T Consensus 54 Ipl~g~YiP~~gD~VIG~I~~v~~~~W~VDI~s--p~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~~~ 131 (239)
T COG1097 54 IPLEGRYIPEVGDVVIGKIIEVGPSGWKVDIGS--PYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDGE 131 (239)
T ss_pred EeCCCcccCCCCCEEEEEEEEEcccceEEEcCC--ccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCCCc
Confidence 455566778899999999999999999999988 7999999999966553 4678999999999999999999998
Q ss_pred eeeecccccch
Q psy18072 81 MTTVTPEKADG 91 (174)
Q Consensus 81 l~ls~~~k~~g 91 (174)
..+++++...|
T Consensus 132 ~~L~~k~~~~G 142 (239)
T COG1097 132 VELTLKDEGLG 142 (239)
T ss_pred eEEEeecCCCc
Confidence 88888666433
No 80
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=98.81 E-value=1.2e-09 Score=99.75 Aligned_cols=110 Identities=25% Similarity=0.259 Sum_probs=92.6
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-----------cee
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-----------VMT 82 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-----------~l~ 82 (174)
+.|.+|.|+|+++..||+||+|+. .+.||+|.+.++.. ..+.+|+.+.|+|..|.+.+ .+.
T Consensus 121 e~g~~Y~g~v~~v~~~GvFv~Ln~--~v~GL~~~~d~~~~------~~~~vgdeiiV~v~~vr~~~geidf~~~~~~~Y~ 192 (715)
T COG1107 121 EAGKYYKGIVSRVEKYGVFVELNS--HVRGLIHRRDLGGD------PDYAVGDEIIVQVSDVRPEKGEIDFEPVGLDRYR 192 (715)
T ss_pred ccceeeeccccchhhhcceeecCh--hhhccccccccCCC------CCCCCCCeEEEEeeccCCCCCccceeecCCccch
Confidence 589999999999999999999998 89999999998852 46899999999999999884 233
Q ss_pred eecccccchHHHHHHHHHHHHHHHhhhCCeeEEe--eCceeEeccCHHHHH
Q psy18072 83 TVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ--MAPKVVTASDEAELA 131 (174)
Q Consensus 83 ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k--~~P~~i~~~~~~~~k 131 (174)
.....+++++..+.+.-+.+++.+...|...++| ++|++|+-+|...+.
T Consensus 193 ~~~~~ke~~r~~i~~id~~ig~tV~I~GeV~qikqT~GPTVFtltDetg~i 243 (715)
T COG1107 193 EVQVEKELPRTLIDDLDEMIGKTVRIEGEVTQIKQTSGPTVFTLTDETGAI 243 (715)
T ss_pred hhhhhhhcccccHHHHHhhcCceEEEEEEEEEEEEcCCCEEEEEecCCCce
Confidence 5556677887778888888899998899888884 999999977764443
No 81
>PRK11642 exoribonuclease R; Provisional
Probab=98.79 E-value=1.4e-08 Score=97.16 Aligned_cols=73 Identities=27% Similarity=0.452 Sum_probs=61.2
Q ss_pred cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-----------ccccccCCCCEEEEE
Q psy18072 3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-----------SINKLIRVGKTEPVV 71 (174)
Q Consensus 3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-----------~~~~~l~vGd~V~vr 71 (174)
+.|+|+..+ +|+++.|+|++|++||+||+|.++ +++||||++++.++++. ...+.|++||.|+|+
T Consensus 634 ~~~~~m~~~---iGe~f~G~Is~V~~fGifVeL~~~-~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~Vk 709 (813)
T PRK11642 634 LKCDFMLDQ---VGNVFKGVISSVTGFGFFVRLDDL-FIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVR 709 (813)
T ss_pred HHHhhhhcc---CCcEEEEEEEEeecCceEEEECCC-CeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEE
Confidence 468866662 799999999999999999999873 39999999999876432 234789999999999
Q ss_pred EEEEeCCC
Q psy18072 72 VIRVDKEK 79 (174)
Q Consensus 72 Vi~Vd~~~ 79 (174)
|++|+..+
T Consensus 710 V~~vD~~~ 717 (813)
T PRK11642 710 VEAVNMDE 717 (813)
T ss_pred EEEeecCC
Confidence 99999755
No 82
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.79 E-value=2.9e-08 Score=78.98 Aligned_cols=75 Identities=20% Similarity=0.314 Sum_probs=60.7
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-----------ccccccCCCCEEEEEEEEEeC-----
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-----------SINKLIRVGKTEPVVVIRVDK----- 77 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-----------~~~~~l~vGd~V~vrVi~Vd~----- 77 (174)
.+|+++.|+|++++++|+||+|. .++|++|.+++...++. +....+++||.|++||++++.
T Consensus 80 ~~gEvv~G~V~~v~~~GifV~lg---~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~ 156 (179)
T TIGR00448 80 ELGEIVEGEVIEIVEFGAFVSLG---PFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRP 156 (179)
T ss_pred cCCCEEEEEEEEEEeeEEEEEeC---CceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCC
Confidence 37999999999999999999994 48999999998865432 234789999999999999984
Q ss_pred -CCceeeecccccch
Q psy18072 78 -EKVMTTVTPEKADG 91 (174)
Q Consensus 78 -~~~l~ls~~~k~~g 91 (174)
...+.+|.+.+-+|
T Consensus 157 ~~~~I~lt~k~~~LG 171 (179)
T TIGR00448 157 EGSKIGLTMRQPLLG 171 (179)
T ss_pred CcceEEEEeccCcCC
Confidence 23567777666555
No 83
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.78 E-value=1.1e-08 Score=81.62 Aligned_cols=76 Identities=20% Similarity=0.380 Sum_probs=60.5
Q ss_pred CCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhh-----------ccccccCCCCEEEEEEEEEeCCC--
Q psy18072 13 PEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIR-----------SINKLIRVGKTEPVVVIRVDKEK-- 79 (174)
Q Consensus 13 p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~-----------~~~~~l~vGd~V~vrVi~Vd~~~-- 79 (174)
|..|++|.|.|+++.+||+||.|.+ ..||||+|++.+.++. .-...+++|+.|+|||+++....
T Consensus 79 P~~gEVV~GeVv~~~~~G~fV~igp---~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~ 155 (183)
T COG1095 79 PFRGEVVEGEVVEVVEFGAFVRIGP---LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRR 155 (183)
T ss_pred eccccEEEEEEEEEeecceEEEecc---ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCc
Confidence 4579999999999999999999986 8999999999987432 13348999999999999988754
Q ss_pred ----ceeeecccccch
Q psy18072 80 ----VMTTVTPEKADG 91 (174)
Q Consensus 80 ----~l~ls~~~k~~g 91 (174)
.+.+|.+.+-+|
T Consensus 156 ~~~~~I~lTmrq~~LG 171 (183)
T COG1095 156 PRESKIGLTMRQPGLG 171 (183)
T ss_pred cccceEEEEeccccCC
Confidence 345555555333
No 84
>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=98.74 E-value=5.3e-08 Score=69.22 Aligned_cols=75 Identities=12% Similarity=0.042 Sum_probs=62.3
Q ss_pred cCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeecccc
Q psy18072 11 KYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVTPEK 88 (174)
Q Consensus 11 ~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~~~k 88 (174)
..|++||.|.|+|+.+....++|.|.. .+.|++|.+.+... .+..+..|++||.|.|||.++++.....+++.++
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s--~~~a~L~~~~f~ga-tk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~~~ 76 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGG--SEPASLSYLAFEGA-TKRNRPNLNVGDLVYARVVKANRDMEPELSCVDS 76 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCC--CcceEechHHcccc-cccccccCCCCCEEEEEEEecCCCCCeEEEEeCC
Confidence 356799999999999999999999988 68999999887432 3334678999999999999999877677777653
No 85
>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=98.74 E-value=2.8e-08 Score=93.07 Aligned_cols=73 Identities=27% Similarity=0.493 Sum_probs=61.1
Q ss_pred cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-----------hccccccCCCCEEEEE
Q psy18072 3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-----------RSINKLIRVGKTEPVV 71 (174)
Q Consensus 3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-----------~~~~~~l~vGd~V~vr 71 (174)
+.|+|+.++ +|.++.|+|++|+++|+||.|.++ +++||||++++.++++ ++....|++||.|+|+
T Consensus 563 ~~~~yl~~~---iG~~~~g~I~~v~~~GifV~L~~~-~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vk 638 (654)
T TIGR00358 563 LKCRYLLDK---VGTEFSGEISSVTRFGMFVRLDDN-GIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVK 638 (654)
T ss_pred HHHHhhhhC---CCcEEEEEEEeEEcCcEEEEecCC-ceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEE
Confidence 358876663 699999999999999999999854 5999999999987652 2234789999999999
Q ss_pred EEEEeCCC
Q psy18072 72 VIRVDKEK 79 (174)
Q Consensus 72 Vi~Vd~~~ 79 (174)
|++||..+
T Consensus 639 i~~vd~~~ 646 (654)
T TIGR00358 639 LTEVNMET 646 (654)
T ss_pred EEEEeccc
Confidence 99998754
No 86
>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=98.66 E-value=7e-08 Score=67.99 Aligned_cols=64 Identities=22% Similarity=0.325 Sum_probs=43.9
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCC----------------CCeEEEEEceecchhhhh--ccccccCCCCEEEEEEE
Q psy18072 12 YPEVEDVVMVTVISIAEMGAYVHLLEY----------------NNIEGMILLSELSRRRIR--SINKLIRVGKTEPVVVI 73 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~GafV~L~~~----------------~~~~GlI~iSels~~~v~--~~~~~l~vGd~V~vrVi 73 (174)
+|++|++|.|+|+++++.-|++.|... ..+.|+||.+++...... .+.+.|++||.|+|+|+
T Consensus 1 lP~vGdiV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~Vi 80 (82)
T PF10447_consen 1 LPKVGDIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVI 80 (82)
T ss_dssp ---TT-EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEE
T ss_pred CCCCCCEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEe
Confidence 478999999999999999999888654 147999999988754433 35789999999999999
Q ss_pred EE
Q psy18072 74 RV 75 (174)
Q Consensus 74 ~V 75 (174)
+.
T Consensus 81 Sl 82 (82)
T PF10447_consen 81 SL 82 (82)
T ss_dssp EE
T ss_pred eC
Confidence 74
No 87
>KOG1067|consensus
Probab=98.53 E-value=9.5e-08 Score=87.21 Aligned_cols=68 Identities=24% Similarity=0.317 Sum_probs=62.3
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeee
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTV 84 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls 84 (174)
.|-+|+|+|+++.++|+||.|.+ ...||+|+|+|+.+++.++.+.+.+||.|.|+.+..|+.+.+.++
T Consensus 668 ~g~vy~~tIt~~rd~G~~V~l~p--~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~~g~~~ls 735 (760)
T KOG1067|consen 668 FGGVYTATITEIRDTGVMVELYP--MQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDPRGGIMLS 735 (760)
T ss_pred eeeEEEEEEeeecccceEEEecC--CchhhccchhcccccccChHHHHhhcceeEEEEEeecCccceeeh
Confidence 68889999999999999999977 899999999999999999999999999999999999987755443
No 88
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.48 E-value=6.6e-07 Score=81.05 Aligned_cols=94 Identities=18% Similarity=0.199 Sum_probs=69.8
Q ss_pred hhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC---ceeee
Q psy18072 8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK---VMTTV 84 (174)
Q Consensus 8 ~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~---~l~ls 84 (174)
|...-.+.|++|+|+|.++.++|+||.|. +++||||.++++ ++..|++||.|+|.|++|+..+ .+-+|
T Consensus 127 ~~eyk~~~GeIV~G~V~ri~~~giiVDLg---gvea~LP~sE~i------p~E~~~~GdrIka~I~~Vd~~~kg~qIilS 197 (470)
T PRK09202 127 YEEYKDRVGEIITGVVKRVERGNIIVDLG---RAEAILPRKEQI------PRENFRPGDRVRAYVYEVRKEARGPQIILS 197 (470)
T ss_pred HHHHHhhcCCEEEEEEEEEecCCEEEEEC---CeEEEecHHHcC------CCccCCCCCEEEEEEEEEecCCCCCeEEEE
Confidence 33333358999999999999999999993 699999999985 5688999999999999999864 35555
Q ss_pred cccccchHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072 85 TPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ 116 (174)
Q Consensus 85 ~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k 116 (174)
...+ . .+...++ .++=+...|.+.++
T Consensus 198 Rt~p--~--~l~~Lf~--~EVPEI~~G~ieIk 223 (470)
T PRK09202 198 RTHP--E--FLKKLFE--QEVPEIADGLIEIK 223 (470)
T ss_pred eCcH--H--HHHHHHH--HhCcccccCeEEEE
Confidence 5544 3 2333332 23335567887775
No 89
>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=98.38 E-value=6.9e-06 Score=73.43 Aligned_cols=61 Identities=21% Similarity=0.275 Sum_probs=52.3
Q ss_pred cCCCCCCEEEEEEEEEecc--eEEEEECCCCCeEEEEEceecchh------------hhhccccccCCCCEEEEEEEE
Q psy18072 11 KYPEVEDVVMVTVISIAEM--GAYVHLLEYNNIEGMILLSELSRR------------RIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 11 ~~p~~GdiV~G~V~~i~~~--GafV~L~~~~~~~GlI~iSels~~------------~v~~~~~~l~vGd~V~vrVi~ 74 (174)
..+ +|++|.|+|.+|.+. ||||.|.. +..||||++++.+. +..++.+.+++||.|.|+|++
T Consensus 22 ~~~-vGnIY~GrV~~i~p~l~aAFVdiG~--~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K 96 (414)
T TIGR00757 22 RQL-KGNIYKGRVTRILPSLQAAFVDIGL--EKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVK 96 (414)
T ss_pred cCC-CCCEEEEEEeeecCCCceEEEEcCC--CceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEee
Confidence 344 899999999999998 99999987 78999999998643 234566789999999999998
No 90
>PRK05054 exoribonuclease II; Provisional
Probab=98.34 E-value=1.3e-06 Score=81.93 Aligned_cols=75 Identities=24% Similarity=0.298 Sum_probs=57.6
Q ss_pred cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh--hh----------ccccccCCCCEEEE
Q psy18072 3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR--IR----------SINKLIRVGKTEPV 70 (174)
Q Consensus 3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~--v~----------~~~~~l~vGd~V~v 70 (174)
+.|+|+.+. +-.|..+.|.|++|+++|+||+|.++ +++||||++.+...+ +. .-.+.|++||.|+|
T Consensus 550 ~~~~y~~~~-~G~~~~f~g~I~~v~~~G~fV~l~~~-~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V 627 (644)
T PRK05054 550 LYARYLKDK-AGTDTRFAAEIIDISRGGMRVRLLEN-GAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDV 627 (644)
T ss_pred HHHHHHhhc-cCCCeEEEEEEEeeecCcEEEEEeCC-ceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEE
Confidence 367866653 21245999999999999999999874 599999999986531 11 11257999999999
Q ss_pred EEEEEeCCC
Q psy18072 71 VVIRVDKEK 79 (174)
Q Consensus 71 rVi~Vd~~~ 79 (174)
+|.+||..+
T Consensus 628 ~v~~vd~~~ 636 (644)
T PRK05054 628 TLAEVRMET 636 (644)
T ss_pred EEEEEcccc
Confidence 999999753
No 91
>KOG1070|consensus
Probab=98.30 E-value=1.2e-06 Score=86.35 Aligned_cols=75 Identities=25% Similarity=0.323 Sum_probs=66.3
Q ss_pred hhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeecc
Q psy18072 8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTP 86 (174)
Q Consensus 8 ~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~ 86 (174)
|.+.. +|.++.|+|-.+.++||||++.+ ++.||.|.|++++.++.+...+|.+||+|.|+|+++|.++ .+.++++
T Consensus 594 ~~~~~--pg~~~~G~l~~~~~~g~~V~F~g--~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nvd~ek~rm~l~~r 669 (1710)
T KOG1070|consen 594 FEQAI--PGKITKGTLCAIKENGAFVTFTG--GLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNVDDEKRRMPLGLR 669 (1710)
T ss_pred hhhcC--CCceEEEEEeeeccCCeEEEecC--ccccccchhhhhhhhhcChhhhcccccEEEEEEEecCchhceeehhhh
Confidence 44443 59999999999999999999977 9999999999999999999999999999999999999876 4555543
No 92
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=98.25 E-value=6.6e-06 Score=58.49 Aligned_cols=61 Identities=13% Similarity=0.109 Sum_probs=50.1
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhc-----------cccccCCCCEEEEEEEEEeCC
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRS-----------INKLIRVGKTEPVVVIRVDKE 78 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~-----------~~~~l~vGd~V~vrVi~Vd~~ 78 (174)
+|+++.|+|+++.++|+||.+.+ +.+|+|.+.+......+ -...+.+|+.|++||+.+..+
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gp---l~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~ 72 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGP---LSIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRVD 72 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcC---ceEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEEc
Confidence 48999999999999999999976 88999999886543211 245699999999999998764
No 93
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.19 E-value=8.2e-06 Score=71.79 Aligned_cols=92 Identities=20% Similarity=0.209 Sum_probs=68.1
Q ss_pred ccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC---ceeeecc
Q psy18072 10 EKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK---VMTTVTP 86 (174)
Q Consensus 10 ~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~---~l~ls~~ 86 (174)
....+.|++|+|+|.++.+.|+||.|. +++|+||.+++. ++..|++||.++|.|++|+..+ .+.+|..
T Consensus 129 ef~~k~GeiV~G~V~~~~~~~~~Vdlg---~vEa~LP~~E~i------p~e~~~~Gd~Ika~V~~V~~~~kgp~IivSRt 199 (362)
T PRK12327 129 EFSEREGDIVTGVVQRRDNRFVYVNLG---KIEAVLPPAEQI------PGETYKHGDRIKVYVVKVEKTTKGPQIFVSRT 199 (362)
T ss_pred HHHHhcCCEEEEEEEEEeCCcEEEEeC---CeEEEecHHHcC------CCCCCCCCCEEEEEEEEEecCCCCCeEEEEeC
Confidence 333358999999999999999999994 599999988764 3578999999999999999654 4666665
Q ss_pred cccchHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072 87 EKADGLKALQEAIDTIKAKIEQLGGVFQVQ 116 (174)
Q Consensus 87 ~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k 116 (174)
.+ . .+...++ .++=+...|.+.++
T Consensus 200 ~p--~--~v~~Lfe--~EVPEI~~G~VeIk 223 (362)
T PRK12327 200 HP--G--LVKRLFE--LEVPEIYDGTVEIK 223 (362)
T ss_pred CH--H--HHHHHHH--HhCccccCCeEEEE
Confidence 55 3 2333332 23335567877775
No 94
>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=98.19 E-value=9.7e-06 Score=70.80 Aligned_cols=88 Identities=19% Similarity=0.273 Sum_probs=65.8
Q ss_pred CCCCEEEEEEEEEecce-EEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC---ceeeeccccc
Q psy18072 14 EVEDVVMVTVISIAEMG-AYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK---VMTTVTPEKA 89 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~G-afV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~---~l~ls~~~k~ 89 (174)
+.|++|+|+|.++.+.| +||.| + +.+|+||.++.. +...|++||.++|.|++|+... .+.+|...+
T Consensus 130 k~GeiV~G~V~~v~~~g~v~Vdi-G--~~ea~LP~~E~i------p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt~~- 199 (341)
T TIGR01953 130 KEGEIISGTVKRVNRRGNLYVEL-G--KTEGILPKKEQI------PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHP- 199 (341)
T ss_pred hcCCEEEEEEEEEecCCcEEEEE-C--CeEEEecHHHcC------CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeCcH-
Confidence 58999999999999888 69999 4 699999999877 3467999999999999999653 356665555
Q ss_pred chHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072 90 DGLKALQEAIDTIKAKIEQLGGVFQVQ 116 (174)
Q Consensus 90 ~g~~~i~~~~~~i~~~l~~~~g~l~~k 116 (174)
. .+...++ .++=+..+|.+.++
T Consensus 200 -~--~v~~Lfe--~EVPEI~dG~VeI~ 221 (341)
T TIGR01953 200 -E--FVKELLK--LEVPEIADGIIEIK 221 (341)
T ss_pred -H--HHHHHHH--HhCccccCCeEEEE
Confidence 3 2333333 23335577887774
No 95
>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=98.08 E-value=8.1e-06 Score=76.56 Aligned_cols=75 Identities=25% Similarity=0.347 Sum_probs=57.2
Q ss_pred cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch--hhh-----h---cc--ccccCCCCEEEE
Q psy18072 3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR--RRI-----R---SI--NKLIRVGKTEPV 70 (174)
Q Consensus 3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~--~~v-----~---~~--~~~l~vGd~V~v 70 (174)
+.|+|+.++.- .|..+.|+|++++.+|+||.|.+. +++||||++.+.. .++ . .+ ...|++||.|+|
T Consensus 546 ~~~~yl~~~~g-~~~~f~g~I~~v~~~g~~v~l~~~-~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V 623 (639)
T TIGR02062 546 LYARFLADKAA-KNTRFAAEIVDISRGGMRVRLLEN-GAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDV 623 (639)
T ss_pred HHHHHHhhccC-CCcEEEEEEEeeeCCcEEEEEecC-ceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEE
Confidence 35776666421 355999999999999999999763 6999999999865 222 1 11 136999999999
Q ss_pred EEEEEeCCC
Q psy18072 71 VVIRVDKEK 79 (174)
Q Consensus 71 rVi~Vd~~~ 79 (174)
+|.+||..+
T Consensus 624 ~v~~vd~~~ 632 (639)
T TIGR02062 624 VLTEVRMET 632 (639)
T ss_pred EEEEecccc
Confidence 999998653
No 96
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=98.05 E-value=8.1e-06 Score=77.28 Aligned_cols=72 Identities=25% Similarity=0.414 Sum_probs=59.9
Q ss_pred cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh-----------hccccccCCCCEEEEE
Q psy18072 3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI-----------RSINKLIRVGKTEPVV 71 (174)
Q Consensus 3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v-----------~~~~~~l~vGd~V~vr 71 (174)
+.|+|+... +|..+.|+|++++.||+||.|+++ +++|+||++.+...++ ......+++||.|+|+
T Consensus 613 ~~~~~m~~~---vg~~f~g~V~~v~~~g~~V~l~~~-~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~ 688 (706)
T COG0557 613 LKAEYMKKR---VGEEFDGVVTGVTSFGFFVELPEL-GLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVK 688 (706)
T ss_pred HHHHHHHHh---cCCEEEEEEEEEEeccEEEEeccc-ccccceEcccCCCceeeeccccceeeccccccccccCCEEEEE
Confidence 367765553 699999999999999999999985 3999999999986543 2345689999999999
Q ss_pred EEEEeCC
Q psy18072 72 VIRVDKE 78 (174)
Q Consensus 72 Vi~Vd~~ 78 (174)
|++++..
T Consensus 689 v~~v~~~ 695 (706)
T COG0557 689 VTSVDLD 695 (706)
T ss_pred EEEEccc
Confidence 9999874
No 97
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=98.01 E-value=3.2e-05 Score=61.65 Aligned_cols=62 Identities=11% Similarity=0.130 Sum_probs=51.1
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh-----------h-hccccccCCCCEEEEEEEEEeCC
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR-----------I-RSINKLIRVGKTEPVVVIRVDKE 78 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~-----------v-~~~~~~l~vGd~V~vrVi~Vd~~ 78 (174)
-+|+++.|+|+++.++|+||++.. ++++||.+++.... . .+-...+..|+.|++||+.+..+
T Consensus 80 f~gEVv~g~V~~v~~~G~~v~~Gp---~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~ 153 (176)
T PTZ00162 80 FKDEVLDAIVTDVNKLGFFAQAGP---LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYD 153 (176)
T ss_pred CCCCEEEEEEEEEecceEEEEeeC---eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEec
Confidence 379999999999999999999965 77999999987431 1 12246899999999999998764
No 98
>KOG1070|consensus
Probab=97.80 E-value=7.6e-05 Score=74.19 Aligned_cols=72 Identities=21% Similarity=0.298 Sum_probs=65.3
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC-ceeeeccc
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK-VMTTVTPE 87 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~-~l~ls~~~ 87 (174)
+.|++|.|.|..+.+.|+||.|.. +++|++++|+++..+...+.+.|.+|+.|.+||++++... .+.++++.
T Consensus 1161 k~g~iv~G~V~nv~~~glfi~ls~--~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~ve~~s~riel~Lk~ 1233 (1710)
T KOG1070|consen 1161 KIGDIVRGFVKNVETKGLFIALSR--KVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSVEEDSKRIELSLKN 1233 (1710)
T ss_pred ccCceeEEEEEEecCCcEEEEEcc--ceEEEEEccccccchhhhhhccCCccceeeeEEEEeeccCceEEEEEec
Confidence 489999999999999999999988 8999999999999999999999999999999999999876 55555544
No 99
>KOG3409|consensus
Probab=97.78 E-value=8.2e-05 Score=59.10 Aligned_cols=85 Identities=22% Similarity=0.232 Sum_probs=65.6
Q ss_pred hhccCCCCCCEEEEEEEEEecceEEEEECC-----C-CCeEEEEEceecchh--hhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLE-----Y-NNIEGMILLSELSRR--RIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 8 ~~~~~p~~GdiV~G~V~~i~~~GafV~L~~-----~-~~~~GlI~iSels~~--~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
+..-+|..|++|.++|..+...-|-|.|.. + ..+.|+||...+... ---.+.+.|++||.|.|+|++.....
T Consensus 61 ~~~~LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~ 140 (193)
T KOG3409|consen 61 FNELLPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGS 140 (193)
T ss_pred hhhcCCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCC
Confidence 345678899999999999987777666653 2 147999998876531 11235678999999999999977777
Q ss_pred ceeeecccccchH
Q psy18072 80 VMTTVTPEKADGL 92 (174)
Q Consensus 80 ~l~ls~~~k~~g~ 92 (174)
.+-|++...++|.
T Consensus 141 ~y~LTtAeneLGV 153 (193)
T KOG3409|consen 141 NYLLTTAENELGV 153 (193)
T ss_pred cEEEEEecccceE
Confidence 8899998888885
No 100
>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=97.66 E-value=0.00026 Score=48.68 Aligned_cols=56 Identities=18% Similarity=0.214 Sum_probs=49.4
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh---hccccccCCCCEE-EEEEE
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI---RSINKLIRVGKTE-PVVVI 73 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v---~~~~~~l~vGd~V-~vrVi 73 (174)
|++|.|+|..-++.+++|+|.++ ++.|+||..++++ .+ +..-..+++||.+ .+.|+
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~-~l~a~l~~~HLsD-~~~k~~~~~~klrvG~~L~~~lvL 60 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPE-EIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL 60 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCC-CcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE
Confidence 78999999999999999999986 5999999999998 43 3355789999999 99999
No 101
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.53 E-value=0.00058 Score=45.14 Aligned_cols=60 Identities=25% Similarity=0.338 Sum_probs=34.7
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCceeeec
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKVMTTVT 85 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~l~ls~ 85 (174)
+|++.+.+|..+.++|+|+.... .-+-+||.+++. ..+++||.|.|-|-. |..+.+.+|+
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~--~~~vlLp~~e~~--------~~~~~Gd~v~VFvY~-D~~~rl~AT~ 60 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGE--GKEVLLPKSEVP--------EPLKVGDEVEVFVYL-DKEGRLVATT 60 (61)
T ss_dssp --------EEEE-SSEEEEEETT---EEEEEEGGG--------------TTSEEEEEEEE--TTS-EEEE-
T ss_pred CCCCcceEEEEEeCCEEEEECCC--CCEEEechHHcC--------CCCCCCCEEEEEEEE-CCCCCEEEec
Confidence 48899999999999999999766 689999999887 569999999998754 5555565554
No 102
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=97.53 E-value=0.00043 Score=61.14 Aligned_cols=94 Identities=15% Similarity=0.226 Sum_probs=66.8
Q ss_pred hhccCCCCCCEEEEEEEEEecc-eEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCCc----ee
Q psy18072 8 YAEKYPEVEDVVMVTVISIAEM-GAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEKV----MT 82 (174)
Q Consensus 8 ~~~~~p~~GdiV~G~V~~i~~~-GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~~----l~ 82 (174)
|.....++|++|.|+|.++... ++||.|. +.+|+||.++.. ++..|++||.++|.|.+|..... +-
T Consensus 131 ~~ey~~~~Geiv~g~V~r~~~~~~i~vdlg---~~ea~LP~~eqi------p~E~~~~Gdrik~~i~~V~~~~k~gp~Ii 201 (374)
T PRK12328 131 FEKYKKKVGKIVFGTVVRVDNEENTFIEID---EIRAVLPMKNRI------KGEKFKVGDVVKAVLKRVKIDKNNGILIE 201 (374)
T ss_pred HHHHHHhcCcEEEEEEEEEecCCCEEEEcC---CeEEEeCHHHcC------CCCcCCCCCEEEEEEEEEecCCCCCCEEE
Confidence 3344446899999999999764 5899985 599999988755 45889999999999999988643 34
Q ss_pred eecccccchHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072 83 TVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ 116 (174)
Q Consensus 83 ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k 116 (174)
+|...+ + .+...++ .++=+..+|.+.++
T Consensus 202 lSRt~p--~--~v~~Lfe--~EVPEI~dG~VeIk 229 (374)
T PRK12328 202 LSRTSP--K--FLEALLE--LEVPEIKDGEVIII 229 (374)
T ss_pred EEcCCH--H--HHHHHHH--HhCccccCCeEEEE
Confidence 444444 3 2333333 23335577887774
No 103
>KOG1856|consensus
Probab=97.52 E-value=0.00016 Score=70.83 Aligned_cols=63 Identities=33% Similarity=0.452 Sum_probs=56.8
Q ss_pred CCCEEEEEEEEEecce---EEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 15 VEDVVMVTVISIAEMG---AYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~G---afV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
.|.+|.++|++|+..- +-|.+.+ ++.|+||.+.+|.+.+++|...+++||+|.+||++++..+
T Consensus 985 ~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 985 EGAIVPVTVTKVTHRRGICVRVRLDC--GVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKIDKER 1050 (1299)
T ss_pred cCceEEEeeeEEEecccceeEEEecC--CCceeeeccccChhhccCHHHhhccCceEEEEeeeeeHhh
Confidence 7999999999996543 4567777 8999999999999999999999999999999999999887
No 104
>PRK11712 ribonuclease G; Provisional
Probab=97.47 E-value=0.002 Score=58.96 Aligned_cols=59 Identities=20% Similarity=0.303 Sum_probs=48.0
Q ss_pred CCCEEEEEEEEEec--ceEEEEECCCCCeEEEEEceecchh------------hhhccccccCCCCEEEEEEEEE
Q psy18072 15 VEDVVMVTVISIAE--MGAYVHLLEYNNIEGMILLSELSRR------------RIRSINKLIRVGKTEPVVVIRV 75 (174)
Q Consensus 15 ~GdiV~G~V~~i~~--~GafV~L~~~~~~~GlI~iSels~~------------~v~~~~~~l~vGd~V~vrVi~V 75 (174)
+|++|.|+|.+|.+ .+|||.|.. +..||+|++++... ....+.+.+++||.|-|+|++-
T Consensus 38 vGnIY~G~V~~v~pg~~AAFVdIG~--~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke 110 (489)
T PRK11712 38 VGNIYKGRVSRVLPGMQAAFVDIGL--DKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD 110 (489)
T ss_pred cccEEEEEEeecCCCCceeEEeeCC--CccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence 89999999999965 389999988 89999999987321 1223456799999999999983
No 105
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=97.42 E-value=0.00095 Score=60.10 Aligned_cols=97 Identities=14% Similarity=0.123 Sum_probs=68.9
Q ss_pred hhccCCCCCCEEEEEEEEEecceEEEEECC-CCC--eEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC----c
Q psy18072 8 YAEKYPEVEDVVMVTVISIAEMGAYVHLLE-YNN--IEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK----V 80 (174)
Q Consensus 8 ~~~~~p~~GdiV~G~V~~i~~~GafV~L~~-~~~--~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~----~ 80 (174)
|.....++|++|+|+|.++...+++|.|.. ++. .+|+||.++.. ++..|++|+.|+|.|.+|.... .
T Consensus 145 ~~ef~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi------p~E~y~~Gdrika~i~~V~~~~~kGpq 218 (449)
T PRK12329 145 QEEFQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL------PNDNYRANATFKVFLKEVSEGPRRGPQ 218 (449)
T ss_pred HHHHHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC------CCCcCCCCCEEEEEEEEeecCCCCCCE
Confidence 334444689999999999988899999942 223 89999988754 4588999999999999997752 3
Q ss_pred eeeecccccchHHHHHHHHHHHHHHHhhhCCeeEEe
Q psy18072 81 MTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ 116 (174)
Q Consensus 81 l~ls~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k 116 (174)
+.+|...+ + .+...++ .++=+...|.+.++
T Consensus 219 IilSRt~p--~--lv~~Lfe--~EVPEI~dG~VeIk 248 (449)
T PRK12329 219 LFVSRANA--G--LVVYLFE--NEVPEIEEGVVRIV 248 (449)
T ss_pred EEEEcCCH--H--HHHHHHH--hhCcccccCeEEEE
Confidence 55555555 4 2333333 23335577888775
No 106
>PRK10811 rne ribonuclease E; Reviewed
Probab=97.23 E-value=0.00067 Score=65.95 Aligned_cols=61 Identities=18% Similarity=0.285 Sum_probs=49.6
Q ss_pred CCCCCEEEEEEEEEec--ceEEEEECCCCCeEEEEEceecchhhhh---------ccccccCCCCEEEEEEEEE
Q psy18072 13 PEVEDVVMVTVISIAE--MGAYVHLLEYNNIEGMILLSELSRRRIR---------SINKLIRVGKTEPVVVIRV 75 (174)
Q Consensus 13 p~~GdiV~G~V~~i~~--~GafV~L~~~~~~~GlI~iSels~~~v~---------~~~~~l~vGd~V~vrVi~V 75 (174)
+.+|+||.|+|.+|.+ .+|||.|.. +..||||++++...++. ++...+++||.|-|.|.+-
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~--gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE 107 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGA--ERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE 107 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecC--CcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence 3489999999999954 488999998 89999999998644321 3456799999999999983
No 107
>KOG3013|consensus
Probab=96.56 E-value=0.0029 Score=53.31 Aligned_cols=81 Identities=22% Similarity=0.259 Sum_probs=67.0
Q ss_pred hccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch------hh----hhccccccCCCCEEEEEEEEEeCC
Q psy18072 9 AEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR------RR----IRSINKLIRVGKTEPVVVIRVDKE 78 (174)
Q Consensus 9 ~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~------~~----v~~~~~~l~vGd~V~vrVi~Vd~~ 78 (174)
....|++||+|.|+|..|.+.-|=|++.. +..+.+..|.+.- ++ -...+.+|+.||.|.|.|-.+-.+
T Consensus 79 ~rY~pEvGDvVVgRV~eVq~KRWkvd~ns--k~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~d 156 (301)
T KOG3013|consen 79 SRYAPEVGDVVVGRVIEVQQKRWKVDLNS--KQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHD 156 (301)
T ss_pred hhcCCccCCEEEEEeeeeecceeEEeccc--ccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhccC
Confidence 45567899999999999999999999988 8999999887642 11 124678999999999999999999
Q ss_pred Cceeeecccccch
Q psy18072 79 KVMTTVTPEKADG 91 (174)
Q Consensus 79 ~~l~ls~~~k~~g 91 (174)
+.+++.++....|
T Consensus 157 Gs~sLhTRS~KYG 169 (301)
T KOG3013|consen 157 GSLSLHTRSLKYG 169 (301)
T ss_pred CeEEEEecchhcc
Confidence 9998888776444
No 108
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=96.42 E-value=0.035 Score=50.83 Aligned_cols=62 Identities=23% Similarity=0.313 Sum_probs=51.3
Q ss_pred CCCEEEEEEEEEecc--eEEEEECCCCCeEEEEEceecchhhhhc-----cccccCCCCEEEEEEEEEeCCC
Q psy18072 15 VEDVVMVTVISIAEM--GAYVHLLEYNNIEGMILLSELSRRRIRS-----INKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~--GafV~L~~~~~~~GlI~iSels~~~v~~-----~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
+|.+|.|+|++|.+. .|||.+.. .-.||+|.+++.+ +++. +...++.||.+-|.|++-....
T Consensus 37 ~gniy~grv~~i~p~~~aafvdig~--~r~gfl~~~~~~~-~~~~~~~~~i~~~lr~~~~~~Vqv~ke~~G~ 105 (487)
T COG1530 37 VGNIYKGRVTRVLPSLEAAFVDIGL--ERNGFLHLSEIVP-YFRAVLEEKIKVRLRGGQATLVQVVKEPRGT 105 (487)
T ss_pred ecCceEEEecccCccchhheeeccC--CccceEEecccch-hhhhcccccceeeecCCceEEEEEEeecCcc
Confidence 799999999999654 78999987 7899999999998 4433 3468999999999999855443
No 109
>KOG3298|consensus
Probab=95.66 E-value=0.058 Score=42.59 Aligned_cols=61 Identities=15% Similarity=0.103 Sum_probs=42.3
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecch-----------hhhhccccccCCCCEEEEEEEEEeCC
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSR-----------RRIRSINKLIRVGKTEPVVVIRVDKE 78 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~-----------~~v~~~~~~l~vGd~V~vrVi~Vd~~ 78 (174)
.|++|.|+|+.+...|+|+++.+ ++-++..--... .+..+-...+.+|..|+++|+.+.-+
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~GP---l~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~ 152 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSGP---LEVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVD 152 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEeccc---eEeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEe
Confidence 69999999999999999999977 333332111111 11112223799999999999987654
No 110
>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=94.02 E-value=0.37 Score=36.28 Aligned_cols=61 Identities=20% Similarity=0.081 Sum_probs=43.5
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchh-h-----------h-hccccccCCCCEEEEEEEEEeC
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRR-R-----------I-RSINKLIRVGKTEPVVVIRVDK 77 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~-~-----------v-~~~~~~l~vGd~V~vrVi~Vd~ 77 (174)
+|+++.|+|.+.+..|+.|.|.-| -+=+||.+.|... + + ....-.+..|+.|+.||.++..
T Consensus 3 ~gEvl~g~I~~~~~~Gi~vslgFF--ddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAEGIRVSLGFF--DDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp TT-EEEEEEEEEETTEEEEEECCE--EEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CCCEEEEEEEecCCCcEEEEeccc--ccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 699999999999999999999653 3567777766531 1 1 2334467999999999999876
No 111
>KOG1004|consensus
Probab=92.86 E-value=0.55 Score=38.74 Aligned_cols=65 Identities=15% Similarity=0.060 Sum_probs=48.6
Q ss_pred CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 12 YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
.|.+||.|.|+|+.-...+.-|.|.. .--|+|+.-.+...- +.-+-.+++||.|-|||...+++.
T Consensus 62 iP~~~D~VIGiV~~~~gd~ykVDigg--~~~a~L~~laFe~At-krNrPnl~vGdliyakv~~a~~~~ 126 (230)
T KOG1004|consen 62 IPVKGDHVIGIVTSKSGDIYKVDIGG--SEPASLSYLAFEGAT-KRNRPNLQVGDLIYAKVVDANKDM 126 (230)
T ss_pred cCCCCCEEEEEEEeccCceEEEecCC--CCeeeeeeccccCcc-ccCCCccccccEEEEEEEecCCCc
Confidence 45689999999999888888999976 567777765554321 112246999999999999876544
No 112
>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=92.33 E-value=0.96 Score=33.16 Aligned_cols=51 Identities=6% Similarity=0.089 Sum_probs=43.5
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
.|.+|.|+|..|...-+||.+.. +..++++...... +.|..|..|.+|+..
T Consensus 23 ~gk~V~G~I~hvv~ddLYIDfG~--KFhcVc~rp~~~~-------~~y~~G~rV~lrLkd 73 (104)
T PF10246_consen 23 EGKIVIGKIFHVVDDDLYIDFGG--KFHCVCKRPAVNG-------EKYVRGSRVRLRLKD 73 (104)
T ss_pred cCCEEEEEEEEEecCceEEEeCC--ceeEEEecccccc-------cccccCCEEEEEECC
Confidence 79999999999988899999988 8999998665432 468889999999874
No 113
>PRK15464 cold shock-like protein CspH; Provisional
Probab=89.95 E-value=1.2 Score=30.17 Aligned_cols=51 Identities=12% Similarity=0.173 Sum_probs=38.8
Q ss_pred EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
++|+|+... ..|. ||..+. ++-+-|+|+|.+..... +.+.+||.|...|..
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~-g~~DvFvH~s~l~~~g~----~~l~~G~~V~f~v~~ 57 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSD-GRKEVQVHISAFTPRDA----EVLIPGLRVEFCRVN 57 (70)
T ss_pred ceEEEEEEECCCCeEEEccCC-CCccEEEEehhehhcCC----CCCCCCCEEEEEEEE
Confidence 479999984 4676 787765 24689999999964322 468999999998876
No 114
>PRK15463 cold shock-like protein CspF; Provisional
Probab=89.06 E-value=1.5 Score=29.65 Aligned_cols=51 Identities=14% Similarity=0.149 Sum_probs=38.6
Q ss_pred EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
++|+|+... ..|. ||.... ++-+-|+|+|.+..... ..+++|+.|...|..
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~-g~~DvFvH~sal~~~g~----~~l~~G~~V~f~v~~ 57 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSD-GRKDVQVHISALNLRDA----EELTTGLRVEFCRIN 57 (70)
T ss_pred ceEEEEEEeCCCceEEEecCC-CCccEEEEehhhhhcCC----CCCCCCCEEEEEEEE
Confidence 479999984 4676 777765 24789999999975422 468899999998775
No 115
>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=88.79 E-value=2.1 Score=29.03 Aligned_cols=54 Identities=15% Similarity=0.016 Sum_probs=38.9
Q ss_pred EEEEEEEEEecceEEE-EECCCCCeEEEEEcee-cchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072 18 VVMVTVISIAEMGAYV-HLLEYNNIEGMILLSE-LSRRRIRSINKLIRVGKTEPVVVIRVDKE 78 (174)
Q Consensus 18 iV~G~V~~i~~~GafV-~L~~~~~~~GlI~iSe-ls~~~v~~~~~~l~vGd~V~vrVi~Vd~~ 78 (174)
.+.|+|+..-+.+.|- .|.+ +..=+.|+|= +...+ -.+.+||.|.|.+...+..
T Consensus 6 e~~G~V~e~L~~~~f~V~l~n--g~~vla~i~GKmr~~r-----I~I~~GD~V~Ve~spyd~t 61 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELEN--GHEVLAHISGKIRMHY-----IRILPGDKVKVELSPYDLT 61 (68)
T ss_pred EEEEEEEEECCCCEEEEEECC--CCEEEEEecCcchhcc-----EEECCCCEEEEEECcccCC
Confidence 4789999997777764 8877 7777777773 22122 3588999999987765543
No 116
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=88.15 E-value=2 Score=30.60 Aligned_cols=55 Identities=18% Similarity=0.111 Sum_probs=39.6
Q ss_pred EEEEEEEEEecceEE-EEECCCCCeEEEEEcee-cchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 18 VVMVTVISIAEMGAY-VHLLEYNNIEGMILLSE-LSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 18 iV~G~V~~i~~~Gaf-V~L~~~~~~~GlI~iSe-ls~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
.+.|+|+.+-+.+.| |.|.+ +..=+-|+|= +...+ -.+.+||.|.|.+...|..+
T Consensus 8 e~~G~V~e~Lp~~~frV~Len--G~~vla~isGKmR~~r-----IrIl~GD~V~VE~spYDltk 64 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLEN--GVEVGAYASGRMRKHR-----IRILAGDRVTLELSPYDLTK 64 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCC--CCEEEEEeccceeeee-----EEecCCCEEEEEECcccCCc
Confidence 589999999777766 48887 6666777662 22222 34789999999998777654
No 117
>PRK09890 cold shock protein CspG; Provisional
Probab=87.35 E-value=2.8 Score=28.23 Aligned_cols=51 Identities=4% Similarity=0.117 Sum_probs=37.7
Q ss_pred EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
++|+|.... ..|. ||.-.+ ++-+-|+|+|.+...-+ ..+.+|+.|...+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~-g~~dvFvH~s~l~~~~~----~~l~~G~~V~f~~~~ 57 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDD-GSKDVFVHFTAIQSNEF----RTLNENQKVEFSIEQ 57 (70)
T ss_pred ceEEEEEEECCCCcEEEecCC-CCceEEEEEeeeccCCC----CCCCCCCEEEEEEEE
Confidence 479999884 3565 777665 14789999999975432 468899999997765
No 118
>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=87.30 E-value=5.5 Score=25.87 Aligned_cols=51 Identities=16% Similarity=0.125 Sum_probs=35.4
Q ss_pred EEEEEEEEec-ceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 19 VMVTVISIAE-MGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 19 V~G~V~~i~~-~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
.+|+|....+ .|. ||.-.+- .-+=++|.|.+.... ...++.|+.|...+..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~-~~diFfh~s~~~~~~----~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDG-GEDIFFHISDLSGNG----FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTS-SSEEEEEGGGBCSSS----STS--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEccc-ceeEEeccccccccc----cccCCCCCEEEEEEEE
Confidence 4799999854 233 5555541 458999999998543 2568899999999987
No 119
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=86.61 E-value=3.5 Score=29.60 Aligned_cols=53 Identities=19% Similarity=0.305 Sum_probs=34.7
Q ss_pred EEEEEEEEEecce--EEEEECCCC-CeEEEEEceecchhhhhccccccCCCCEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEYN-NIEGMILLSELSRRRIRSINKLIRVGKTEPV 70 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~~-~~~GlI~iSels~~~v~~~~~~l~vGd~V~v 70 (174)
.+.|.|.++...| +||.|.... .++.++..+......+......+++|+.|.|
T Consensus 3 ~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v 58 (108)
T cd04322 3 SVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGV 58 (108)
T ss_pred EEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEE
Confidence 4789999997654 799997622 3566665554433333333344899999866
No 120
>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane
Probab=86.48 E-value=1.2 Score=33.99 Aligned_cols=20 Identities=30% Similarity=0.421 Sum_probs=14.4
Q ss_pred HHHHHHHHHhcccccCCCCc
Q psy18072 131 ARQMERAEAENAEVAADDDE 150 (174)
Q Consensus 131 k~~~~~l~k~~~e~~gd~~~ 150 (174)
++--.+|..-+++||.|+++
T Consensus 101 ~kyk~rLk~LG~eVSddE~~ 120 (136)
T PF04871_consen 101 KKYKERLKELGEEVSDDEDS 120 (136)
T ss_pred HHHHHHHHHcCCCccCCccc
Confidence 33446677889999988765
No 121
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=85.58 E-value=2.6 Score=27.34 Aligned_cols=55 Identities=13% Similarity=0.100 Sum_probs=33.8
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEE-EEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGM-ILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~Gl-I~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
...+.|+|.++...|.++.+.- .+.|. .-.+.++...... -.|++|+.|.+.+-.
T Consensus 6 ~N~l~g~I~~i~~~g~~~~v~l--~~~~~~~l~a~i~~~~~~~--l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 6 RNQLKGKVVAIEDGDVNAEVDL--LLGGGTKLTAVITLESVAE--LGLKPGKEVYAVIKA 61 (69)
T ss_pred ccEEEEEEEEEEECCCeEEEEE--EECCCCEEEEEecHHHHhh--CCCCCCCEEEEEEEC
Confidence 3578999999987777665532 12222 2233444433332 348999999998754
No 122
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=84.56 E-value=0.034 Score=48.34 Aligned_cols=47 Identities=13% Similarity=0.084 Sum_probs=27.8
Q ss_pred hccCCCCCCEEEEEEEEE-ecceEEEE------ECCCCCeEEEEEceecchhhhhcc
Q psy18072 9 AEKYPEVEDVVMVTVISI-AEMGAYVH------LLEYNNIEGMILLSELSRRRIRSI 58 (174)
Q Consensus 9 ~~~~p~~GdiV~G~V~~i-~~~GafV~------L~~~~~~~GlI~iSels~~~v~~~ 58 (174)
...|+ .|++|.|+|..+ ..+|+|++ ..+ .++++.|+++++...+.++
T Consensus 100 ~e~~~-~g~~v~~~V~~ia~~~g~~~eely~~i~~p--l~~~~gh~y~af~~~v~~~ 153 (319)
T PTZ00248 100 EEKFS-KSKKVHSIMRHIAQKHGMSVEELYTKIIWP--LYKKYGHALDALKEALTNP 153 (319)
T ss_pred HHhCc-CCCEEEEEEEEchhhcCCCHHHHHHHHHHH--HHHhcCCHHHHHHHHhcCc
Confidence 44554 677777777777 34677765 222 4566667666665544433
No 123
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=84.52 E-value=5.2 Score=34.26 Aligned_cols=51 Identities=16% Similarity=0.277 Sum_probs=35.4
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEE
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrV 72 (174)
++|.+....|.+.++||+|+.=.++. -.=++|.++.-. +.+.+||.|+|-|
T Consensus 4 ~iG~~~~l~V~~~~~~g~fL~~~~~~-~~ilL~k~~~~~-------~e~evGdev~vFi 54 (287)
T COG2996 4 KIGQINSLEVVEFSDFGYFLDAGEDG-TTILLPKSEPEE-------DELEVGDEVTVFI 54 (287)
T ss_pred cccceEEEEEEEeeceeEEEecCCCc-eEEeccccCCcC-------CccccCcEEEEEE
Confidence 37999999999999999999876631 255666664321 3455666666543
No 124
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=84.22 E-value=4.8 Score=27.01 Aligned_cols=51 Identities=10% Similarity=0.141 Sum_probs=37.4
Q ss_pred EEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 19 VMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 19 V~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
+.|+|.... ..|. ||.-.. ++-+-|+|+|.+..... ..+++|+.|...+..
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~-g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~ 57 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDD-GSKDVFVHFSAIQNDGY----KSLDEGQKVSFTIES 57 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCC-CCccEEEEEeeccccCC----CCCCCCCEEEEEEEE
Confidence 479998884 3455 676655 14789999999974322 468999999998775
No 125
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=82.33 E-value=6.3 Score=26.40 Aligned_cols=53 Identities=9% Similarity=0.119 Sum_probs=38.7
Q ss_pred EEEEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072 18 VVMVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV 75 (174)
Q Consensus 18 iV~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V 75 (174)
.++|+|+... ..|. ||..++ ++-+-|+|+|.+..... ..+.+|+.|...+..-
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~-g~~dvfvH~s~l~~~g~----~~l~~G~~V~f~~~~~ 57 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPED-GSKDVFVHFSAIQTNGF----KTLAEGQRVEFEITNG 57 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCC-CCeeEEEEeecccccCC----CCCCCCCEEEEEEEEC
Confidence 4679999884 3566 777655 14689999999874322 4688999999987753
No 126
>PRK10943 cold shock-like protein CspC; Provisional
Probab=82.05 E-value=5.3 Score=26.78 Aligned_cols=53 Identities=11% Similarity=0.135 Sum_probs=38.9
Q ss_pred EEEEEEEEEec-ceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072 18 VVMVTVISIAE-MGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV 75 (174)
Q Consensus 18 iV~G~V~~i~~-~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V 75 (174)
.++|+|+.... .|. ||.-.. ++-+-|+|+|.+..... ..+..|+.|...+..-
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~-g~~dvFvH~s~l~~~g~----~~l~~G~~V~f~~~~~ 57 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPAD-GSKDVFVHFSAIQGNGF----KTLAEGQNVEFEIQDG 57 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCC-CCeeEEEEhhHccccCC----CCCCCCCEEEEEEEEC
Confidence 36899998843 565 776654 14799999999874422 4688999999988763
No 127
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=80.64 E-value=6.9 Score=26.73 Aligned_cols=52 Identities=12% Similarity=0.050 Sum_probs=38.2
Q ss_pred EEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEe
Q psy18072 20 MVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76 (174)
Q Consensus 20 ~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd 76 (174)
+|+|+-.. ..|. ||..+. ++-+-|+|+|.+...-. ..+..||.|...+..-.
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~-gg~dVFvH~s~i~~~g~----~~l~~G~~V~f~~~~~~ 56 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEG-GGEDIFAHYSTIQMDGY----RTLKAGQSVQFDVHQGP 56 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCC-CCccEEEEEeeccccCC----CCCCCCCEEEEEEEECC
Confidence 48888874 3566 776654 25799999999974422 46889999999887643
No 128
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=79.13 E-value=5.7 Score=33.93 Aligned_cols=58 Identities=19% Similarity=0.118 Sum_probs=44.2
Q ss_pred cccchhhcc-CCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072 3 LSCRFYAEK-YPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV 75 (174)
Q Consensus 3 ~~~r~~~~~-~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V 75 (174)
|.++.+... .|..|.+=.|.|.+....|.+|.+.. ..++..+ ..+.+|..|.++|.+.
T Consensus 92 L~ip~h~~~~~~~~Ge~ReG~v~~~~~~~~~v~iG~----~~~~~l~-----------~~~~~~~RvTvri~~~ 150 (272)
T COG2106 92 LRIPSHTVSTSPKEGEYREGLVIRRGKKGNLVDIGK----DKLAKLS-----------SPAPPGARVTVRIISR 150 (272)
T ss_pred CCCCCccCcCCccceeecceEEEEecCCceEEEecC----Ccceecc-----------CCCCCCceEEEEEEec
Confidence 666655444 67799999999999999999998843 3333322 3388999999999987
No 129
>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=76.00 E-value=4.1 Score=26.06 Aligned_cols=51 Identities=16% Similarity=0.100 Sum_probs=29.8
Q ss_pred CCEEEEEEEEEecce----EEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEE
Q psy18072 16 EDVVMVTVISIAEMG----AYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73 (174)
Q Consensus 16 GdiV~G~V~~i~~~G----afV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi 73 (174)
-..+.|+|..+.+.| +++.+.+...+.+.|+... ... =.+++|+.|.+.+-
T Consensus 4 ~N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~-----~~~--L~L~~G~~V~~~ik 58 (64)
T PF03459_consen 4 RNQLPGTVESIENLGSEVEVTLDLGGGETLTARITPES-----AEE--LGLKPGDEVYASIK 58 (64)
T ss_dssp SEEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHH-----HHH--CT-STT-EEEEEE-
T ss_pred CcEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHH-----HHH--cCCCCCCEEEEEEe
Confidence 346899999999988 4445544101455554332 222 23889999999774
No 130
>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=75.90 E-value=7.5 Score=25.90 Aligned_cols=50 Identities=10% Similarity=0.099 Sum_probs=36.6
Q ss_pred EEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 20 MVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 20 ~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
+|+|.-.. ..|. ||..+. ++-+-++|+|.+..... ..++.|+.|...+..
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~-g~~dvfvH~s~~~~~g~----~~l~~G~~V~f~~~~ 54 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEG-VDGDIFAHYSTIQMDGY----RTLKAGQKVQFEVVQ 54 (68)
T ss_pred CeEEEEEeCCCCeEEEecCC-CCccEEEEHHHhhhcCC----CCCCCCCEEEEEEEE
Confidence 48888873 4566 776655 14789999999874322 468999999997765
No 131
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=75.87 E-value=3.9 Score=27.61 Aligned_cols=59 Identities=14% Similarity=-0.053 Sum_probs=40.8
Q ss_pred EEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC
Q psy18072 18 VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77 (174)
Q Consensus 18 iV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~ 77 (174)
...++|..+...-|.|.|.+.. --..+|.+.--+.-++.-++.+++|+.+.|.+.....
T Consensus 3 ~htA~VQh~~kdfAvvSL~~t~-~L~a~p~~sHLNdtfrf~seklkvG~~l~v~lk~~~~ 61 (69)
T cd05701 3 RHTAIVQHADKDFAIVSLATTG-DLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNC 61 (69)
T ss_pred ccchhhhhhhhceEEEEeeccc-cEEEEEchhhccccccccceeeeccceEEEEEecCcc
Confidence 4567777887777889998743 4455555543344455556889999999999986543
No 132
>KOG1832|consensus
Probab=74.88 E-value=1.9 Score=42.70 Aligned_cols=6 Identities=17% Similarity=0.362 Sum_probs=2.6
Q ss_pred HHHHHH
Q psy18072 134 MERAEA 139 (174)
Q Consensus 134 ~~~l~k 139 (174)
+||+.-
T Consensus 1397 IGR~r~ 1402 (1516)
T KOG1832|consen 1397 IGRRRP 1402 (1516)
T ss_pred hcccCC
Confidence 444443
No 133
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=74.72 E-value=1.1 Score=41.07 Aligned_cols=74 Identities=26% Similarity=0.276 Sum_probs=56.6
Q ss_pred cccchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhh------------hccccccCCCCEEEE
Q psy18072 3 LSCRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRI------------RSINKLIRVGKTEPV 70 (174)
Q Consensus 3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v------------~~~~~~l~vGd~V~v 70 (174)
|-|||...+.- ....+.+.|..|...|+-|+|.+ ++...|||.+-+...+- -+-...+++||.|.|
T Consensus 550 LY~r~L~~k~~-~~~~F~AEI~Di~R~G~RvrLle-NGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk~~D~i~V 627 (645)
T COG4776 550 LYARFLADKAG-TNTRFAAEIQDISRGGMRVRLLE-NGAIAFIPAPLIHANREELVCNQENGTVQIKGETVYKVGDVIDV 627 (645)
T ss_pred HHHHHhccccc-cCchhhhhhhhhccCceEEEecc-CCcceecchhhhccchhheEecCCCceEEEccEEEEeeccEEEE
Confidence 46898877665 78889999999999999999976 36888998876654321 112367899999999
Q ss_pred EEEEEeCC
Q psy18072 71 VVIRVDKE 78 (174)
Q Consensus 71 rVi~Vd~~ 78 (174)
++..|+..
T Consensus 628 ~l~eVr~e 635 (645)
T COG4776 628 TLAEVRME 635 (645)
T ss_pred EeHHHHHh
Confidence 99887653
No 134
>PRK14998 cold shock-like protein CspD; Provisional
Probab=74.17 E-value=13 Score=25.33 Aligned_cols=52 Identities=12% Similarity=0.050 Sum_probs=38.1
Q ss_pred EEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEe
Q psy18072 20 MVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76 (174)
Q Consensus 20 ~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd 76 (174)
.|+|.-.. ..|. ||.... ++-+-|+|+|.|..... ..+..|+.|...+..-.
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~-g~~dVFvH~s~l~~~g~----~~l~~G~~V~f~~~~~~ 56 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEG-GGEDIFAHYSTIQMDGY----RTLKAGQSVRFDVHQGP 56 (73)
T ss_pred CeEEEEEeCCCceEEEecCC-CCccEEEEeeeecccCC----CCCCCCCEEEEEEEECC
Confidence 48888874 3566 777655 24789999999874322 56889999999987643
No 135
>COG1278 CspC Cold shock proteins [Transcription]
Probab=73.42 E-value=7.6 Score=26.28 Aligned_cols=50 Identities=16% Similarity=0.214 Sum_probs=34.7
Q ss_pred EEEEEEEe-cceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 20 MVTVISIA-EMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 20 ~G~V~~i~-~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
.|+|.-.. ..|+ ||.-.+ ++-+-|+|+|.+....+ ..|..||.|...|..
T Consensus 3 ~GtVKwfn~~KGfGFI~p~~-G~~DvFVH~Sai~~~g~----~~L~eGQ~V~f~~~~ 54 (67)
T COG1278 3 TGTVKWFNATKGFGFITPED-GGKDVFVHISAIQRAGF----RTLREGQKVEFEVEQ 54 (67)
T ss_pred cceEEEeeCCCcceEcCCCC-CCcCEEEEeeeeccCCC----cccCCCCEEEEEEec
Confidence 46776663 3454 555444 23688999999975544 468899999988875
No 136
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=72.12 E-value=13 Score=24.80 Aligned_cols=56 Identities=18% Similarity=0.225 Sum_probs=33.4
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~ 77 (174)
|+..+=+|..+...|--+-... .+.|+.- ...|+..-...+-+|+.++|.|+.||.
T Consensus 1 G~~L~LvV~~~~edgsv~fs~g--~v~g~tv----~AtryH~~g~nl~pGqK~kaviLhvD~ 56 (65)
T cd05700 1 GDQLKLVVQDVTEDGSVMFSGG--QVSGLTV----LASRYHKEGVNVTPGCKLKAVILHVDF 56 (65)
T ss_pred CceEEEEEeeeccCCcEEEecC--CcCCcEE----EEEEEEecceecCCCceeEEEEEEEee
Confidence 4556666777655444333333 4556521 122222234678899999999999986
No 137
>COG1915 Uncharacterized conserved protein [Function unknown]
Probab=71.29 E-value=73 Score=28.14 Aligned_cols=103 Identities=17% Similarity=0.179 Sum_probs=54.1
Q ss_pred ceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC---------c--eeeecccccchHHHHHH
Q psy18072 29 MGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK---------V--MTTVTPEKADGLKALQE 97 (174)
Q Consensus 29 ~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~---------~--l~ls~~~k~~g~~~i~~ 97 (174)
.|-+|++.+. ...+.|-+..-...-.-.+-+.++.||.|.|-+..|+--. . +--+-...+.....+-.
T Consensus 109 ~geWi~Ve~~-~MD~aIvv~p~~~~A~ck~ire~k~Gd~VvVg~~Girvippe~pre~~~~F~FM~~~vSsErp~e~~i~ 187 (415)
T COG1915 109 NGEWIEVEGQ-RMDCAIVVTPEPRRARCKPIRELKKGDLVVVGVEGIRVIPPERPREKTGEFEFMGSGVSSERPVETLIE 187 (415)
T ss_pred CCEEEEEcce-eeeeEEEEecCCCcceeeEhhHhccCCEEEEccceeEecCCCCCCcCCceEEeecCCCCcCCcHHHHHH
Confidence 3555555543 3566666553332211123346889999988666554322 0 10111111223333333
Q ss_pred HHHHHHHHHhhhCCeeEEeeCceeEeccCHHHHHH
Q psy18072 98 AIDTIKAKIEQLGGVFQVQMAPKVVTASDEAELAR 132 (174)
Q Consensus 98 ~~~~i~~~l~~~~g~l~~k~~P~~i~~~~~~~~k~ 132 (174)
.+.|=...++.+||++.+..+|.+|---...++..
T Consensus 188 ~IA~E~~ei~~kgGkIvvv~GPaviHtg~~~~la~ 222 (415)
T COG1915 188 QIAWEIREIRDKGGKIVVVAGPAVIHTGAAQHLAH 222 (415)
T ss_pred HHHHHHHHHHhcCCcEEEEecCeEEecCcHHHHHH
Confidence 33333446677899999999999987444444433
No 138
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=70.18 E-value=2.7 Score=40.66 Aligned_cols=15 Identities=13% Similarity=0.136 Sum_probs=9.9
Q ss_pred ccCHHHHHHHHHHHH
Q psy18072 124 ASDEAELARQMERAE 138 (174)
Q Consensus 124 ~~~~~~~k~~~~~l~ 138 (174)
.+...++..++.-|.
T Consensus 619 ~~t~~~l~~ll~vl~ 633 (784)
T PF04931_consen 619 HLTESGLQLLLDVLD 633 (784)
T ss_pred hcCHHHHHHHHHHhc
Confidence 456667777766666
No 139
>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=68.59 E-value=18 Score=23.26 Aligned_cols=51 Identities=12% Similarity=0.053 Sum_probs=35.9
Q ss_pred EEEEEEEec-ceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072 20 MVTVISIAE-MGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV 75 (174)
Q Consensus 20 ~G~V~~i~~-~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V 75 (174)
.|+|+...+ .|. ||...+. +-+=++|.+.+...- ...+++|+.|...+..-
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~-g~diffh~~~~~~~~----~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDG-GEDVFVHISALEGDG----FRSLEEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCeEEEecCCC-CcCEEEEhhHhhccC----CCcCCCCCEEEEEEEEC
Confidence 588887744 344 5555442 478899999987432 25689999999988764
No 140
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=67.42 E-value=15 Score=25.80 Aligned_cols=51 Identities=20% Similarity=0.246 Sum_probs=31.1
Q ss_pred EEEEEEEEEe---cce-EEEEECCCCCeEEEEEceecchh-hhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIA---EMG-AYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~---~~G-afV~L~~~~~~~GlI~iSels~~-~v~~~~~~l~vGd~V~vr 71 (174)
.|.|.|+++. ..| +|+.|.+- .+.|+.--+... ..+.+...++.||.|.|.
T Consensus 2 ~v~GeVs~~~~~~~sGH~yFtlkD~---~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~ 57 (91)
T cd04482 2 RVTGKVVEEPRTIEGGHVFFKISDG---TGEIDCAAYEPTKEFRDVVRLLIPGDEVTVY 57 (91)
T ss_pred EEEEEEeCCeecCCCCCEEEEEECC---CcEEEEEEECcccccccccCCCCCCCEEEEE
Confidence 5889999884 346 89999651 233433222111 134555779999988764
No 141
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=67.20 E-value=30 Score=25.05 Aligned_cols=59 Identities=20% Similarity=0.195 Sum_probs=40.9
Q ss_pred CCCCCCEEEEEEEEEecceEE-EEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072 12 YPEVEDVVMVTVISIAEMGAY-VHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE 78 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~Gaf-V~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~ 78 (174)
.| ....+.|+|+.....+.| |.+.+ +..=+.|++-=. +. +-.++.||.|.|.....+..
T Consensus 17 ~p-~e~e~~g~V~~~lG~~~~~V~~~d--G~~~la~i~GK~----Rk-~IwI~~GD~VlVe~~~~~~~ 76 (100)
T PRK04012 17 MP-EEGEVFGVVEQMLGANRVRVRCMD--GVERMGRIPGKM----KK-RMWIREGDVVIVAPWDFQDE 76 (100)
T ss_pred CC-CCCEEEEEEEEEcCCCEEEEEeCC--CCEEEEEEchhh----cc-cEEecCCCEEEEEecccCCC
Confidence 44 455689999999777665 46666 667677765322 22 24689999999998776643
No 142
>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=67.16 E-value=17 Score=22.52 Aligned_cols=48 Identities=15% Similarity=0.105 Sum_probs=28.2
Q ss_pred EEEEEEe-cceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072 21 VTVISIA-EMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV 75 (174)
Q Consensus 21 G~V~~i~-~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V 75 (174)
|+|.... .+| ||..... ..+-+||.+.+.. ....+..||.|.+++..-
T Consensus 2 G~i~~~~~g~g-fv~~~~~-~~~i~v~~~~~~~-----~~~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 2 GVVKWFNKGFG-FIRPDDG-GKDVFVHPSQIQG-----GLKSLREGDEVEFKVVSP 50 (64)
T ss_pred eEEEEEcCCee-EEecCCC-CccEEEEhHHhhc-----CCCcCCCCCEEEEEEEEc
Confidence 5555443 344 4444432 2467887765421 114577899999999763
No 143
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=66.99 E-value=36 Score=23.90 Aligned_cols=52 Identities=17% Similarity=0.255 Sum_probs=33.3
Q ss_pred EEEEEEEEEecce---EEEEECCC-CCeEEEEEcee--cchhhhhccccccCCCCEEEE
Q psy18072 18 VVMVTVISIAEMG---AYVHLLEY-NNIEGMILLSE--LSRRRIRSINKLIRVGKTEPV 70 (174)
Q Consensus 18 iV~G~V~~i~~~G---afV~L~~~-~~~~GlI~iSe--ls~~~v~~~~~~l~vGd~V~v 70 (174)
.+.|.|.++...| +|+.|... +.+..+++... .....+.. -..++.|+.|.|
T Consensus 3 ~i~Gwv~~~R~~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~-~~~l~~es~V~V 60 (102)
T cd04320 3 LIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKW-AGSLSKESIVDV 60 (102)
T ss_pred EEEEEEEEeecCCCceEEEEEecCCceEEEEEeCCcccCCHHHHHH-HhcCCCccEEEE
Confidence 4789999998777 89999763 24666666443 22222221 135788988766
No 144
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=66.84 E-value=21 Score=32.77 Aligned_cols=52 Identities=17% Similarity=0.264 Sum_probs=35.9
Q ss_pred EEEEEEEEEecce--EEEEECCC-CCeEEEEEceecchhhhhccccccCCCCEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEY-NNIEGMILLSELSRRRIRSINKLIRVGKTEPV 70 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~-~~~~GlI~iSels~~~v~~~~~~l~vGd~V~v 70 (174)
.|.|.|.++...| +|+.|.+. +.++.++....+....+..+.. +++|+.|.|
T Consensus 58 ~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~-l~~g~~v~v 112 (491)
T PRK00484 58 SVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKK-LDLGDIIGV 112 (491)
T ss_pred EEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhc-CCCCCEEEE
Confidence 5889999998776 79999762 2467777665554333333333 889998866
No 145
>KOG4078|consensus
Probab=66.59 E-value=20 Score=27.93 Aligned_cols=53 Identities=13% Similarity=0.186 Sum_probs=43.9
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV 75 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V 75 (174)
-.|.+|.|+|..|...-+|+.+.. ++..++..-.+.. ..|..|-.|..|++..
T Consensus 81 a~gklV~GkIfhiV~~DlYIDFG~--KFhcVC~rP~~n~-------e~Y~~GaRVrlRl~Dl 133 (173)
T KOG4078|consen 81 AKGKLVIGKIFHIVEEDLYIDFGG--KFHCVCKRPALNG-------EAYQKGARVRLRLIDL 133 (173)
T ss_pred cCCcEEEeeeeeeeccceEEecCC--eEEEEEcCcCcCH-------HHhhcCceEEEEEcCh
Confidence 368999999999998899999987 7888888776653 5677899999988853
No 146
>KOG4134|consensus
Probab=66.52 E-value=4 Score=34.04 Aligned_cols=65 Identities=18% Similarity=0.303 Sum_probs=47.5
Q ss_pred cchhhccCCCCCCEEEEEEEEEecc--eEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 5 CRFYAEKYPEVEDVVMVTVISIAEM--GAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 5 ~r~~~~~~p~~GdiV~G~V~~i~~~--GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
+.||.- -|++|++..|.|-.+... |+.|. . -+.+-||..+++.+| ..+..+++..++|.+.|..+
T Consensus 98 adfyVf-~Pk~Gd~LeG~Vn~vS~sHIglLIh--g--~FNASIpk~nip~dw-----~fI~md~eee~~v~ntD~gn 164 (253)
T KOG4134|consen 98 ADFYVF-RPKAGDILEGVVNHVSRSHIGLLIH--G--VFNASIPKTNIPADW-----EFIAMDQEEEIRVKNTDIGN 164 (253)
T ss_pred eeEEEE-CCCCCCeeeeeeeecchhhhceeeh--h--hhhccCCCCCCccce-----eeecCCchhhhceeeccccc
Confidence 345543 357999999999988654 55542 2 456778877776555 37889999999999998765
No 147
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=64.79 E-value=37 Score=23.43 Aligned_cols=56 Identities=25% Similarity=0.112 Sum_probs=37.5
Q ss_pred CCEEEEEEEEEecce-EEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC
Q psy18072 16 EDVVMVTVISIAEMG-AYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77 (174)
Q Consensus 16 GdiV~G~V~~i~~~G-afV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~ 77 (174)
.-.+.|+|..+-..+ +.|.+.+ +..=+-|++-=-+. .+-.+.+||.|.|.....+.
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~ed--g~~~~ahI~GKmr~----~~i~I~~GD~V~Ve~~~~d~ 62 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELEN--GHERLAHISGKMRK----NRIRILPGDVVLVELSPYDL 62 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecC--CcEEEEEccCcchh----eeEEeCCCCEEEEEeccccc
Confidence 456899999996654 4677777 55666665532111 12358899999999887664
No 148
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=64.22 E-value=43 Score=25.53 Aligned_cols=59 Identities=19% Similarity=0.147 Sum_probs=39.8
Q ss_pred CCCCCCEEEEEEEEEecce---------EEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 12 YPEVEDVVMVTVISIAEMG---------AYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~G---------afV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
++..|.+.+=+|..+...| |.|+|.+ +-..+.|+... -.+.+++|..|++++......+
T Consensus 60 ls~~G~V~t~Tv~~~~~~~~~~~~P~viaiV~l~~--~~~i~~~i~~~-------~p~~v~iGm~V~~v~~~~~~~~ 127 (140)
T COG1545 60 LSGEGKVETYTVVYVKPPGFSLEEPYVIAIVELEE--GGRILGQLVDV-------DPDDVEIGMKVEAVFRKREEDG 127 (140)
T ss_pred eCCCeEEEEEEEEeeCCCCcccCCCEEEEEEEeCC--CCceEEEEEec-------CcccccCCCEEEEEEEEccccC
Confidence 4557888888888876654 5566655 33555555541 1247899999999999766544
No 149
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=63.43 E-value=28 Score=32.09 Aligned_cols=54 Identities=15% Similarity=0.212 Sum_probs=36.6
Q ss_pred EEEEEEEEEecce--EEEEECCC-CCeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEY-NNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~-~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
.|.|.|.++...| +|+.|... +.++.++..+.+...........+++|+.|.|.
T Consensus 57 ~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~ 113 (496)
T TIGR00499 57 SIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVT 113 (496)
T ss_pred EEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEE
Confidence 4789999998765 79999763 247777776665443332223357899988663
No 150
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=61.74 E-value=52 Score=23.20 Aligned_cols=52 Identities=17% Similarity=0.204 Sum_probs=31.3
Q ss_pred EEEEEEEEEecce--EEEEECCCC-CeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEYN-NIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~~-~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
.+.|.|.++...| +|+.|.... .+..++..+ +....+..+ ..++.|+.|.|.
T Consensus 3 ~v~Gwv~~~R~~gk~~Fi~lrD~~g~iQ~v~~~~-~~~~~~~~~-~~l~~~s~v~V~ 57 (103)
T cd04319 3 TLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKD-LNEEAYREA-KKVGIESSVIVE 57 (103)
T ss_pred EEEEEEEeEEcCCCeEEEEEecCCeeEEEEEeCC-CCHHHHHHH-hCCCCCCEEEEE
Confidence 4789999997654 899997621 244444433 222222222 357889988763
No 151
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=61.05 E-value=86 Score=28.26 Aligned_cols=118 Identities=19% Similarity=0.202 Sum_probs=71.7
Q ss_pred CCEEEEEEEEEe--cce-EEEEECCCC-CeEEEEEceecchhhhhccccccCCCCEEEEEE-EEEeCC-Ccee--eeccc
Q psy18072 16 EDVVMVTVISIA--EMG-AYVHLLEYN-NIEGMILLSELSRRRIRSINKLIRVGKTEPVVV-IRVDKE-KVMT--TVTPE 87 (174)
Q Consensus 16 GdiV~G~V~~i~--~~G-afV~L~~~~-~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrV-i~Vd~~-~~l~--ls~~~ 87 (174)
.=+|.|.|++++ ..| +|..|-+-. .+.+.+..+.. ..+.-.++.|+.|.|+. +++.+. +.++ .....
T Consensus 19 ~v~V~GEisn~~~~~sGH~YFtLkD~~a~i~~vmf~~~~-----~~l~f~~~~G~~V~v~g~v~~y~~~G~~ql~v~~i~ 93 (432)
T TIGR00237 19 QVWIQGEISNFTQPVSGHWYFTLKDENAQVRCVMFRGNN-----NRLKFRPQNGQQVLVRGGISVYEPRGDYQIICFEMQ 93 (432)
T ss_pred cEEEEEEecCCeeCCCceEEEEEEcCCcEEEEEEEcChh-----hCCCCCCCCCCEEEEEEEEEEECCCCcEEEEEEEec
Confidence 668999999995 456 799997522 35665555432 23335578999997755 234333 3233 33333
Q ss_pred ccchHHHHHHHHHHHHHHHhhhCCeeEE---e---eCce---eEeccCHHHHHHHHHHHHHh
Q psy18072 88 KADGLKALQEAIDTIKAKIEQLGGVFQV---Q---MAPK---VVTASDEAELARQMERAEAE 140 (174)
Q Consensus 88 k~~g~~~i~~~~~~i~~~l~~~~g~l~~---k---~~P~---~i~~~~~~~~k~~~~~l~k~ 140 (174)
+ .|...+....+.+.+.|.+.| -|.- + .-|+ +||..+.+++...+-.+.+.
T Consensus 94 ~-~G~G~l~~~~~~lk~~L~~eG-lfd~~~k~~lP~~p~~i~vits~~~aa~~D~~~~~~~r 153 (432)
T TIGR00237 94 P-AGEGLLQLAYEQLKEKLAAEG-LFDQEYKKPLPHFPKRVGVITSQTGAALADILHILKRR 153 (432)
T ss_pred c-CChHHHHHHHHHHHHHHHHCC-CCCchhcCCCCCCCCEEEEEeCCccHHHHHHHHHHHhh
Confidence 3 388899999999999998654 3322 1 2344 34444556666555555544
No 152
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=60.88 E-value=47 Score=22.87 Aligned_cols=49 Identities=16% Similarity=0.210 Sum_probs=33.9
Q ss_pred CCCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCC
Q psy18072 14 EVEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKE 78 (174)
Q Consensus 14 ~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~ 78 (174)
+.|+++...|..+.+.|==+..-+ ++-=|+| -..+|+.|+++|.++.++
T Consensus 14 eeGe~y~V~I~d~g~~GDGiarve--GfvVFVp--------------~a~~Gd~V~vkI~~v~~~ 62 (73)
T COG3269 14 EEGETYEVEIEDVGDQGDGIARVE--GFVVFVP--------------GAEVGDEVKVKITKVKPN 62 (73)
T ss_pred ccCCEEEEEEEEeccCCCceEEEE--EEEEEeC--------------CCCCCCeeeEEEEEeecc
Confidence 489999999999976654333211 2333333 356899999999998764
No 153
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=59.03 E-value=44 Score=21.24 Aligned_cols=50 Identities=18% Similarity=0.179 Sum_probs=30.9
Q ss_pred EEEEEEEEE-ec--ceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISI-AE--MGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i-~~--~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
.|.|.|.++ .. .-+|+.|.+ + .|.|...-+. .......+.+++|+.|.++
T Consensus 2 ~v~G~V~~~~~~~~~~~~~~l~D--~-tg~i~~~~~~-~~~~~~~~~l~~g~~v~v~ 54 (75)
T PF01336_consen 2 TVEGRVTSIRRSGGKIVFFTLED--G-TGSIQVVFFN-EEYERFREKLKEGDIVRVR 54 (75)
T ss_dssp EEEEEEEEEEEEETTEEEEEEEE--T-TEEEEEEEET-HHHHHHHHTS-TTSEEEEE
T ss_pred EEEEEEEEEEcCCCCEEEEEEEE--C-CccEEEEEcc-HHhhHHhhcCCCCeEEEEE
Confidence 378899888 33 346778876 2 2555544433 2333445789999999775
No 154
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=58.94 E-value=36 Score=28.00 Aligned_cols=46 Identities=9% Similarity=0.069 Sum_probs=32.1
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
-+.+.|+|..+.+.-++|+...|+.- |.+- .+....+++||.|+|.
T Consensus 39 ~~tiEGrVvEV~~~~i~iesk~yn~~---v~i~-------~d~~~nvKVGD~VKaT 84 (213)
T PRK06763 39 FSTIEGRVVEVDNGVIVIKSKQYEEP---VSVY-------IDSLSNVKVGDEVKAT 84 (213)
T ss_pred cceeeeEEEEEeCCEEEEEeccCCCc---eEEE-------ecCCCCcccCcEEEEc
Confidence 45799999999998889998887632 1111 1112456999999884
No 155
>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=58.46 E-value=48 Score=22.02 Aligned_cols=51 Identities=22% Similarity=0.083 Sum_probs=35.3
Q ss_pred CEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC
Q psy18072 17 DVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77 (174)
Q Consensus 17 diV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~ 77 (174)
.-+.|+|.+|.+...-|.|.. +- -+-...++. -+.+++|..|.+-.-.++.
T Consensus 3 ~~veG~I~~id~~~~titLdD--Gk-sy~lp~ef~-------~~~L~~G~kV~V~yd~~~g 53 (61)
T PF07076_consen 3 ADVEGTIKSIDPETMTITLDD--GK-SYKLPEEFD-------FDGLKPGMKVVVFYDEVDG 53 (61)
T ss_pred ccceEEEEEEcCCceEEEecC--CC-EEECCCccc-------ccccCCCCEEEEEEEccCC
Confidence 358999999999999999987 32 222223332 1579999888776665554
No 156
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=58.44 E-value=35 Score=30.73 Aligned_cols=52 Identities=19% Similarity=0.191 Sum_probs=34.8
Q ss_pred EEEEEEEEEecce--EEEEECCC-CCeEEEEEceecchhhhhccccccCCCCEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEY-NNIEGMILLSELSRRRIRSINKLIRVGKTEPV 70 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~-~~~~GlI~iSels~~~v~~~~~~l~vGd~V~v 70 (174)
.+.|.|.++...| +|+.|..- +.++.++..+.++...+..+ ..+++|+.|.|
T Consensus 16 ~i~G~v~~~R~~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~-~~l~~~s~v~v 70 (428)
T TIGR00458 16 TFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWA-KKLNLESVVAV 70 (428)
T ss_pred EEEEEEEEEecCCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHH-hCCCCCcEEEE
Confidence 3789999998877 89999762 24677776655443333323 45778888765
No 157
>PF12857 TOBE_3: TOBE-like domain; InterPro: IPR024765 The TOBE (transport-associated OB) domain [] always occurs as a dimer and it is found in ABC transporters immediately after the ATPase domain. This entry represents a TOBE-like domain, found in the C terminus of ATPase subunit CysA. CysA is part of the CysATWP ABC transporter complex, involved in sulphate/thiosulphate import [, ].
Probab=58.11 E-value=31 Score=22.02 Aligned_cols=53 Identities=23% Similarity=0.167 Sum_probs=32.8
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
..-+.|+|..|...|..|.|.=.....|=.---+++... .. -.+..||.|.++
T Consensus 4 ~~~l~a~V~~v~~~G~~vRlEl~~~~~~~~iEvel~~~~-~~--l~l~~G~~V~l~ 56 (58)
T PF12857_consen 4 EGGLPARVRRVRPVGPEVRLELKRLDDGEPIEVELPRER-RQ--LGLQPGDRVYLR 56 (58)
T ss_pred CCcEeEEEEEEEecCCeEEEEEEECCCCCEEEEEeCHhH-Hh--cCCCCCCEEEEE
Confidence 456789999999999988775210111222223556554 33 346679999876
No 158
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=57.53 E-value=39 Score=22.72 Aligned_cols=50 Identities=16% Similarity=0.190 Sum_probs=28.8
Q ss_pred EEEEEEEEE-ecce-EEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISI-AEMG-AYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i-~~~G-afV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
.|.|.|++. ...| +|+.|.+- .+-|+.--+.... ..+...++.|+.|.+.
T Consensus 2 ~v~GeVs~~~~~~GHvyfsLkD~---~a~i~cv~f~~~~-~~~~~~l~~Gd~V~v~ 53 (73)
T cd04487 2 HIEGEVVQIKQTSGPTIFTLRDE---TGTVWAAAFEEAG-VRAYPEVEVGDIVRVT 53 (73)
T ss_pred EEEEEEeccccCCCCEEEEEEcC---CEEEEEEEEchhc-cCCcCCCCCCCEEEEE
Confidence 478888876 3445 89999651 2333322111111 2244678999988663
No 159
>PRK08572 rps17p 30S ribosomal protein S17P; Reviewed
Probab=57.25 E-value=29 Score=25.66 Aligned_cols=64 Identities=16% Similarity=0.017 Sum_probs=39.3
Q ss_pred ccchhhccCCCCCCEEEEEEEEE-ecceEEEEECCC---CCeEEEEEceecchhhhhccc-cccCCCCEEEE
Q psy18072 4 SCRFYAEKYPEVEDVVMVTVISI-AEMGAYVHLLEY---NNIEGMILLSELSRRRIRSIN-KLIRVGKTEPV 70 (174)
Q Consensus 4 ~~r~~~~~~p~~GdiV~G~V~~i-~~~GafV~L~~~---~~~~GlI~iSels~~~v~~~~-~~l~vGd~V~v 70 (174)
+|+|+-.-.+ .|.++.|+|++- .+.-+.|++... ..|.=++..+.-. .+.+.. ...++||.|..
T Consensus 18 ~cP~~g~l~i-rgk~l~G~VvS~Km~KTvvV~v~r~~~hpkY~K~i~r~kky--~aHDe~cn~~kvGD~V~I 86 (108)
T PRK08572 18 NCPFHGTLPV-RGQVLEGTVVSDKMHKTVVVEREYLHYVPKYERYEKRRSRI--HAHNPPCIDAKVGDKVKI 86 (108)
T ss_pred CCCCcceeee-eeEEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeE--EEECCCCCCCCCCCEEEE
Confidence 5999887766 799999999987 556777777541 1233333222100 112222 35899999865
No 160
>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=56.83 E-value=45 Score=21.26 Aligned_cols=44 Identities=14% Similarity=-0.073 Sum_probs=25.5
Q ss_pred EEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 21 VTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 21 G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
|++....+.-.||...+ ...+=|||..++. .--.||.|.|+++.
T Consensus 1 G~~~~~~~GfGFv~~~~-~~~DifIp~~~l~---------~A~~gD~V~v~i~~ 44 (58)
T PF08206_consen 1 GTLKIHPKGFGFVIPDD-GGEDIFIPPRNLN---------GAMDGDKVLVRITP 44 (58)
T ss_dssp EEEEE-SSS-EEEEECT--TEEEEE-HHHHT---------TS-TT-EEEEEEEE
T ss_pred CEEEEEcCCCEEEEECC-CCCCEEECHHHHC---------CCCCCCEEEEEEec
Confidence 45544333234666665 2577788877765 34479999999998
No 161
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=56.52 E-value=38 Score=31.30 Aligned_cols=54 Identities=17% Similarity=0.141 Sum_probs=35.3
Q ss_pred EEEEEEEEEecce--EEEEECCC-CCeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEY-NNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~-~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
.|.|.|.++...| +|+.|.+. +.++.++..+.+....+...-..+.+|+.|.|.
T Consensus 69 ~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~ 125 (505)
T PRK12445 69 SVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGAR 125 (505)
T ss_pred EEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEE
Confidence 5799999998775 79999762 246777765555432222112458899988663
No 162
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=54.23 E-value=63 Score=21.58 Aligned_cols=50 Identities=16% Similarity=0.106 Sum_probs=31.9
Q ss_pred EEEEEEEEEecc--eEEEEECC-CC--CeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIAEM--GAYVHLLE-YN--NIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~~~--GafV~L~~-~~--~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
.+.|.|.++... .+|+.|.+ .+ .++.++..+....... ..+++|+.|.|.
T Consensus 3 ~v~Gwv~~~R~~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~----~~l~~gs~V~v~ 57 (82)
T cd04318 3 TVNGWVRSVRDSKKISFIELNDGSCLKNLQVVVDKELTNFKEI----LKLSTGSSIRVE 57 (82)
T ss_pred EEEEeEEEEEcCCcEEEEEEECCCCccCEEEEEeCcccCHHHH----hcCCCceEEEEE
Confidence 478999999654 57999955 22 2677776543321111 457899888664
No 163
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=53.92 E-value=77 Score=22.48 Aligned_cols=52 Identities=13% Similarity=0.192 Sum_probs=31.3
Q ss_pred EEEEEEEEecce--EEEEECCCC-CeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 19 VMVTVISIAEMG--AYVHLLEYN-NIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 19 V~G~V~~i~~~G--afV~L~~~~-~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
+.|.|.+++..| +|+.|.... .+..++..++.....+..+ ..+++|+.|.|.
T Consensus 17 v~Gwv~~~R~~g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~-~~l~~es~V~V~ 71 (108)
T cd04316 17 VAGWVHEIRDLGGIKFVILRDREGIVQVTAPKKKVDKELFKTV-RKLSRESVISVT 71 (108)
T ss_pred EEEEEEeeeccCCeEEEEEecCCeeEEEEEeCCCCCHHHHHHH-hCCCCcCEEEEE
Confidence 679999997654 689887622 3555555333322222222 458889888663
No 164
>KOG0943|consensus
Probab=53.53 E-value=8.2 Score=39.83 Aligned_cols=6 Identities=17% Similarity=0.462 Sum_probs=2.3
Q ss_pred HHHHHH
Q psy18072 101 TIKAKI 106 (174)
Q Consensus 101 ~i~~~l 106 (174)
.|.+.+
T Consensus 1682 e~qesl 1687 (3015)
T KOG0943|consen 1682 EIQESL 1687 (3015)
T ss_pred hhhhcc
Confidence 333333
No 165
>KOG3130|consensus
Probab=52.65 E-value=8 Score=34.98 Aligned_cols=7 Identities=29% Similarity=0.434 Sum_probs=3.0
Q ss_pred eCceeEe
Q psy18072 117 MAPKVVT 123 (174)
Q Consensus 117 ~~P~~i~ 123 (174)
+.|.-++
T Consensus 204 skP~~v~ 210 (514)
T KOG3130|consen 204 SKPDTVI 210 (514)
T ss_pred CCchhhh
Confidence 4444444
No 166
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=51.65 E-value=41 Score=24.62 Aligned_cols=64 Identities=11% Similarity=-0.006 Sum_probs=39.2
Q ss_pred ccchhhccCCCCCCEEEEEEEEE-ecceEEEEECCC---CCeEEEEEceecchhhhhccc-cccCCCCEEEE
Q psy18072 4 SCRFYAEKYPEVEDVVMVTVISI-AEMGAYVHLLEY---NNIEGMILLSELSRRRIRSIN-KLIRVGKTEPV 70 (174)
Q Consensus 4 ~~r~~~~~~p~~GdiV~G~V~~i-~~~GafV~L~~~---~~~~GlI~iSels~~~v~~~~-~~l~vGd~V~v 70 (174)
+|+|+-.-.+ .|.+..|+|++- .+.-+.|++... ..|.=++..+.=. .+.+.. ...++||.|.+
T Consensus 16 ~cpf~g~l~i-rgk~l~G~VvS~Km~KTivV~V~r~~~hpkY~K~i~r~kky--~aHDe~cn~~kvGD~V~I 84 (102)
T TIGR03630 16 KCPFHGHLKV-RGQILEGVVVSDKMNKTVVVEREYLYYDRKYERYERRRSKI--HAHNPPCIDVKEGDIVII 84 (102)
T ss_pred CCCccceeee-eeEEEEEEEEecCCCceEEEEEEEEEecCCccEEEEEeeeE--EEECCCCCCCCCCCEEEE
Confidence 6998887766 799999999887 566788877641 1222333222100 011222 35789999765
No 167
>KOG1991|consensus
Probab=50.71 E-value=16 Score=36.41 Aligned_cols=20 Identities=10% Similarity=0.159 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHhcccccCC
Q psy18072 128 AELARQMERAEAENAEVAAD 147 (174)
Q Consensus 128 ~~~k~~~~~l~k~~~e~~gd 147 (174)
.++++|+..+-+.++|.+++
T Consensus 872 ~~Lp~ala~ra~~~ee~~~e 891 (1010)
T KOG1991|consen 872 LSLPEALAERAQVEEEDSEE 891 (1010)
T ss_pred HHHHHHHHHHHHhhcccccc
Confidence 57888888877777775444
No 168
>KOG3297|consensus
Probab=50.36 E-value=56 Score=26.59 Aligned_cols=61 Identities=18% Similarity=0.061 Sum_probs=42.4
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhh-------------h----hccccccCCCCEEEEEEEEEeC
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRR-------------I----RSINKLIRVGKTEPVVVIRVDK 77 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~-------------v----~~~~~~l~vGd~V~vrVi~Vd~ 77 (174)
+|+++.|+|.+.+..|+-|.|.-+ -+=+||.+-|...- - ....=++.+|..|+.||.+...
T Consensus 81 ~gEVi~gki~~cs~eG~rvtl~FF--dDI~IP~~~L~~p~~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~f 158 (202)
T KOG3297|consen 81 VGEVITGKIKECSEEGLRVTLGFF--DDIFIPKEMLPEPCVFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDESF 158 (202)
T ss_pred cceEEEEEeecCCccceEEEEEee--eceeechhhCCCCcccccccEEEEEEecccCCCCceeEecCCCeEEEEEeeecc
Confidence 799999999999999999988642 23344444443211 0 1122468899999999998754
No 169
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=50.05 E-value=62 Score=21.05 Aligned_cols=51 Identities=18% Similarity=0.150 Sum_probs=31.9
Q ss_pred EEEEEEEEEe--cce-EEEEECCCC-CeEEEEEceecchhhhhccccccCCCCEEEEEEE
Q psy18072 18 VVMVTVISIA--EMG-AYVHLLEYN-NIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73 (174)
Q Consensus 18 iV~G~V~~i~--~~G-afV~L~~~~-~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi 73 (174)
.+.|.|+++. ..| +|+.|.+.. .+++.+..+.+ ......++.|+.|.+...
T Consensus 3 ~v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~~~~-----~~~~~~l~~g~~v~v~g~ 57 (78)
T cd04489 3 WVEGEISNLKRPSSGHLYFTLKDEDASIRCVMWRSNA-----RRLGFPLEEGMEVLVRGK 57 (78)
T ss_pred EEEEEEecCEECCCcEEEEEEEeCCeEEEEEEEcchh-----hhCCCCCCCCCEEEEEEE
Confidence 4677787774 456 788887622 34555554322 334578999998866543
No 170
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=50.04 E-value=64 Score=22.11 Aligned_cols=52 Identities=13% Similarity=0.102 Sum_probs=35.2
Q ss_pred EEEEEEEEecceEE-EEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC
Q psy18072 19 VMVTVISIAEMGAY-VHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77 (174)
Q Consensus 19 V~G~V~~i~~~Gaf-V~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~ 77 (174)
+.|+|+.....+.| |.+.+ +..-+.|++-= ++. +-.+++||.|.|.....+.
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~--g~~~la~i~gK----~rk-~iwI~~GD~V~Ve~~~~d~ 54 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFD--GKKRLCRIRGK----MRK-RVWINEGDIVLVAPWDFQD 54 (77)
T ss_pred EEEEEEEEcCCCEEEEEECC--CCEEEEEEchh----hcc-cEEEcCCCEEEEEeccccC
Confidence 57899998776665 56666 66666665532 222 3568999999998776543
No 171
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=49.01 E-value=39 Score=28.76 Aligned_cols=49 Identities=12% Similarity=0.091 Sum_probs=36.7
Q ss_pred hhccCCCCCCE-----EEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccc
Q psy18072 8 YAEKYPEVEDV-----VMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSIN 59 (174)
Q Consensus 8 ~~~~~p~~Gdi-----V~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~ 59 (174)
+.++|. +||. +.|+|.+|.-+-..+...+ +..=.||.|.+....+.+.+
T Consensus 126 ~~rpf~-vGD~I~i~~~~G~V~~I~~r~T~i~t~d--~~~v~IPNs~~~~~~i~N~s 179 (286)
T PRK10334 126 MFRPFR-AGEYVDLGGVAGTVLSVQIFSTTMRTAD--GKIIVIPNGKIIAGNIINFS 179 (286)
T ss_pred hcCCCC-CCCEEEECCEEEEEEEEEeEEEEEEcCC--CCEEEEcchHhcCCeeEEcC
Confidence 456675 8998 4788988876666666655 78889999999877776654
No 172
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=48.24 E-value=60 Score=30.72 Aligned_cols=54 Identities=15% Similarity=0.190 Sum_probs=34.6
Q ss_pred EEEEEEEEEecce---EEEEE-CCCCCeEEEEEceecc--hhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIAEMG---AYVHL-LEYNNIEGMILLSELS--RRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~~~G---afV~L-~~~~~~~GlI~iSels--~~~v~~~~~~l~vGd~V~vr 71 (174)
.|.|.|.++...| +|+.| ...+.++.++....+. ...+......+.+|+.|.|.
T Consensus 136 ~v~Grv~~~R~~G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~ 195 (585)
T PTZ00417 136 NVTGRIMRVSASGQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIV 195 (585)
T ss_pred EEEEEEEeeecCCCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEE
Confidence 5889999999887 79999 4333567777654331 22222222457888888664
No 173
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=47.98 E-value=84 Score=21.15 Aligned_cols=51 Identities=10% Similarity=0.045 Sum_probs=30.2
Q ss_pred EEEEEEEEEecce--EEEEECCCC-CeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEYN-NIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~~-~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
.+.|.|.++...| +|+.|.+.. .+..++..+.... +..+ ..+++|+.|.|+
T Consensus 3 ~v~Gwv~~~R~~g~~~Fi~LrD~~~~iQ~v~~~~~~~~--~~~~-~~l~~es~V~V~ 56 (84)
T cd04323 3 KVFGWVHRLRSQKKLMFLVLRDGTGFLQCVLSKKLVTE--FYDA-KSLTQESSVEVT 56 (84)
T ss_pred EEEEEEEEEecCCCcEEEEEEcCCeEEEEEEcCCcchh--HHHH-hcCCCcCEEEEE
Confidence 4789999997654 899997621 2344443332211 2222 358889988763
No 174
>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins. They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.
Probab=47.59 E-value=6.2 Score=30.61 Aligned_cols=7 Identities=14% Similarity=0.363 Sum_probs=3.9
Q ss_pred eCceeEe
Q psy18072 117 MAPKVVT 123 (174)
Q Consensus 117 ~~P~~i~ 123 (174)
++|--|+
T Consensus 96 sGPVhis 102 (149)
T PF03066_consen 96 SGPVHIS 102 (149)
T ss_dssp SS-EEEE
T ss_pred CCCEEee
Confidence 6776666
No 175
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=47.57 E-value=69 Score=23.62 Aligned_cols=51 Identities=12% Similarity=0.083 Sum_probs=31.0
Q ss_pred EEEEEEEEEecce--EEEEECCC-CCeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEY-NNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~-~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
.+.|.|.++...| +|+.|... +.+..++..+... . +..+ ..+++|+.|.|.
T Consensus 18 ~i~Gwv~~~R~~gk~~Fi~LrD~~g~~Q~v~~~~~~~-~-~~~~-~~l~~gs~V~V~ 71 (135)
T cd04317 18 TLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEEAP-E-FELA-EKLRNESVIQVT 71 (135)
T ss_pred EEEEeEehhcccCCEEEEEEecCCeeEEEEEeCCchh-H-HHHH-hCCCCccEEEEE
Confidence 3789999997664 89999762 2355555433221 1 1111 358899988764
No 176
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=47.51 E-value=94 Score=21.58 Aligned_cols=54 Identities=17% Similarity=0.169 Sum_probs=36.5
Q ss_pred CCEEEEEEEEEecceEE-EEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEe
Q psy18072 16 EDVVMVTVISIAEMGAY-VHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76 (174)
Q Consensus 16 GdiV~G~V~~i~~~Gaf-V~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd 76 (174)
...+.|+|+.....+.| |.+.+ +..=+.|++-=.++ +=.++.||.|.|.....+
T Consensus 4 e~q~~g~V~~~lG~~~~~V~~~d--G~~~la~ipgK~Rk-----~iwI~~GD~VlVe~~~~~ 58 (83)
T smart00652 4 DGQEIAQVVKMLGNGRLEVMCAD--GKERLARIPGKMRK-----KVWIRRGDIVLVDPWDFQ 58 (83)
T ss_pred CCcEEEEEEEEcCCCEEEEEECC--CCEEEEEEchhhcc-----cEEEcCCCEEEEEecCCC
Confidence 45688999999776665 46666 66666665532222 346899999999776544
No 177
>PLN02502 lysyl-tRNA synthetase
Probab=47.21 E-value=68 Score=30.09 Aligned_cols=54 Identities=17% Similarity=0.212 Sum_probs=34.4
Q ss_pred EEEEEEEEEecce--EEEEECCC-CCeEEEEEceecchhh--hhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEY-NNIEGMILLSELSRRR--IRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~-~~~~GlI~iSels~~~--v~~~~~~l~vGd~V~vr 71 (174)
.|.|.|.++...| +|+.|... +.++.++....+.... +..+...+++|+.|.|.
T Consensus 112 ~v~GrV~~~R~~Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~ 170 (553)
T PLN02502 112 SVAGRIMAKRAFGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVT 170 (553)
T ss_pred EEEEEEEEEecCCCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEE
Confidence 4689999998776 69999762 2456666544443211 22333458899998663
No 178
>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=46.40 E-value=74 Score=20.09 Aligned_cols=50 Identities=14% Similarity=0.124 Sum_probs=30.7
Q ss_pred CCCEEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~ 77 (174)
+|+.+...|.+..+.|.++.-.+. +..=+++-. ..+ +|+.++|+|.++..
T Consensus 4 ~G~~~~VlVe~~~~~g~~~gr~~~-~~~V~v~~~-----------~~~-iG~~v~v~I~~~~~ 53 (61)
T PF01938_consen 4 VGKTLEVLVEELGDEGQGIGRTDN-GKVVFVPGG-----------LPL-IGEFVKVRITKAKK 53 (61)
T ss_dssp TTEEEEEEEEEE-TTSEEEEEET--TEEEEETT-------------T---TEEEEEEEEEE-S
T ss_pred CCcEEEEEEEEecCCCEEEEEeCC-CeEEEECCC-----------CCC-CCCEEEEEEEEeeC
Confidence 799999999998866766644331 233333322 112 79999999999875
No 179
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=46.14 E-value=48 Score=24.88 Aligned_cols=56 Identities=13% Similarity=0.088 Sum_probs=34.7
Q ss_pred EEEEEEEEecce--EEEEECCCCCeEEEEEceecchh-hhhccccccCCCCEEEE--EEEEEe
Q psy18072 19 VMVTVISIAEMG--AYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPV--VVIRVD 76 (174)
Q Consensus 19 V~G~V~~i~~~G--afV~L~~~~~~~GlI~iSels~~-~v~~~~~~l~vGd~V~v--rVi~Vd 76 (174)
+.|+|+.+.+.+ +-+...+ +++-|||+.-=+.. .-+-....++.||.|++ .++++|
T Consensus 42 ~~G~v~~i~~T~HA~~i~~~~--G~eiLiHiGidTv~l~g~gF~~~vk~Gd~V~~G~~l~~~D 102 (124)
T cd00210 42 VDGTIVQIFPTKHAIGIESDS--GVEILIHIGIDTVKLNGEGFTSHVEEGQRVKQGDKLLEFD 102 (124)
T ss_pred CCeEEEEEccCCCEEEEEeCC--CcEEEEEeeeeeeecCCCceEEEecCCCEEcCCCEEEEEc
Confidence 679999996644 3356555 89999998843221 11223355777777766 455554
No 180
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=45.56 E-value=54 Score=30.45 Aligned_cols=56 Identities=18% Similarity=0.236 Sum_probs=43.4
Q ss_pred CEEEEEEEEEecce--EEEEECCCC-CeEEEEEceecchhhhhccccccCCCCEEEEEE
Q psy18072 17 DVVMVTVISIAEMG--AYVHLLEYN-NIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72 (174)
Q Consensus 17 diV~G~V~~i~~~G--afV~L~~~~-~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrV 72 (174)
=.+-|+|..+..+| +|+.|...+ .++-+|....+....+....+.+.+||.|-|+-
T Consensus 64 v~vAGRi~~~R~~GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G 122 (502)
T COG1190 64 VSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEG 122 (502)
T ss_pred eEEecceeeecccCceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCCEEeeee
Confidence 34789999998887 788887632 578888887777766777778889999997754
No 181
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=44.55 E-value=77 Score=23.35 Aligned_cols=53 Identities=23% Similarity=0.169 Sum_probs=24.5
Q ss_pred CEEEEEEEEEec--ceEEEEECC--CC--CeEEEEEceecchhhhhccccccCCCCEEEEEEE
Q psy18072 17 DVVMVTVISIAE--MGAYVHLLE--YN--NIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73 (174)
Q Consensus 17 diV~G~V~~i~~--~GafV~L~~--~~--~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi 73 (174)
=.|+|+|..|.. .+-++-+.. .+ ++...+...+-.+.. ...++.||.|.++=.
T Consensus 70 i~vtG~V~~I~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~----~~~l~~G~~Vti~G~ 128 (144)
T PF12869_consen 70 IEVTGTVSSIDKGFGDNYVVLLGTENGFAGVQCYFSNDQEKRAS----VAKLKKGQKVTIKGI 128 (144)
T ss_dssp EEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGGGHHH----HHH--TTSEEEEEEE
T ss_pred EEEEEEEEEEEEcCCCcEEEEccCCCCceeEEEEEccchhhhhh----HhcCCCCCEEEEEEE
Confidence 358999999953 333444433 11 233333333311111 134999999977543
No 182
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=44.27 E-value=43 Score=19.81 Aligned_cols=35 Identities=20% Similarity=0.232 Sum_probs=26.3
Q ss_pred CCCEEEEEEEEEe-cceEEEEECCCCCeEEEEEceec
Q psy18072 15 VEDVVMVTVISIA-EMGAYVHLLEYNNIEGMILLSEL 50 (174)
Q Consensus 15 ~GdiV~G~V~~i~-~~GafV~L~~~~~~~GlI~iSel 50 (174)
-|..+.|+|.++. +..+.|.+..|+ ....++.++|
T Consensus 11 d~~wyra~V~~~~~~~~~~V~f~DyG-~~~~v~~~~l 46 (48)
T cd04508 11 DGKWYRAKITSILSDGKVEVFFVDYG-NTEVVPLSDL 46 (48)
T ss_pred CCeEEEEEEEEECCCCcEEEEEEcCC-CcEEEeHHHc
Confidence 4889999999997 556788887775 4556666554
No 183
>PRK09439 PTS system glucose-specific transporter subunit; Provisional
Probab=43.03 E-value=70 Score=25.34 Aligned_cols=57 Identities=16% Similarity=0.114 Sum_probs=34.4
Q ss_pred EEEEEEEEecce--EEEEECCCCCeEEEEEceecchh-hhhccccccCCCCEEEE--EEEEEeC
Q psy18072 19 VMVTVISIAEMG--AYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPV--VVIRVDK 77 (174)
Q Consensus 19 V~G~V~~i~~~G--afV~L~~~~~~~GlI~iSels~~-~v~~~~~~l~vGd~V~v--rVi~Vd~ 77 (174)
+.|+|+.+.+.+ +-+...+ +++=|||+.==+-. .-+-....++.||.|++ .++++|.
T Consensus 64 ~dG~V~~vf~T~HAigi~t~~--G~eiLIHiGiDTV~L~G~gF~~~Vk~Gd~Vk~G~~L~~~D~ 125 (169)
T PRK09439 64 VDGTIGKIFETNHAFSIESDS--GVELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDPIIEFDL 125 (169)
T ss_pred CCeEEEEEcCCCCEEEEEeCC--CcEEEEEEeecccccCCCceEEEecCCCEEeCCCEEEEEcH
Confidence 678998885443 3355556 89999998721111 01122356777888776 5566554
No 184
>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=41.99 E-value=40 Score=22.99 Aligned_cols=45 Identities=22% Similarity=0.245 Sum_probs=28.3
Q ss_pred EEEEEEEEec----ceEEEEECCC----CCeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 19 VMVTVISIAE----MGAYVHLLEY----NNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 19 V~G~V~~i~~----~GafV~L~~~----~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
|.|.|+.+.+ .|+||.=..- ..-+|+.--.- . ...+++||.|++.
T Consensus 2 v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~~-------~-~~~~~~Gd~V~vt 54 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYTG-------S-GADVAVGDLVRVT 54 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEecC-------C-CCCCCCCCEEEEE
Confidence 7899999965 6999886521 01345433211 0 2568899999774
No 185
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=41.95 E-value=77 Score=32.23 Aligned_cols=54 Identities=17% Similarity=0.327 Sum_probs=35.9
Q ss_pred EEEEEEEEEecce--EEEEECCC-CCeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEY-NNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~-~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
.|.|.|.++...| +|+.|.+. +.++.++..+.+....+......+.+|+.|.|+
T Consensus 655 ~v~Grv~~~R~~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~ 711 (1094)
T PRK02983 655 SVSGRVLRIRDYGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVT 711 (1094)
T ss_pred EEEEEEEEEeeCCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEE
Confidence 5789999998776 79999762 246777766555433222233457888888663
No 186
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.77 E-value=1.8e+02 Score=23.65 Aligned_cols=52 Identities=10% Similarity=0.153 Sum_probs=35.9
Q ss_pred EEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEE-EEEeCCC
Q psy18072 18 VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV-IRVDKEK 79 (174)
Q Consensus 18 iV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrV-i~Vd~~~ 79 (174)
.+.|+|..+.+..+.|...+. +|+=.+|.+.+. .++.|+.+.+-+ +.|+.+.
T Consensus 4 ~l~G~v~~~~~~~vvidv~GV-GY~v~vs~~~~~---------~l~~g~~v~l~t~~~vrED~ 56 (196)
T PRK13901 4 KIYGKIIEKKESSIVIMATPF-EFELLVSSFCLA---------ELRLLEDVEILTYLHTREDE 56 (196)
T ss_pred EEEEEEEEEeCCEEEEEeCCE-EEEEEecHHHHH---------hcCCCCcEEEEEEEEEecCC
Confidence 578999999888888887664 366666654432 346799888766 4454444
No 187
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=41.31 E-value=47 Score=26.88 Aligned_cols=38 Identities=21% Similarity=0.226 Sum_probs=28.0
Q ss_pred cchhhccCCCCCCEEEEEEEEEecceEEEEECCCCCeEEEEE
Q psy18072 5 CRFYAEKYPEVEDVVMVTVISIAEMGAYVHLLEYNNIEGMIL 46 (174)
Q Consensus 5 ~r~~~~~~p~~GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~ 46 (174)
.++....|. +||+|.++|.+.. ...++.+.. +--|.|.
T Consensus 112 ~~~~~d~f~-~GDivrA~Vis~~-~~~~Lst~~--~dlGVI~ 149 (188)
T COG1096 112 VEKLSDAFR-IGDIVRARVISTG-DPIQLSTKG--NDLGVIY 149 (188)
T ss_pred ccccccccc-cccEEEEEEEecC-CCeEEEecC--CcceEEE
Confidence 344556664 9999999999987 678888876 5556655
No 188
>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=41.22 E-value=96 Score=20.47 Aligned_cols=23 Identities=17% Similarity=0.118 Sum_probs=20.5
Q ss_pred CCCEEEEEEEEEecceEEEEECC
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLE 37 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~ 37 (174)
.+..+.|++..|...|+.+.+..
T Consensus 21 ~~~~~~~~~~diS~~G~~~~~~~ 43 (102)
T PF07238_consen 21 GGSSFQGTIVDISEGGCAFRSPK 43 (102)
T ss_dssp TTEEEEEEEEEETTSEEEEEECT
T ss_pred CCcEEEEEEEEECccceEEEECC
Confidence 67889999999999999999854
No 189
>KOG1832|consensus
Probab=41.10 E-value=15 Score=36.74 Aligned_cols=32 Identities=41% Similarity=0.535 Sum_probs=12.0
Q ss_pred HHHHhcccccCCCCccccccCCCCCCCCCccc
Q psy18072 136 RAEAENAEVAADDDEDEEDFDNERDGDEGEDE 167 (174)
Q Consensus 136 ~l~k~~~e~~gd~~~~~~~~~~~~~~~~~~~~ 167 (174)
|+..=+.--.-|||+++|++++++|-|||||+
T Consensus 1393 r~yEIGR~r~~~dd~DeeeD~e~Ed~dEddd~ 1424 (1516)
T KOG1832|consen 1393 RMYEIGRRRPTDDDSDEEEDDETEDEDEDDDE 1424 (1516)
T ss_pred hhhhhcccCCCccccCccccchhhcccccccc
Confidence 44444444333333333333333333333333
No 190
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=40.53 E-value=1.9e+02 Score=23.12 Aligned_cols=47 Identities=9% Similarity=-0.010 Sum_probs=34.0
Q ss_pred EEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 18 VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 18 iV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
.+.|+|..+.+..+.|...+. +|+=.+|.+.+. . ++.|+.+++-+.-
T Consensus 4 ~l~G~v~~~~~~~~ii~~~Gv-GY~v~v~~~~~~--------~-l~~g~~v~l~t~~ 50 (186)
T PRK14600 4 SLSGIVEEVRSDYIILNVGNV-GYIVYLSAKVLS--------T-CKIGDNIKLYIET 50 (186)
T ss_pred eEEEEEEEEcCCEEEEEECCE-EEEEEecHHHHH--------h-hCCCCeEEEEEEE
Confidence 578999999988888887654 366666654443 2 5789999887653
No 191
>KOG3241|consensus
Probab=40.43 E-value=19 Score=29.14 Aligned_cols=6 Identities=0% Similarity=-0.280 Sum_probs=2.5
Q ss_pred HHHHHH
Q psy18072 98 AIDTIK 103 (174)
Q Consensus 98 ~~~~i~ 103 (174)
+|.+|.
T Consensus 95 vCAKC~ 100 (227)
T KOG3241|consen 95 VCAKCC 100 (227)
T ss_pred HHHHHh
Confidence 344443
No 192
>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=39.21 E-value=33 Score=24.07 Aligned_cols=25 Identities=28% Similarity=0.356 Sum_probs=19.1
Q ss_pred CCCCCEEEEEEEEEec-ceEEEEECC
Q psy18072 13 PEVEDVVMVTVISIAE-MGAYVHLLE 37 (174)
Q Consensus 13 p~~GdiV~G~V~~i~~-~GafV~L~~ 37 (174)
.++||+|.|+|.++.+ .-.++.+..
T Consensus 61 f~~GDiV~AkVis~~~~~~~~Lst~~ 86 (92)
T cd05791 61 FRPGDIVRAKVISLGDASSYYLSTAE 86 (92)
T ss_pred cCCCCEEEEEEEEcCCCCCcEEEecC
Confidence 3699999999999864 456666654
No 193
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=38.97 E-value=75 Score=19.43 Aligned_cols=35 Identities=17% Similarity=0.196 Sum_probs=26.6
Q ss_pred CCCEEEEEEEEEec-ceEEEEECCCCCeEEEEEceec
Q psy18072 15 VEDVVMVTVISIAE-MGAYVHLLEYNNIEGMILLSEL 50 (174)
Q Consensus 15 ~GdiV~G~V~~i~~-~GafV~L~~~~~~~GlI~iSel 50 (174)
-|..+.|+|.++.+ ..++|.+.+|+ ....++.++|
T Consensus 15 d~~wyra~I~~~~~~~~~~V~f~D~G-~~~~v~~~~l 50 (57)
T smart00333 15 DGEWYRARIIKVDGEQLYEVFFIDYG-NEEVVPPSDL 50 (57)
T ss_pred CCCEEEEEEEEECCCCEEEEEEECCC-ccEEEeHHHe
Confidence 68899999999977 67888888775 4456665554
No 194
>TIGR00830 PTBA PTS system, glucose subfamily, IIA component. These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are demonstrably homologous. These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-c
Probab=38.85 E-value=76 Score=23.72 Aligned_cols=56 Identities=11% Similarity=0.017 Sum_probs=34.8
Q ss_pred EEEEEEEEecce--EEEEECCCCCeEEEEEceecchh-hhhccccccCCCCEEEE--EEEEEe
Q psy18072 19 VMVTVISIAEMG--AYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPV--VVIRVD 76 (174)
Q Consensus 19 V~G~V~~i~~~G--afV~L~~~~~~~GlI~iSels~~-~v~~~~~~l~vGd~V~v--rVi~Vd 76 (174)
+.|+|+.+.+.+ +-+...+ +.+-|||+.-=+-. .-+-....++.||.|++ .++++|
T Consensus 42 ~~G~v~~v~~T~HA~gi~~~~--G~evLiHiGidTV~L~G~gF~~~v~~Gd~V~~G~~l~~~D 102 (121)
T TIGR00830 42 VDGKIGKIFPTKHAFGIESDS--GVEILIHIGIDTVKLNGEGFTSHVEEGQRVKKGDPLLEFD 102 (121)
T ss_pred CCeEEEEEccCCCEEEEEeCC--CcEEEEEeeeceeecCCCceEEEecCCCEEcCCCEEEEEc
Confidence 678999986644 3355555 89999998732211 11122356778888776 555555
No 195
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=38.02 E-value=1.1e+02 Score=27.53 Aligned_cols=51 Identities=18% Similarity=0.178 Sum_probs=32.5
Q ss_pred EEEEEEEEecce--EEEEECCC-CCeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 19 VMVTVISIAEMG--AYVHLLEY-NNIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 19 V~G~V~~i~~~G--afV~L~~~-~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
+.|.|.++...| +|+.|... +.++.++..+.. ...+..+ ..+++|+.|.|.
T Consensus 21 i~GrV~~~R~~gk~~Fl~LrD~~g~iQ~v~~~~~~-~~~~~~~-~~L~~gs~V~v~ 74 (437)
T PRK05159 21 LAGWVHEIRDLGGIAFLILRDRSGIIQVVVKKKVD-EELFETI-KKLKRESVVSVT 74 (437)
T ss_pred EEEEeEeeecCCCeEEEEEEcCCcEEEEEEeCCcc-HHHHHHH-hCCCCCcEEEEE
Confidence 789999997766 89999762 236666655433 2222222 357788887664
No 196
>PF11213 DUF3006: Protein of unknown function (DUF3006); InterPro: IPR021377 This family of proteins has no known function.
Probab=35.61 E-value=1.3e+02 Score=19.94 Aligned_cols=41 Identities=20% Similarity=0.037 Sum_probs=29.7
Q ss_pred EEEEEEEecceEEEEECCCCCe-EEEEEceecchhhhhccccccCCCCEEEE
Q psy18072 20 MVTVISIAEMGAYVHLLEYNNI-EGMILLSELSRRRIRSINKLIRVGKTEPV 70 (174)
Q Consensus 20 ~G~V~~i~~~GafV~L~~~~~~-~GlI~iSels~~~v~~~~~~l~vGd~V~v 70 (174)
+++|-+|...-|.+.+.+ +- .-.||.+.|. .-.+.||.+.+
T Consensus 1 k~ivDRiE~~~AVl~~~~--~~~~~~vp~~~LP--------~~~keGDvl~i 42 (71)
T PF11213_consen 1 KAIVDRIEGDYAVLELED--GEKEIDVPRSRLP--------EGAKEGDVLEI 42 (71)
T ss_pred CeEEEEEeCCEEEEEECC--CeEEEEEEHHHCC--------CCCCcccEEEE
Confidence 367778876667777766 44 5677777776 67899998877
No 197
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.47 E-value=2.4e+02 Score=22.72 Aligned_cols=51 Identities=12% Similarity=-0.050 Sum_probs=34.4
Q ss_pred EEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC
Q psy18072 18 VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77 (174)
Q Consensus 18 iV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~ 77 (174)
.+.|+|..+.+..+.|+..+. +|+=+++.+.+. ..-++|+.+++.+.-+-.
T Consensus 4 ~i~G~i~~~~~~~viie~~Gv-GY~v~vs~~~~~--------~l~~~g~~v~l~t~~~vr 54 (195)
T PRK14604 4 SIRGIIQSIGNDHLIVETGGV-GLLIYAPRSVLA--------AIGAIGDEVFLYTHLIVR 54 (195)
T ss_pred eEEEEEEEEcCCEEEEEECCE-EEEEEeCHHHHH--------HhccCCCeEEEEEEEEEe
Confidence 578999999888888887653 366666644432 223679999886655433
No 198
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=35.05 E-value=84 Score=24.77 Aligned_cols=33 Identities=15% Similarity=0.081 Sum_probs=25.0
Q ss_pred ccchhhccCCCCCCEEEEEEEEE-ecceEEEEECC
Q psy18072 4 SCRFYAEKYPEVEDVVMVTVISI-AEMGAYVHLLE 37 (174)
Q Consensus 4 ~~r~~~~~~p~~GdiV~G~V~~i-~~~GafV~L~~ 37 (174)
+|+|+-.--. -|.++.|+|++- .+.-+.|+...
T Consensus 57 kCPf~G~~~i-Rgril~G~VvS~KM~KTIVV~ve~ 90 (158)
T PTZ00241 57 KCPFTGNVSI-RGRILRGVVISTKMKRTIIIRRDY 90 (158)
T ss_pred CCCccceeeE-cceEEEEEEEEccCCccEEEEEEE
Confidence 6998876555 899999999887 45567776643
No 199
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=34.96 E-value=68 Score=25.38 Aligned_cols=52 Identities=19% Similarity=0.347 Sum_probs=29.7
Q ss_pred cceEEEEECC-CCCeEEEEEcee----cchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 28 EMGAYVHLLE-YNNIEGMILLSE----LSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 28 ~~GafV~L~~-~~~~~GlI~iSe----ls~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
..|+|+.=.. |..+-|++.+.. ++-.........+++||.|.++|+++...+
T Consensus 23 G~Gty~~~~~i~as~~G~~~id~~~~~Isv~P~~~~~~~~~~GdiV~GkV~~i~~~g 79 (189)
T PRK09521 23 GEGTYEDNGEVYASVVGKVFIDDINRKISVIPFKKTPPLLKKGDIVYGRVVDVKEQR 79 (189)
T ss_pred CCCEEeeCCEEEEEeeEEEEEcCCCCEEEEecCcCCCCCCCCCCEEEEEEEEEcCCe
Confidence 3566663111 113456666532 111222222356789999999999998765
No 200
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=34.95 E-value=79 Score=26.49 Aligned_cols=55 Identities=11% Similarity=0.132 Sum_probs=32.3
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCe-EEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNI-EGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~-~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
-..+.|+|.+|...|..+.+.- .+ .|-.-...++..-... -.+++|+.|.|.+..
T Consensus 199 rN~l~g~V~~i~~~~~~~~V~l--~l~~g~~l~A~IT~~s~~~--L~L~~G~~V~a~iKa 254 (263)
T PRK10676 199 DNQLPGTISHIERGAEQSEVLM--ALPDGQTLCATVPNNEAAR--LSLQQGDAVTAYFNA 254 (263)
T ss_pred hheEEEEEEEEEeCCCcEEEEE--EeCCCCEEEEEecHHHHHh--cCCCCCCEEEEEEEc
Confidence 4679999999976665444321 11 1222233344433333 248999999998864
No 201
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=34.94 E-value=3.3e+02 Score=24.26 Aligned_cols=120 Identities=18% Similarity=0.202 Sum_probs=71.1
Q ss_pred CCCEEEEEEEEEec--ce-EEEEECCCC-CeEEEEEceecchhhhhccccccCCCCEEEEEE-EEEeC-CCceeeeccc-
Q psy18072 15 VEDVVMVTVISIAE--MG-AYVHLLEYN-NIEGMILLSELSRRRIRSINKLIRVGKTEPVVV-IRVDK-EKVMTTVTPE- 87 (174)
Q Consensus 15 ~GdiV~G~V~~i~~--~G-afV~L~~~~-~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrV-i~Vd~-~~~l~ls~~~- 87 (174)
..=+|.|.|++++. .| +|+.|-+-. .+.+.+..+... .+.-.++.|+.|.|.. +++.+ .+.+++....
T Consensus 24 ~~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~-----~~~~~~~~G~~v~v~g~~~~y~~~g~~ql~v~~i 98 (438)
T PRK00286 24 GQVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSAR-----RLKFKPEEGMKVLVRGKVSLYEPRGDYQLIVEEI 98 (438)
T ss_pred CcEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhh-----cCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEEe
Confidence 46679999999953 46 899997621 356666655432 3345688999997754 33333 3334333221
Q ss_pred ccchHHHHHHHHHHHHHHHhhhCCeeEE---ee---Cce---eEeccCHHHHHHHHHHHHHh
Q psy18072 88 KADGLKALQEAIDTIKAKIEQLGGVFQV---QM---APK---VVTASDEAELARQMERAEAE 140 (174)
Q Consensus 88 k~~g~~~i~~~~~~i~~~l~~~~g~l~~---k~---~P~---~i~~~~~~~~k~~~~~l~k~ 140 (174)
...|...+....+.+++.|.+.| -|.. +. -|+ +||..+.+++...+-.+.+.
T Consensus 99 ~~~g~G~l~~~~~~lk~~L~~eG-lfd~~~k~~lP~~p~~I~viTs~~gAa~~D~~~~~~~r 159 (438)
T PRK00286 99 EPAGIGALAAAFEQLKEKLAAEG-LFDPERKKPLPFFPKRIGVITSPTGAAIRDILTVLRRR 159 (438)
T ss_pred eeCCccHHHHHHHHHHHHHHHCC-CCChhhcCCCCCCCCEEEEEeCCccHHHHHHHHHHHhc
Confidence 12366788888888999998654 3322 22 233 34444556665555555444
No 202
>PF15243 ANAPC15: Anaphase-promoting complex subunit 15
Probab=34.94 E-value=43 Score=24.01 Aligned_cols=22 Identities=5% Similarity=0.077 Sum_probs=10.2
Q ss_pred HHHHH-HHHHHHHHhhhCCeeEE
Q psy18072 94 ALQEA-IDTIKAKIEQLGGVFQV 115 (174)
Q Consensus 94 ~i~~~-~~~i~~~l~~~~g~l~~ 115 (174)
++.+. ..||..+-++.....++
T Consensus 32 ~~Eq~~q~Wl~sI~ekd~nlvPI 54 (92)
T PF15243_consen 32 QQEQQHQAWLQSIAEKDNNLVPI 54 (92)
T ss_pred HHHHHHHHHHHHHHHhccCcCcc
Confidence 44444 34444444544454555
No 203
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=34.75 E-value=42 Score=31.83 Aligned_cols=15 Identities=13% Similarity=0.375 Sum_probs=9.9
Q ss_pred cccCCCCEEEEEEEE
Q psy18072 60 KLIRVGKTEPVVVIR 74 (174)
Q Consensus 60 ~~l~vGd~V~vrVi~ 74 (174)
..+.+...+++-|+.
T Consensus 68 ~~l~~~~~~~iyViD 82 (622)
T PF02724_consen 68 EFLELDEDVTIYVID 82 (622)
T ss_pred HHhCCCCceEEEEEe
Confidence 456666777777774
No 204
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=34.30 E-value=1.8e+02 Score=22.79 Aligned_cols=57 Identities=14% Similarity=0.228 Sum_probs=38.0
Q ss_pred CCCCCCEEEEEEEEEecceEE-EEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEe
Q psy18072 12 YPEVEDVVMVTVISIAEMGAY-VHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~Gaf-V~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd 76 (174)
+|+.|+ +.|+|+.....+.| |.+.+ +..=|.|++-=.+.+ -.+++||.|.|.+-..+
T Consensus 28 ~~eegq-~~g~V~~~LGn~~f~V~c~d--G~~rLa~I~GKmRK~-----IWI~~GD~VlVel~~yd 85 (155)
T PTZ00329 28 FKEEGQ-EYAQVLRMLGNGRLEAYCFD--GVKRLCHIRGKMRKR-----VWINIGDIILVSLRDFQ 85 (155)
T ss_pred cCCCCc-EEEEEEEEcCCCEEEEEECC--CCEEEEEeeccceee-----EEecCCCEEEEeccCCC
Confidence 454555 68999998776665 46666 677777776422222 46889999999764443
No 205
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=34.24 E-value=1.3e+02 Score=19.53 Aligned_cols=50 Identities=14% Similarity=0.024 Sum_probs=29.6
Q ss_pred CEEEEEEEEEecceE-EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEE
Q psy18072 17 DVVMVTVISIAEMGA-YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73 (174)
Q Consensus 17 diV~G~V~~i~~~Ga-fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi 73 (174)
..+.|+|+.....+. -|.+.+ +..=+.+++- ++-+. -.++.||.|.|.+-
T Consensus 3 ~e~~~~V~~~lG~~~~~V~~~d--g~~~l~~i~g---K~r~~--iwI~~GD~V~V~~~ 53 (65)
T PF01176_consen 3 GEVIGRVTEMLGNNLFEVECED--GEERLARIPG---KFRKR--IWIKRGDFVLVEPS 53 (65)
T ss_dssp TEEEEEEEEEESSSEEEEEETT--SEEEEEEE-H---HHHTC--C---TTEEEEEEES
T ss_pred cEEEEEEEEECCCCEEEEEeCC--CCEEEEEecc---ceeee--EecCCCCEEEEEec
Confidence 357899999866655 466766 6655555542 22222 35889999988763
No 206
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=34.17 E-value=1.7e+02 Score=26.19 Aligned_cols=58 Identities=16% Similarity=0.209 Sum_probs=32.7
Q ss_pred chhhccCCCCCCEEEEEEEEE-ecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072 6 RFYAEKYPEVEDVVMVTVISI-AEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV 75 (174)
Q Consensus 6 r~~~~~~p~~GdiV~G~V~~i-~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V 75 (174)
++.+.+|. .|++|+..|.-= .-.|=.+.... +.+-+++... .....+|+.|+|||++-
T Consensus 346 p~lp~PF~-rGevv~aevV~~Gr~kGEmlavAr-dRvIav~~~~----------~~~~~vG~~vkvrIvr~ 404 (414)
T COG2100 346 PRLPKPFK-RGEVVKAEVVLPGRLKGEMLAVAR-DRVIAVINSN----------EGALLVGDRVKVRIVRT 404 (414)
T ss_pred CCCCCccc-cCcEEEEEEEecceecceEEEEec-ccEEEEecCc----------hhhhccCceEEEEEEEc
Confidence 34566675 999999988742 11233333321 0111111111 12578999999999984
No 207
>PF00358 PTS_EIIA_1: phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1; InterPro: IPR001127 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. ; GO: 0005351 sugar:hydrogen symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane; PDB: 3OUR_D 1GPR_A 1F3G_A 2F3G_B 1F3Z_A 1O2F_A 1GLB_F 1GGR_A 1GLA_F 1GLE_F ....
Probab=34.16 E-value=68 Score=24.29 Aligned_cols=57 Identities=18% Similarity=0.121 Sum_probs=32.9
Q ss_pred EEEEEEEEecc--eEEEEECCCCCeEEEEEceecchh-hhhccccccCCCCEEEE--EEEEEeC
Q psy18072 19 VMVTVISIAEM--GAYVHLLEYNNIEGMILLSELSRR-RIRSINKLIRVGKTEPV--VVIRVDK 77 (174)
Q Consensus 19 V~G~V~~i~~~--GafV~L~~~~~~~GlI~iSels~~-~v~~~~~~l~vGd~V~v--rVi~Vd~ 77 (174)
+.|+|+.+.+. .+-++..+ +++-|||+--=+-. .-+-....++.||.|++ .++.+|.
T Consensus 46 ~~G~v~~i~~T~HAi~i~s~~--G~eiLiHiGidTv~L~G~gF~~~v~~G~~V~~G~~L~~~D~ 107 (132)
T PF00358_consen 46 VDGTVTMIFPTKHAIGIRSDN--GVEILIHIGIDTVKLNGEGFETLVKEGDKVKAGQPLIEFDL 107 (132)
T ss_dssp SSEEEEEE-TTSSEEEEEETT--SEEEEEE-SBSGGGGTTTTEEESS-TTSEE-TTEEEEEE-H
T ss_pred eeEEEEEEcCCCCEEEEEeCC--CCEEEEEEccchhhcCCcceEEEEeCCCEEECCCEEEEEcH
Confidence 46899999664 44445556 89999998743322 12233467788888876 4555543
No 208
>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins. They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.
Probab=34.16 E-value=13 Score=28.72 Aligned_cols=10 Identities=20% Similarity=0.311 Sum_probs=4.7
Q ss_pred EEEEEceecc
Q psy18072 42 EGMILLSELS 51 (174)
Q Consensus 42 ~GlI~iSels 51 (174)
.--|+++.++
T Consensus 29 ~h~L~L~~v~ 38 (149)
T PF03066_consen 29 EHQLSLRQVC 38 (149)
T ss_dssp CEEEEEEEEE
T ss_pred ccEEEEEEee
Confidence 3444555544
No 209
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=34.03 E-value=75 Score=19.39 Aligned_cols=23 Identities=13% Similarity=0.089 Sum_probs=18.3
Q ss_pred CCCEEEEEEEEEecceEEE-EECC
Q psy18072 15 VEDVVMVTVISIAEMGAYV-HLLE 37 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV-~L~~ 37 (174)
.+..+.|++.+|.+.|+.+ +..+
T Consensus 11 ~~~~~~G~~~gId~~G~L~v~~~~ 34 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDDGALLVRTED 34 (48)
T ss_dssp TSCEEEEEEEEEETTSEEEEEETT
T ss_pred CCeEEEEEEEEECCCCEEEEEECC
Confidence 4788999999999999855 4544
No 210
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=33.87 E-value=1.3e+02 Score=28.97 Aligned_cols=55 Identities=20% Similarity=0.291 Sum_probs=36.0
Q ss_pred CEEEEEEEEEecce--EEEEECCC-CCeEEEEEceec-chhhhhccccccCCCCEEEEE
Q psy18072 17 DVVMVTVISIAEMG--AYVHLLEY-NNIEGMILLSEL-SRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 17 diV~G~V~~i~~~G--afV~L~~~-~~~~GlI~iSel-s~~~v~~~~~~l~vGd~V~vr 71 (174)
=.|.|.|.++...| +|+.|-.. +.++.++...++ +...+......+.+|+.|.|.
T Consensus 110 V~vaGrV~~~R~~Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~ 168 (659)
T PTZ00385 110 VRVAGRVTSVRDIGKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGAD 168 (659)
T ss_pred EEEEEEEEeeeccCCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEE
Confidence 35789999997765 68888652 247777776554 332233333568889988653
No 211
>PLN02850 aspartate-tRNA ligase
Probab=33.39 E-value=1.5e+02 Score=27.63 Aligned_cols=54 Identities=19% Similarity=0.230 Sum_probs=34.4
Q ss_pred CCE--EEEEEEEEecce--EEEEECC-CCCeEEEEEcee--cchhhhhccccccCCCCEEEE
Q psy18072 16 EDV--VMVTVISIAEMG--AYVHLLE-YNNIEGMILLSE--LSRRRIRSINKLIRVGKTEPV 70 (174)
Q Consensus 16 Gdi--V~G~V~~i~~~G--afV~L~~-~~~~~GlI~iSe--ls~~~v~~~~~~l~vGd~V~v 70 (174)
|+. |.|.|.++...| +|+.|.. .+.+++++..+. ++...++.+ ..+++|+.|.|
T Consensus 81 g~~V~v~Grv~~~R~~gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~-~~l~~es~V~V 141 (530)
T PLN02850 81 GSEVLIRGRVHTIRGKGKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYA-KQLSRESVVDV 141 (530)
T ss_pred CCEEEEEEEEEEEccCCCeEEEEEEeCCcCEEEEEECCccccCHHHHHHH-hCCCCCCEEEE
Confidence 444 689999997665 7888865 235888887664 343322222 35777777755
No 212
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=33.01 E-value=1.7e+02 Score=26.54 Aligned_cols=52 Identities=17% Similarity=0.166 Sum_probs=30.8
Q ss_pred EEEEEEEEEecce--EEEEECCCC-CeEEEEEceecchhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEYN-NIEGMILLSELSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~~-~~~GlI~iSels~~~v~~~~~~l~vGd~V~vr 71 (174)
.|.|.|.++...| +||.|..-. .++..+..+. ....+..+ ..++.|+.|.|+
T Consensus 20 ~i~G~v~~~R~~g~~~Fi~lrD~~g~iq~~~~~~~-~~~~~~~~-~~l~~~s~v~v~ 74 (450)
T PRK03932 20 TVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDN-GEEYFEEI-KKLTTGSSVIVT 74 (450)
T ss_pred EEEEEEEEEEeCCCeEEEEEECCCCcEEEEEEcCC-ChHHHHHH-hcCCCCcEEEEE
Confidence 3789999997766 899997622 2344444333 22222222 347778777664
No 213
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=32.97 E-value=1.3e+02 Score=19.90 Aligned_cols=46 Identities=24% Similarity=0.396 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhhhCCeeEE-eeCceeEe----------ccCHHHHHHHHHHHHHhc
Q psy18072 96 QEAIDTIKAKIEQLGGVFQV-QMAPKVVT----------ASDEAELARQMERAEAEN 141 (174)
Q Consensus 96 ~~~~~~i~~~l~~~~g~l~~-k~~P~~i~----------~~~~~~~k~~~~~l~k~~ 141 (174)
++.++.|+-.|...||.+.+ .-.+..+. .++...++..+++.+++.
T Consensus 2 ~~~l~~IrP~L~~dGGdv~lv~v~~~~V~V~l~GaC~gC~~s~~Tl~~~Ie~~L~~~ 58 (68)
T PF01106_consen 2 EEVLEEIRPYLQSDGGDVELVDVDDGVVYVRLTGACSGCPSSDMTLKQGIEQALREA 58 (68)
T ss_dssp HHHHHHCHHHHHHTTEEEEEEEEETTEEEEEEESSCCSSCCHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhChHHHhcCCcEEEEEecCCEEEEEEEeCCCCCCCHHHHHHHHHHHHHHHH
Confidence 45666789999999999888 22222444 456678888888877764
No 214
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=32.74 E-value=1.9e+02 Score=20.82 Aligned_cols=50 Identities=16% Similarity=0.153 Sum_probs=33.7
Q ss_pred CCEEEEEEEEEecceEE-EEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEE
Q psy18072 16 EDVVMVTVISIAEMGAY-VHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVV 72 (174)
Q Consensus 16 GdiV~G~V~~i~~~Gaf-V~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrV 72 (174)
...+.|+|+.....+.| |.+.+ +..=+.|++-=.+. .-.++.||.|.|..
T Consensus 18 e~e~~g~V~~~lG~~~~~V~~~d--G~~~la~i~GK~Rk-----~iwI~~GD~VlVsp 68 (99)
T TIGR00523 18 EGEILGVIEQMLGAGRVKVRCLD--GKTRLGRIPGKLKK-----RIWIREGDVVIVKP 68 (99)
T ss_pred CCEEEEEEEEEcCCCEEEEEeCC--CCEEEEEEchhhcc-----cEEecCCCEEEEEE
Confidence 46799999999776665 46666 56666665532211 34689999999844
No 215
>PF02598 Methyltrn_RNA_3: Putative RNA methyltransferase; InterPro: IPR003750 This entry describes proteins of unknown function.; PDB: 1K3R_B.
Probab=32.53 E-value=1.4e+02 Score=25.59 Aligned_cols=58 Identities=14% Similarity=0.119 Sum_probs=32.5
Q ss_pred cccchhhccCCCCCCEEEEEEEEEecce---EEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 3 LSCRFYAEKYPEVEDVVMVTVISIAEMG---AYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 3 ~~~r~~~~~~p~~GdiV~G~V~~i~~~G---afV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
|.++-+....+..|..=.|.|......+ .||.+.- ...+.+.. ..+.+|.+|+|++.+
T Consensus 102 L~~phH~~~~~~~~~yREGvv~~~~~~~~~~~~VdiGl----~~~v~i~~----------~~l~~g~RVTV~~~~ 162 (291)
T PF02598_consen 102 LDAPHHMSRSDEWGPYREGVVVRKPSKGGKGSYVDIGL----DKPVEIDK----------QELPPGTRVTVRIKS 162 (291)
T ss_dssp ---TTS--SS--TT-EEEEEEEEE-SSS---EEEESSS----SEEEESSS--------------SS-EEEEEEEE
T ss_pred CCCCccccCCccccceeEEEEEeCCCCCCceEEEEeCC----CcEEeecc----------cccCCCCEEEEEecC
Confidence 5666566455568999999999986655 9999854 33333322 268899999999988
No 216
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=32.53 E-value=1.8e+02 Score=20.48 Aligned_cols=53 Identities=21% Similarity=0.177 Sum_probs=35.0
Q ss_pred CCCEEEEEEEEEec--ce-EEEEECCCC-CeEEEEEceecchhhhhccc-cccCCCCEEEEEE
Q psy18072 15 VEDVVMVTVISIAE--MG-AYVHLLEYN-NIEGMILLSELSRRRIRSIN-KLIRVGKTEPVVV 72 (174)
Q Consensus 15 ~GdiV~G~V~~i~~--~G-afV~L~~~~-~~~GlI~iSels~~~v~~~~-~~l~vGd~V~vrV 72 (174)
..-.|.|.|++++. .| +|..|-+-. .+.+.+..+. ...+. ..++.|+.|.|+.
T Consensus 22 ~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~-----~~~i~~~~l~~G~~V~v~g 79 (99)
T PF13742_consen 22 PNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSR-----ARRIRGFDLKDGDKVLVRG 79 (99)
T ss_pred CCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHH-----HhhCCCCCCCCCCEEEEEE
Confidence 46679999999965 44 588887611 2444444333 33444 6789999998765
No 217
>PLN00208 translation initiation factor (eIF); Provisional
Probab=31.59 E-value=1.9e+02 Score=22.51 Aligned_cols=58 Identities=12% Similarity=0.135 Sum_probs=38.4
Q ss_pred CCCCCCEEEEEEEEEecceEE-EEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC
Q psy18072 12 YPEVEDVVMVTVISIAEMGAY-VHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~Gaf-V~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~ 77 (174)
+|..| .+.|+|+.....+.| |.+.+ +..=|.|++-=.+.+ -.+++||.|.|.+-..+.
T Consensus 28 ~p~eg-q~~g~V~~~lGn~~~~V~c~d--G~~rLa~IpGKmRKr-----IWI~~GD~VlVel~~~d~ 86 (145)
T PLN00208 28 FKEDG-QEYAQVLRMLGNGRCEALCID--GTKRLCHIRGKMRKK-----VWIAAGDIILVGLRDYQD 86 (145)
T ss_pred cCCCC-cEEEEEEEEcCCCEEEEEECC--CCEEEEEEeccceee-----EEecCCCEEEEEccCCCC
Confidence 45445 478999988776665 46665 677777776422222 468999999998665543
No 218
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=31.50 E-value=1.7e+02 Score=20.00 Aligned_cols=50 Identities=16% Similarity=0.136 Sum_probs=34.1
Q ss_pred EEEEEEEEecceEE-EEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE
Q psy18072 19 VMVTVISIAEMGAY-VHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV 75 (174)
Q Consensus 19 V~G~V~~i~~~Gaf-V~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V 75 (174)
+.|+|+.....+.| |.+.+ +..-+.|++-=.+++ -.++.||.|.|.....
T Consensus 2 ~i~~V~~~lG~~~~~V~~~d--g~~~l~~i~gK~Rk~-----iwI~~GD~VlV~~~~~ 52 (78)
T cd04456 2 QIVRVLRMLGNNRHEVECAD--GQRRLVSIPGKLRKN-----IWIKRGDFLIVDPIEE 52 (78)
T ss_pred eEEEEEEECCCCEEEEEECC--CCEEEEEEchhhccC-----EEEcCCCEEEEEeccc
Confidence 56889888766665 56666 666676665322221 4588999999987765
No 219
>KOG1189|consensus
Probab=30.79 E-value=28 Score=34.09 Aligned_cols=12 Identities=25% Similarity=0.410 Sum_probs=7.3
Q ss_pred ecceEEEEECCC
Q psy18072 27 AEMGAYVHLLEY 38 (174)
Q Consensus 27 ~~~GafV~L~~~ 38 (174)
....|.|.|.++
T Consensus 765 pTs~cLV~LtE~ 776 (960)
T KOG1189|consen 765 PTSSCLVNLTEW 776 (960)
T ss_pred cchhhhhccccC
Confidence 445677777663
No 220
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=30.19 E-value=1.7e+02 Score=19.46 Aligned_cols=53 Identities=21% Similarity=0.097 Sum_probs=28.9
Q ss_pred EEEEEEEEEecce-EEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEe
Q psy18072 18 VVMVTVISIAEMG-AYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76 (174)
Q Consensus 18 iV~G~V~~i~~~G-afV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd 76 (174)
.+.|+|++....+ .+|.+.+ +..=+++++- .++.....+.+||.|.+.+...+
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~--g~~~~c~~~G----klr~~~i~i~vGD~V~ve~~~~~ 61 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELEN--GHEVLAHISG----KMRKNYIRILPGDKVTVELSPYD 61 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCC--CCEEEEEEcc----ceeeCCcccCCCCEEEEEEcccC
Confidence 4679999887654 4455544 3222222221 11111233789999999875444
No 221
>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane
Probab=30.03 E-value=42 Score=25.50 Aligned_cols=8 Identities=25% Similarity=0.592 Sum_probs=3.5
Q ss_pred CCCCcccc
Q psy18072 146 ADDDEDEE 153 (174)
Q Consensus 146 gd~~~~~~ 153 (174)
|-+=++++
T Consensus 111 G~eVSddE 118 (136)
T PF04871_consen 111 GEEVSDDE 118 (136)
T ss_pred CCCccCCc
Confidence 44334444
No 222
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=29.78 E-value=29 Score=37.21 Aligned_cols=11 Identities=9% Similarity=0.268 Sum_probs=5.3
Q ss_pred cccCCCCEEEE
Q psy18072 60 KLIRVGKTEPV 70 (174)
Q Consensus 60 ~~l~vGd~V~v 70 (174)
..+..|+.|+.
T Consensus 73 ~~y~~~~~i~m 83 (2849)
T PTZ00415 73 GIYNLGDAIRM 83 (2849)
T ss_pred CEEeccCceee
Confidence 34555555443
No 223
>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=29.69 E-value=1.5e+02 Score=18.83 Aligned_cols=46 Identities=11% Similarity=0.000 Sum_probs=31.8
Q ss_pred EEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEE
Q psy18072 18 VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVI 73 (174)
Q Consensus 18 iV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi 73 (174)
.+.|+|..+.+.-+.++..+. +++=++|.+.+. .++.++.+++-+-
T Consensus 4 ~l~G~v~~~~~~~vvi~~~Gv-Gy~v~v~~~~~~---------~l~~~~~v~l~t~ 49 (61)
T PF01330_consen 4 YLKGKVVEKNPDYVVIDVNGV-GYEVFVPSNTLS---------ELPEGGEVKLYTY 49 (61)
T ss_dssp EEEEEEEEEESSEEEEEETTE-EEEEEE-HHHHH---------TS-TTSEEEEEEE
T ss_pred EEEEEEEEEcCCEEEEEECCE-EEEEEeCCchHH---------hCCCCCEEEEEEE
Confidence 478999999999999998764 477777766543 4666776655443
No 224
>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=29.65 E-value=2.6e+02 Score=22.33 Aligned_cols=49 Identities=10% Similarity=0.056 Sum_probs=34.7
Q ss_pred EEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEe
Q psy18072 18 VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76 (174)
Q Consensus 18 iV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd 76 (174)
.+.|+|..+.+..+.|+..+. +|+=+++.+.+. .++.|+.|++-+--+-
T Consensus 4 ~l~G~v~~~~~~~vvi~v~Gv-GY~v~v~~~~~~---------~l~~g~~v~l~t~~~v 52 (191)
T TIGR00084 4 FLFGKVIEVSKPKIIIEVNGV-GYELQVPMTCAY---------ELNLEQKAQVFTHLVV 52 (191)
T ss_pred eEEEEEEEEcCCEEEEEECCE-EEEEEecHHHHH---------hcCCCCeEEEEEEEEE
Confidence 578999999998899988654 466666655443 3456998888665543
No 225
>PF06347 SH3_4: Bacterial SH3 domain; InterPro: IPR010466 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region.
Probab=29.27 E-value=71 Score=19.71 Aligned_cols=24 Identities=17% Similarity=0.133 Sum_probs=16.4
Q ss_pred ecceEEEEECCCCCeEEEEEceecc
Q psy18072 27 AEMGAYVHLLEYNNIEGMILLSELS 51 (174)
Q Consensus 27 ~~~GafV~L~~~~~~~GlI~iSels 51 (174)
...+-|+.+. +++..|.|+.+.|+
T Consensus 31 ~~~~~W~~V~-~~g~~GWv~~~~lw 54 (55)
T PF06347_consen 31 ECRGGWCKVR-ADGRTGWVHKSLLW 54 (55)
T ss_pred EccCCeEEEE-ECCeEEeEEeeecc
Confidence 3445555555 45899999988774
No 226
>PHA02608 67 prohead core protein; Provisional
Probab=28.11 E-value=95 Score=21.65 Aligned_cols=14 Identities=36% Similarity=0.399 Sum_probs=7.6
Q ss_pred HHHHhcccccCCCC
Q psy18072 136 RAEAENAEVAADDD 149 (174)
Q Consensus 136 ~l~k~~~e~~gd~~ 149 (174)
..+-++++..++++
T Consensus 42 sv~iEGEe~ed~dd 55 (80)
T PHA02608 42 SVMIEGEEPEDDDD 55 (80)
T ss_pred HHhhcCCCCccccc
Confidence 34556666655533
No 227
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=27.20 E-value=2.9e+02 Score=21.27 Aligned_cols=50 Identities=18% Similarity=0.127 Sum_probs=33.8
Q ss_pred hhccCCCCCCE-----EEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhcccc
Q psy18072 8 YAEKYPEVEDV-----VMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINK 60 (174)
Q Consensus 8 ~~~~~p~~Gdi-----V~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~ 60 (174)
+..+|. +||. +.|+|.++.-.-..++-.+ +-.=.||.|.+....+.+.+.
T Consensus 57 ~~~pf~-vGD~I~i~~~~G~V~~I~l~~t~l~~~~--g~~v~IPNs~l~~~~i~N~s~ 111 (206)
T PF00924_consen 57 FERPFK-VGDRIEIGGVEGRVEEIGLRSTRLRTWD--GEIVIIPNSKLISSPIVNYSR 111 (206)
T ss_dssp CC-SS--TT-EEESSS-EEEEEEE-SSEEEEEETT--S-EEEEEHHHHHCS-EEETTT
T ss_pred ccCCcc-CCCEEEEEEeehHHHhcCcceeeeecCC--CCEEEEEchheeeEEEEEeec
Confidence 456775 8998 5799999988777777655 788899999998777766554
No 228
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=26.90 E-value=1.6e+02 Score=20.94 Aligned_cols=21 Identities=24% Similarity=0.346 Sum_probs=16.8
Q ss_pred CCCEEEEEEEEEecceEEEEECC
Q psy18072 15 VEDVVMVTVISIAEMGAYVHLLE 37 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~GafV~L~~ 37 (174)
+=.++.|+|.++.+ +-|++.+
T Consensus 16 p~~i~~G~V~s~~P--L~I~i~~ 36 (100)
T PF10844_consen 16 PVDIVIGTVVSVPP--LKIKIDQ 36 (100)
T ss_pred CceeEEEEEEeccc--EEEEECC
Confidence 45678999999988 7777766
No 229
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=26.64 E-value=7.3e+02 Score=25.63 Aligned_cols=47 Identities=9% Similarity=0.105 Sum_probs=33.0
Q ss_pred hhccCCCCCCE-----EEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhc
Q psy18072 8 YAEKYPEVEDV-----VMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRS 57 (174)
Q Consensus 8 ~~~~~p~~Gdi-----V~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~ 57 (174)
+.++|. +||. +.|+|.+|.=+-.-+...+ +..=+||.+.+....+.|
T Consensus 932 ~erPfr-VGD~I~I~~~~GtV~~I~lRsT~Irt~D--g~~IiIPNs~~it~~IiN 983 (1109)
T PRK10929 932 FEKPIR-IGDTVTIRDLTGSVTKINTRATTISDWD--RKEIIVPNKAFITEQFIN 983 (1109)
T ss_pred HhCCCC-CCCEEEECCEEEEEEEEeeeEEEEEeCC--CCEEEEEChhhhcCceEe
Confidence 566775 8998 4578887765555555544 788899999887666544
No 230
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=26.61 E-value=42 Score=36.06 Aligned_cols=8 Identities=38% Similarity=0.268 Sum_probs=3.4
Q ss_pred cchhhccC
Q psy18072 5 CRFYAEKY 12 (174)
Q Consensus 5 ~r~~~~~~ 12 (174)
.+|...+-
T Consensus 17 ~~~~~~~~ 24 (2849)
T PTZ00415 17 VIFAEEKD 24 (2849)
T ss_pred Hhhhhhhc
Confidence 34444443
No 231
>PF14444 S1-like: S1-like
Probab=26.09 E-value=2e+02 Score=18.91 Aligned_cols=43 Identities=19% Similarity=0.191 Sum_probs=23.6
Q ss_pred EEEEEEEEE-ecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 18 VVMVTVISI-AEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 18 iV~G~V~~i-~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
++.|.|+++ .+||+.= + .=+.+.+-++ ....++||.|.|..+.
T Consensus 3 ~~~GvVTkl~~~yG~ID---e----~vFF~~~vv~-------G~~P~vGdrV~v~A~~ 46 (58)
T PF14444_consen 3 VFTGVVTKLCDDYGFID---E----DVFFQTDVVK-------GNVPKVGDRVLVEAIY 46 (58)
T ss_pred eEEEEEEEEeCCcceEc---c----cEEEEcccEe-------cCCCccCCEEEEEEEe
Confidence 578999998 4555421 1 1111111111 1345789999987664
No 232
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=25.96 E-value=54 Score=22.50 Aligned_cols=21 Identities=14% Similarity=0.363 Sum_probs=18.2
Q ss_pred ccccCCCCEEEEEEEEEeCCC
Q psy18072 59 NKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 59 ~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
+..+.+||.|.++|++++.+.
T Consensus 9 ~Esi~IgddI~itVl~i~gnq 29 (73)
T COG1551 9 GESIMIGDDIEITVLSIKGNQ 29 (73)
T ss_pred CceEEecCCeEEEEEEEcCCe
Confidence 467889999999999998765
No 233
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.70 E-value=3.4e+02 Score=21.68 Aligned_cols=50 Identities=6% Similarity=-0.086 Sum_probs=34.2
Q ss_pred EEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEe
Q psy18072 18 VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76 (174)
Q Consensus 18 iV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd 76 (174)
.+.|+|..+.+..+.+...+. +|+=+++.+.+. ..-+.|+.+++-+--+-
T Consensus 4 ~l~G~v~~~~~~~vvi~~~Gv-GY~v~~s~~~~~--------~l~~~g~~~~l~t~~~v 53 (194)
T PRK14605 4 SLNGILEASGKDWAVINVSGV-GFRCYMPATSPA--------LIGGLGQRVRVFTHLHV 53 (194)
T ss_pred eEEEEEEEecCCEEEEEECCE-EEEEEeCHHHHH--------hcccCCCeEEEEEEEEE
Confidence 578999999888888887653 466666655443 22357898888665543
No 234
>PRK11281 hypothetical protein; Provisional
Probab=25.62 E-value=7.5e+02 Score=25.51 Aligned_cols=48 Identities=15% Similarity=0.133 Sum_probs=33.3
Q ss_pred hhccCCCCCCEE-----EEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhcc
Q psy18072 8 YAEKYPEVEDVV-----MVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSI 58 (174)
Q Consensus 8 ~~~~~p~~GdiV-----~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~ 58 (174)
+..+|. +||.| .|+|..|.-.---|...+ +..=+||.+.+....+.|.
T Consensus 935 ~eRPfr-IGD~I~I~~~~G~V~~I~lRsT~Irt~D--~~~ViIPNs~~~t~~IiN~ 987 (1113)
T PRK11281 935 FERPVR-IGDTVTIGTFSGTVSKIRIRATTITDFD--RKEVIVPNKAFVTERLINW 987 (1113)
T ss_pred HcCCcC-CCCEEEECCEEEEEEEEEeEEEEEEcCC--CCEEEEechhhhcCceEeC
Confidence 566775 99985 678877755444454444 7788999999877666543
No 235
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=25.23 E-value=2.5e+02 Score=27.33 Aligned_cols=52 Identities=12% Similarity=0.097 Sum_probs=30.8
Q ss_pred EEEEEEEEEecce--EEEEECCC-CCeEEEEEceecchhhhhccccccCCCCEEEE
Q psy18072 18 VVMVTVISIAEMG--AYVHLLEY-NNIEGMILLSELSRRRIRSINKLIRVGKTEPV 70 (174)
Q Consensus 18 iV~G~V~~i~~~G--afV~L~~~-~~~~GlI~iSels~~~v~~~~~~l~vGd~V~v 70 (174)
.+.|.|.++...| +||.|... +.++.++..+..+...+..+ ..++.|+.|.|
T Consensus 22 ~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~-~~L~~EsvV~V 76 (706)
T PRK12820 22 CLAGWVDAFRDHGELLFIHLRDRNGFIQAVFSPEAAPADVYELA-ASLRAEFCVAL 76 (706)
T ss_pred EEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCCcCCHHHHHHH-hcCCCCCEEEE
Confidence 4789999998775 69999762 24666666544333222111 34566665544
No 236
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=24.86 E-value=2.9e+02 Score=25.13 Aligned_cols=54 Identities=19% Similarity=0.110 Sum_probs=32.3
Q ss_pred CCCE--EEEEEEEEecce--EEEEECCC---CCeEEEEEceecchhhhhccccccCCCCEEEE
Q psy18072 15 VEDV--VMVTVISIAEMG--AYVHLLEY---NNIEGMILLSELSRRRIRSINKLIRVGKTEPV 70 (174)
Q Consensus 15 ~Gdi--V~G~V~~i~~~G--afV~L~~~---~~~~GlI~iSels~~~v~~~~~~l~vGd~V~v 70 (174)
.|+. |.|.|.++...| +|+.|... +.++.++... ........+ ..+++|+.|.|
T Consensus 15 ~g~~v~v~Gwv~~~R~~~~~~F~~lrD~~~~g~iQ~v~~~~-~~~~~~~~~-~~l~~gs~V~v 75 (453)
T TIGR00457 15 VGDEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGE-DNPYLFQLL-KSLTTGSSVSV 75 (453)
T ss_pred CCCEEEEEEEeEEEEcCCCeEEEEEECCCCCccEEEEEeCC-cChHHHHHH-HcCCCCcEEEE
Confidence 3553 789999997654 79999762 2467777544 222211111 35777777755
No 237
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.42 E-value=3.6e+02 Score=21.68 Aligned_cols=49 Identities=14% Similarity=-0.017 Sum_probs=33.4
Q ss_pred EEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEe
Q psy18072 18 VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVD 76 (174)
Q Consensus 18 iV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd 76 (174)
.+.|+|..+.+..+.|+..+. +|+=+++.+.+. .++.|+.|++-+--+-
T Consensus 4 ~l~G~i~~~~~~~vvi~~~Gv-GY~V~vs~~~~~---------~l~~g~~v~l~t~~~v 52 (197)
T PRK14603 4 YLSGVVLEKREGSAVLLAGGV-GLEVQCPAPTLA---------RLVEGQEAELHTRLVV 52 (197)
T ss_pred eEEEEEEEecCCEEEEEECCE-EEEEEcCHHHHH---------HcCCCCeEEEEEEEEE
Confidence 578999999888888887553 355555544332 3467999988665543
No 238
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=24.04 E-value=51 Score=21.21 Aligned_cols=22 Identities=14% Similarity=0.373 Sum_probs=17.4
Q ss_pred cccccCCCCEEEEEEEEEeCCC
Q psy18072 58 INKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 58 ~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
+...+.+|+.|.++|++++.+.
T Consensus 8 ~gE~I~Ig~~I~I~Vl~i~~~~ 29 (54)
T PF02599_consen 8 VGESIVIGDDIEITVLEISGGQ 29 (54)
T ss_dssp TT-EEEETTTEEEEEEEEETTE
T ss_pred CCCEEEECCCEEEEEEEEcCCE
Confidence 4467889999999999998554
No 239
>COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism]
Probab=23.54 E-value=2.1e+02 Score=22.47 Aligned_cols=54 Identities=20% Similarity=0.236 Sum_probs=33.2
Q ss_pred EEEEEEEEecc--eEEEEECCCCCeEEEEEce----ecchhhhhccccccCCCCEEEE--EEEEEeC
Q psy18072 19 VMVTVISIAEM--GAYVHLLEYNNIEGMILLS----ELSRRRIRSINKLIRVGKTEPV--VVIRVDK 77 (174)
Q Consensus 19 V~G~V~~i~~~--GafV~L~~~~~~~GlI~iS----els~~~v~~~~~~l~vGd~V~v--rVi~Vd~ 77 (174)
+.|+|..+-+. .+=+...+ +.+=|||+- +|.-..+ ...++.||.|++ .++++|.
T Consensus 49 vdG~v~~iFpTkHAigi~t~~--GvEiLiHiGiDTV~L~GegF---~~~v~~Gd~Vk~Gd~Li~fDl 110 (156)
T COG2190 49 VDGTVVLIFPTKHAIGIETDE--GVEILIHIGIDTVKLNGEGF---ESLVKEGDKVKAGDPLLEFDL 110 (156)
T ss_pred cCcEEEEEeeCCcEEEEEcCC--CcEEEEEeceeeEEECCcce---EEEeeCCCEEccCCEEEEECH
Confidence 57888888444 44445555 899999986 3332222 256777877776 4555543
No 240
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.46 E-value=3.1e+02 Score=22.83 Aligned_cols=60 Identities=23% Similarity=0.154 Sum_probs=34.4
Q ss_pred CCEEEEEEEEEecceEEEEECCCCCeEEEEEceecc---hhhhhccccccCCCC--EEEEEEEEEeCC
Q psy18072 16 EDVVMVTVISIAEMGAYVHLLEYNNIEGMILLSELS---RRRIRSINKLIRVGK--TEPVVVIRVDKE 78 (174)
Q Consensus 16 GdiV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels---~~~v~~~~~~l~vGd--~V~vrVi~Vd~~ 78 (174)
|++|.|++.+..+-|+-+.+.. ...-+|..+|. +...+.+.+.|-.=| .|.++|+.++..
T Consensus 75 Ge~y~G~l~s~~~~G~~~~v~G---~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~~ 139 (225)
T PF09883_consen 75 GETYVGTLISWDEDGYGVDVDG---IFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVEDG 139 (225)
T ss_pred CceEEEEEEeecccceEEEeec---ccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEcccC
Confidence 9999999999977666665532 33444444441 112222223333333 456888887664
No 241
>KOG1885|consensus
Probab=23.34 E-value=1.9e+02 Score=27.08 Aligned_cols=54 Identities=19% Similarity=0.210 Sum_probs=36.3
Q ss_pred EEEEEEEEEecce---EEEEECCCC-CeEEEEEcee-cchhhhhccccccCCCCEEEEE
Q psy18072 18 VVMVTVISIAEMG---AYVHLLEYN-NIEGMILLSE-LSRRRIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 18 iV~G~V~~i~~~G---afV~L~~~~-~~~GlI~iSe-ls~~~v~~~~~~l~vGd~V~vr 71 (174)
.|-|+|.++..+| +|..|.+-+ +++=+..... .+..-+....+.++.||.|.|.
T Consensus 108 svaGRI~s~R~sGsKL~Fydl~~~g~klQvm~~~~~~~~~~~F~~~~~~lkrGDiig~~ 166 (560)
T KOG1885|consen 108 SVAGRIHSKRESGSKLVFYDLHGDGVKLQVMANAKKITSEEDFEQLHKFLKRGDIIGVS 166 (560)
T ss_pred eeeeeEeeeeccCCceEEEEEecCCeEEEEEEehhhcCCHHHHHHHHhhhhccCEEeee
Confidence 4789999998877 677775421 2445555554 2333455667899999999773
No 242
>KOG1999|consensus
Probab=23.19 E-value=4.6e+02 Score=26.65 Aligned_cols=57 Identities=18% Similarity=0.187 Sum_probs=32.9
Q ss_pred CCCCCCEEEEEEEEEecc-eEEEEECCCCCeEEEEEceecchh----hhhccccccCCCCEEEEE
Q psy18072 12 YPEVEDVVMVTVISIAEM-GAYVHLLEYNNIEGMILLSELSRR----RIRSINKLIRVGKTEPVV 71 (174)
Q Consensus 12 ~p~~GdiV~G~V~~i~~~-GafV~L~~~~~~~GlI~iSels~~----~v~~~~~~l~vGd~V~vr 71 (174)
|. +||.|...+-...+. |+...+.. .+-=+++.-+-... ..+.++++|++||.|+|.
T Consensus 408 F~-~GD~VeV~~Gel~glkG~ve~vdg--~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi 469 (1024)
T KOG1999|consen 408 FS-PGDAVEVIVGELKGLKGKVESVDG--TIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVI 469 (1024)
T ss_pred cC-CCCeEEEeeeeeccceeEEEeccC--ceEEEeeccccCCCccccchHhhhhhccCCCeEEEE
Confidence 54 788887777666554 55555554 23223332111111 134567999999998873
No 243
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=23.08 E-value=3.9e+02 Score=21.73 Aligned_cols=53 Identities=15% Similarity=0.058 Sum_probs=36.4
Q ss_pred EEEEEEEEEecceEEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeCCC
Q psy18072 18 VVMVTVISIAEMGAYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 18 iV~G~V~~i~~~GafV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
.+.|+|+.+.+.-+.|+.... +|+-.++.+.+. +.-.+|+.++.-+..+-.+.
T Consensus 4 ~l~G~v~~~~~~~ivie~~GV-GY~i~~~~~~~~--------~l~~~g~~~~l~t~~~vREd 56 (201)
T COG0632 4 YLRGKVTEKNPDYIVIEVNGV-GYEINVPMRTLA--------ELPEVGEEVKLFTHLVVRED 56 (201)
T ss_pred eeEEEEEEecCCEEEEEeCCE-EEEEEcChHHHh--------hcccCCCeEEEEEEEeehhh
Confidence 478999999888777777653 466666655543 22356999988777655444
No 244
>PRK00124 hypothetical protein; Validated
Probab=22.75 E-value=81 Score=24.58 Aligned_cols=76 Identities=11% Similarity=0.129 Sum_probs=45.9
Q ss_pred cccCCCCEEEEE-------EEEEeCCCceeeecccccchHHHHHHHHH--HHHHHHhhhCCeeEEeeCceeEeccCHHHH
Q psy18072 60 KLIRVGKTEPVV-------VIRVDKEKVMTTVTPEKADGLKALQEAID--TIKAKIEQLGGVFQVQMAPKVVTASDEAEL 130 (174)
Q Consensus 60 ~~l~vGd~V~vr-------Vi~Vd~~~~l~ls~~~k~~g~~~i~~~~~--~i~~~l~~~~g~l~~k~~P~~i~~~~~~~~ 130 (174)
...++||.|.-. |+ ..+.+.++.+.+..--.-|...+. .+.+.+...|+. ..+|.-++..|...|
T Consensus 63 ~~~~~gDiVIT~Di~LAa~~l---~Kga~vl~prG~~yt~~nI~~~L~~R~~~~~lR~~G~~---t~Gp~~~~~~Dr~~F 136 (151)
T PRK00124 63 QLAEKGDIVITQDYGLAALAL---EKGAIVLNPRGYIYTNDNIDQLLAMRDLMATLRRSGIR---TGGPKPFTQEDRSRF 136 (151)
T ss_pred HhCCCCCEEEeCCHHHHHHHH---HCCCEEECCCCcCCCHHHHHHHHHHHHHHHHHHHcCCC---CCCCCCCCHHHHHHH
Confidence 567788766321 11 111345555555444344444332 345556655552 358999999999999
Q ss_pred HHHHHHHHHhc
Q psy18072 131 ARQMERAEAEN 141 (174)
Q Consensus 131 k~~~~~l~k~~ 141 (174)
..+|.+++...
T Consensus 137 ~~~L~~~l~~~ 147 (151)
T PRK00124 137 EAELDKLIRRI 147 (151)
T ss_pred HHHHHHHHHHh
Confidence 99999998763
No 245
>TIGR00300 conserved hypothetical protein TIGR00300. All members of the family come from genome projects. A partial length search brings in two plant lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzymes hitting the N-terminal region of the family.
Probab=22.68 E-value=5.9e+02 Score=23.16 Aligned_cols=75 Identities=21% Similarity=0.226 Sum_probs=44.2
Q ss_pred cccCCCCEEEEEEEEEe--CCC--------ceee--ecccccchHHHHHHHHHHHHHHHhhhCCeeEEeeCceeEeccCH
Q psy18072 60 KLIRVGKTEPVVVIRVD--KEK--------VMTT--VTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAPKVVTASDE 127 (174)
Q Consensus 60 ~~l~vGd~V~vrVi~Vd--~~~--------~l~l--s~~~k~~g~~~i~~~~~~i~~~l~~~~g~l~~k~~P~~i~~~~~ 127 (174)
..++.||.|.+-.-.|. +.. .+.. +....+.+...+.+.+.+....++.++|.+-...+|.++---+-
T Consensus 139 r~lk~GD~VVvG~eGI~v~~~~~~~~~~~~~F~FM~s~vS~E~p~~~~~~~ia~~lr~~r~~gG~Iv~V~GPAvvhtga~ 218 (407)
T TIGR00300 139 REIKKGDRVVVGVEGIRVIPPERPREGGTGVFEFMGSGVSSERPVETLIEQIAWEMYEIRDKGGKIGVVAGPAVIHTGAA 218 (407)
T ss_pred cccCCCCEEEECCceeEECCCCCCCccCCceeEecCCCCCcCCccHHHHHHHHHHHHHHHHCCCCEEEEecCeEEecCcH
Confidence 46889999876433222 111 0111 12223345555566666667777888999999999999932233
Q ss_pred HHHHHHH
Q psy18072 128 AELARQM 134 (174)
Q Consensus 128 ~~~k~~~ 134 (174)
.+|.+++
T Consensus 219 ~ala~Li 225 (407)
T TIGR00300 219 QALAHLI 225 (407)
T ss_pred HHHHHHH
Confidence 5555544
No 246
>PF05086 Dicty_REP: Dictyostelium (Slime Mold) REP protein; InterPro: IPR007778 This family consists of REP proteins from a number of Dictyostelium species (Slime molds). REP protein is probably involved in transcription regulation and control of DNA replication, specifically the amplification of plasmid at low copy numbers. The formation of homomultimers may be required for their regulatory activity [].
Probab=22.33 E-value=44 Score=32.77 Aligned_cols=6 Identities=50% Similarity=0.894 Sum_probs=2.5
Q ss_pred cCCCCE
Q psy18072 62 IRVGKT 67 (174)
Q Consensus 62 l~vGd~ 67 (174)
+++|..
T Consensus 787 IKvg~~ 792 (911)
T PF05086_consen 787 IKVGGN 792 (911)
T ss_pred EEECCE
Confidence 344443
No 247
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=22.22 E-value=1.4e+02 Score=17.04 Aligned_cols=22 Identities=18% Similarity=0.409 Sum_probs=16.9
Q ss_pred eCceeEeccCHHHHHHHHHHHHH
Q psy18072 117 MAPKVVTASDEAELARQMERAEA 139 (174)
Q Consensus 117 ~~P~~i~~~~~~~~k~~~~~l~k 139 (174)
..|++|. .+.+.|+.++-+|=-
T Consensus 3 ~~p~vi~-~d~~~Fr~lVQ~LTG 24 (31)
T PF05678_consen 3 SPPTVIH-TDPSNFRALVQRLTG 24 (31)
T ss_pred CCCEEEE-eCHHHHHHHHHHhHC
Confidence 4677666 688999999988753
No 248
>PRK00568 carbon storage regulator; Provisional
Probab=22.07 E-value=65 Score=22.33 Aligned_cols=22 Identities=23% Similarity=0.373 Sum_probs=18.5
Q ss_pred cccccCCCCEEEEEEEEEeCCC
Q psy18072 58 INKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 58 ~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
....+.+|+.|.++|+.+..+.
T Consensus 8 ~gEsI~Igd~I~I~Vl~i~g~~ 29 (76)
T PRK00568 8 VNEGIVIDDNIHIKVISIDRGS 29 (76)
T ss_pred CCCeEEeCCCeEEEEEEEcCCE
Confidence 4467889999999999998765
No 249
>PF11813 DUF3334: Protein of unknown function (DUF3334); InterPro: IPR024513 This family of proteins are functionally uncharacterised. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length.
Probab=21.72 E-value=80 Score=26.17 Aligned_cols=19 Identities=16% Similarity=0.627 Sum_probs=16.9
Q ss_pred cceEEEEECCCCCeEEEEEce
Q psy18072 28 EMGAYVHLLEYNNIEGMILLS 48 (174)
Q Consensus 28 ~~GafV~L~~~~~~~GlI~iS 48 (174)
+.||||-+++ ++.||+-+.
T Consensus 49 DiGCFvlFDG--GFsGLVviN 67 (229)
T PF11813_consen 49 DIGCFVLFDG--GFSGLVVIN 67 (229)
T ss_pred CcceEEEecC--CcceEEEEe
Confidence 6799999988 999999876
No 250
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=21.17 E-value=1.7e+02 Score=25.80 Aligned_cols=56 Identities=13% Similarity=0.078 Sum_probs=33.3
Q ss_pred CCEEEEEEEEEecceE--EEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEEeC
Q psy18072 16 EDVVMVTVISIAEMGA--YVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRVDK 77 (174)
Q Consensus 16 GdiV~G~V~~i~~~Ga--fV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~Vd~ 77 (174)
-.+.-|+|++|.+.+- -|.|.- ++..=.-.++.++.+. =.+++|+.|.|.|.+|.-
T Consensus 293 rNiLp~~v~~i~~~~~~V~v~ld~-~g~~l~Arit~~srd~-----L~l~~G~~v~AqIKsVsv 350 (352)
T COG4148 293 RNILPGKVVGIEDDDGQVDVQLDC-GGKTLWARITPWARDE-----LALKPGQWVYAQIKSVSV 350 (352)
T ss_pred hhccceeEEEEEcCCCcEEEEEEc-CCcEEEEEccHhhHHh-----hcCCCCCeEEEEEEEEEe
Confidence 3467788888865443 444432 1222222334444333 259999999999988753
No 251
>KOG2140|consensus
Probab=21.15 E-value=53 Score=31.11 Aligned_cols=8 Identities=25% Similarity=0.194 Sum_probs=3.2
Q ss_pred EEEEceec
Q psy18072 43 GMILLSEL 50 (174)
Q Consensus 43 GlI~iSel 50 (174)
+++|-.+|
T Consensus 323 ~ILhe~El 330 (739)
T KOG2140|consen 323 YILHEGEL 330 (739)
T ss_pred HHHhHhhH
Confidence 33444443
No 252
>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=21.10 E-value=1.9e+02 Score=27.59 Aligned_cols=48 Identities=17% Similarity=0.158 Sum_probs=32.3
Q ss_pred CCCEEEEEEEEEecce-EEEEECCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEE
Q psy18072 15 VEDVVMVTVISIAEMG-AYVHLLEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIR 74 (174)
Q Consensus 15 ~GdiV~G~V~~i~~~G-afV~L~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~ 74 (174)
....+.|+|... +.| +||.... .-+=+||..++. ..+ .||.|.|+|.+
T Consensus 15 ~~~~~~G~i~~~-~kGfgFv~~~~--~~difI~~~~l~--------~A~-~GD~V~v~i~~ 63 (639)
T TIGR02062 15 QTPRVEGVVKAT-EKGFGFLEVDA--QKSYFIPPPQMK--------KVM-HGDKIIAVIHS 63 (639)
T ss_pred cCceEEEEEEEC-CCccEEEEECC--CCcEEEChHHHc--------cCC-CCCEEEEEEec
Confidence 345788999754 444 6776544 336788877776 445 48888888765
No 253
>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=21.08 E-value=1e+02 Score=21.12 Aligned_cols=19 Identities=26% Similarity=0.268 Sum_probs=14.4
Q ss_pred cccCCCCEEEEEEEEEeCC
Q psy18072 60 KLIRVGKTEPVVVIRVDKE 78 (174)
Q Consensus 60 ~~l~vGd~V~vrVi~Vd~~ 78 (174)
..+++||.|.++++-.+.+
T Consensus 9 ~iYrPGetV~~~~~~~~~~ 27 (99)
T PF01835_consen 9 PIYRPGETVHFRAIVRDLD 27 (99)
T ss_dssp SEE-TTSEEEEEEEEEEEC
T ss_pred cCcCCCCEEEEEEEEeccc
Confidence 6899999999999944444
No 254
>PRK01712 carbon storage regulator; Provisional
Probab=21.00 E-value=85 Score=21.02 Aligned_cols=22 Identities=18% Similarity=0.373 Sum_probs=18.3
Q ss_pred cccccCCCCEEEEEEEEEeCCC
Q psy18072 58 INKLIRVGKTEPVVVIRVDKEK 79 (174)
Q Consensus 58 ~~~~l~vGd~V~vrVi~Vd~~~ 79 (174)
+...+.+|+.|.++|+.+..+.
T Consensus 8 ~gE~I~Igd~I~I~V~~i~~~~ 29 (64)
T PRK01712 8 VGESLMIGDDIEVTVLGVKGNQ 29 (64)
T ss_pred CCCEEEeCCCEEEEEEEEeCCE
Confidence 4567889999999999998654
No 255
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=20.87 E-value=3.4e+02 Score=25.50 Aligned_cols=55 Identities=18% Similarity=0.269 Sum_probs=34.3
Q ss_pred CCCE--EEEEEEEEecce--EEEEECCC-CCeEEEEEcee-cchhhhhccccccCCCCEEEE
Q psy18072 15 VEDV--VMVTVISIAEMG--AYVHLLEY-NNIEGMILLSE-LSRRRIRSINKLIRVGKTEPV 70 (174)
Q Consensus 15 ~Gdi--V~G~V~~i~~~G--afV~L~~~-~~~~GlI~iSe-ls~~~v~~~~~~l~vGd~V~v 70 (174)
.|+. |.|.|.++...| +|+.|..- +.+++++..+. ++...++.+ ..++.|+.|.|
T Consensus 77 ~g~~V~v~Grv~~~R~~Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~-~~l~~esiV~V 137 (550)
T PTZ00401 77 VDKTVLIRARVSTTRKKGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFI-GQIPTESIVDV 137 (550)
T ss_pred CCCEEEEEEEEEEEecCCCeEEEEEEeCCcCEEEEEECCCccCHHHHHHH-hcCCCCCEEEE
Confidence 3544 689999998776 79988762 25788875442 443322222 34677777754
No 256
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.39 E-value=4.5e+02 Score=20.95 Aligned_cols=52 Identities=8% Similarity=0.036 Sum_probs=34.4
Q ss_pred EEEEEEEEEecceEEEEE-CCCCCeEEEEEceecchhhhhccccccCCCCEEEEEEEEE-eCCC
Q psy18072 18 VVMVTVISIAEMGAYVHL-LEYNNIEGMILLSELSRRRIRSINKLIRVGKTEPVVVIRV-DKEK 79 (174)
Q Consensus 18 iV~G~V~~i~~~GafV~L-~~~~~~~GlI~iSels~~~v~~~~~~l~vGd~V~vrVi~V-d~~~ 79 (174)
.+.|+|..+.+..+.|.. .+. +|+=++|.+.+. .++.|+.+++-+--+ +.+.
T Consensus 4 ~l~G~v~~~~~~~vvid~v~GV-GY~v~i~~~~~~---------~l~~g~~v~l~t~~~vrEd~ 57 (183)
T PRK14601 4 AIEGIITKKEPTFIVLKTASGV-SYGIFISLFCSA---------KIQKGEKHELFITQIIKEDS 57 (183)
T ss_pred EEEEEEEEecCCEEEEEcCCCE-EEEEEecHHHHH---------HcCCCCeEEEEEEEEEecCC
Confidence 578999999888888873 443 366666654443 346899988765443 4443
No 257
>KOG0127|consensus
Probab=20.16 E-value=1.2e+02 Score=28.72 Aligned_cols=10 Identities=40% Similarity=0.464 Sum_probs=4.5
Q ss_pred eEEEEEceec
Q psy18072 41 IEGMILLSEL 50 (174)
Q Consensus 41 ~~GlI~iSel 50 (174)
+.|-++.-+.
T Consensus 72 f~Gr~l~v~~ 81 (678)
T KOG0127|consen 72 FEGRILNVDP 81 (678)
T ss_pred ccceeccccc
Confidence 4454444443
Done!