Query 005716
Match_columns 681
No_of_seqs 173 out of 719
Neff 2.3
Searched_HMMs 46136
Date Thu Mar 28 12:40:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005716.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005716hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0539 RpsA Ribosomal protein 100.0 1.8E-32 3.9E-37 293.1 8.9 120 269-412 187-309 (541)
2 COG0539 RpsA Ribosomal protein 99.9 1.6E-25 3.6E-30 240.0 8.6 121 270-413 273-396 (541)
3 PTZ00248 eukaryotic translatio 99.9 1.2E-24 2.7E-29 221.4 7.6 124 273-419 16-152 (319)
4 PRK07899 rpsA 30S ribosomal pr 99.9 3E-24 6.6E-29 227.4 8.3 121 269-413 203-326 (486)
5 PRK13806 rpsA 30S ribosomal pr 99.9 1.4E-23 2.9E-28 220.6 9.3 121 270-413 288-412 (491)
6 PRK12269 bifunctional cytidyla 99.9 1.1E-23 2.4E-28 235.3 8.3 121 270-413 574-698 (863)
7 PRK12269 bifunctional cytidyla 99.9 9.9E-23 2.1E-27 227.8 9.4 122 269-414 488-612 (863)
8 PRK13806 rpsA 30S ribosomal pr 99.9 1.3E-22 2.9E-27 213.2 8.4 124 269-414 197-326 (491)
9 PRK06299 rpsA 30S ribosomal pr 99.9 4.6E-22 1E-26 209.3 9.1 122 269-414 196-320 (565)
10 COG1098 VacB Predicted RNA bin 99.8 1.5E-21 3.2E-26 178.7 5.9 80 271-353 2-84 (129)
11 PRK06676 rpsA 30S ribosomal pr 99.8 9E-21 1.9E-25 191.1 9.1 121 270-414 188-311 (390)
12 COG2183 Tex Transcriptional ac 99.8 7E-21 1.5E-25 210.4 7.6 97 251-349 631-734 (780)
13 TIGR00717 rpsA ribosomal prote 99.8 1.6E-20 3.4E-25 194.8 8.1 121 269-413 182-305 (516)
14 TIGR00717 rpsA ribosomal prote 99.8 3.7E-20 8E-25 192.1 8.6 121 271-414 356-480 (516)
15 PRK06299 rpsA 30S ribosomal pr 99.8 1.3E-19 2.8E-24 190.9 8.6 123 270-415 369-495 (565)
16 PRK00087 4-hydroxy-3-methylbut 99.8 2.8E-19 6E-24 193.5 8.3 122 269-414 472-596 (647)
17 cd05705 S1_Rrp5_repeat_hs14 S1 99.7 4.1E-18 8.9E-23 139.4 7.8 68 272-341 1-74 (74)
18 PRK07400 30S ribosomal protein 99.7 2.8E-18 6.1E-23 173.1 7.4 119 271-413 28-150 (318)
19 PRK07400 30S ribosomal protein 99.7 5.1E-18 1.1E-22 171.2 7.6 114 273-415 117-230 (318)
20 PRK08582 hypothetical protein; 99.7 1.6E-17 3.5E-22 151.3 10.0 78 272-352 3-83 (139)
21 cd05694 S1_Rrp5_repeat_hs2_sc2 99.7 3.2E-17 7E-22 134.6 9.2 72 271-347 1-73 (74)
22 cd05704 S1_Rrp5_repeat_hs13 S1 99.7 6.6E-17 1.4E-21 130.6 8.4 68 272-343 1-72 (72)
23 PRK06676 rpsA 30S ribosomal pr 99.7 3.2E-17 7E-22 165.6 7.2 149 261-437 4-157 (390)
24 cd04461 S1_Rrp5_repeat_hs8_sc7 99.7 9.3E-17 2E-21 131.1 8.1 74 267-342 7-83 (83)
25 cd05686 S1_pNO40 S1_pNO40: pNO 99.7 2.1E-16 4.5E-21 127.2 9.1 67 273-342 2-72 (73)
26 PRK07899 rpsA 30S ribosomal pr 99.7 6.4E-17 1.4E-21 172.1 7.9 142 269-439 30-175 (486)
27 PLN00207 polyribonucleotide nu 99.6 1.1E-16 2.4E-21 180.1 6.7 82 272-356 751-836 (891)
28 PF00575 S1: S1 RNA binding do 99.6 7.2E-16 1.6E-20 121.6 8.9 70 272-343 2-74 (74)
29 cd05698 S1_Rrp5_repeat_hs6_sc5 99.6 1.2E-15 2.6E-20 119.5 8.3 67 275-343 1-70 (70)
30 PRK07252 hypothetical protein; 99.6 1.9E-15 4.1E-20 135.2 9.9 86 272-359 1-90 (120)
31 cd04452 S1_IF2_alpha S1_IF2_al 99.6 2.7E-15 5.8E-20 118.6 9.0 71 272-344 1-76 (76)
32 PRK05807 hypothetical protein; 99.6 2.7E-15 5.8E-20 136.2 9.8 71 272-346 3-76 (136)
33 cd05690 S1_RPS1_repeat_ec5 S1_ 99.6 2.1E-15 4.5E-20 117.3 7.7 65 275-341 1-69 (69)
34 cd05703 S1_Rrp5_repeat_hs12_sc 99.6 2.4E-15 5.2E-20 122.4 8.3 67 275-343 1-72 (73)
35 cd05706 S1_Rrp5_repeat_sc10 S1 99.6 3.9E-15 8.5E-20 117.8 9.1 70 272-343 1-73 (73)
36 cd05684 S1_DHX8_helicase S1_DH 99.6 4.9E-15 1.1E-19 119.7 8.9 70 275-348 1-77 (79)
37 cd05708 S1_Rrp5_repeat_sc12 S1 99.6 1E-14 2.2E-19 114.6 9.0 71 273-345 1-75 (77)
38 cd05696 S1_Rrp5_repeat_hs4 S1_ 99.6 5.7E-15 1.2E-19 119.2 7.6 66 275-342 1-71 (71)
39 cd05697 S1_Rrp5_repeat_hs5 S1_ 99.6 7.5E-15 1.6E-19 115.7 8.0 66 275-342 1-69 (69)
40 PRK08059 general stress protei 99.6 1.1E-14 2.4E-19 129.1 9.6 80 269-350 2-84 (123)
41 cd05707 S1_Rrp5_repeat_sc11 S1 99.6 8.5E-15 1.8E-19 115.1 7.6 65 275-341 1-68 (68)
42 cd05692 S1_RPS1_repeat_hs4 S1_ 99.6 2.1E-14 4.5E-19 109.1 8.8 66 275-343 1-69 (69)
43 cd05691 S1_RPS1_repeat_ec6 S1_ 99.6 1.9E-14 4.2E-19 112.3 8.8 69 275-345 1-72 (73)
44 cd05693 S1_Rrp5_repeat_hs1_sc1 99.5 9.6E-15 2.1E-19 126.4 7.1 72 272-344 1-96 (100)
45 cd05687 S1_RPS1_repeat_ec1_hs1 99.5 3.5E-14 7.7E-19 111.6 8.2 67 275-343 1-70 (70)
46 cd05689 S1_RPS1_repeat_ec4 S1_ 99.5 4E-14 8.6E-19 111.8 8.4 68 272-341 1-72 (72)
47 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 99.5 4.1E-14 8.8E-19 115.7 8.2 72 272-346 4-82 (86)
48 cd04453 S1_RNase_E S1_RNase_E: 99.5 5.4E-14 1.2E-18 119.1 9.1 75 271-346 4-85 (88)
49 PRK11824 polynucleotide phosph 99.5 6.6E-14 1.4E-18 154.0 9.6 89 254-345 586-692 (693)
50 TIGR02696 pppGpp_PNP guanosine 99.5 8.4E-14 1.8E-18 154.5 9.0 68 271-341 644-718 (719)
51 cd05685 S1_Tex S1_Tex: The C-t 99.5 2E-13 4.2E-18 103.9 7.6 65 275-341 1-68 (68)
52 PRK00087 4-hydroxy-3-methylbut 99.5 6.4E-14 1.4E-18 152.2 6.8 141 267-435 295-439 (647)
53 cd04472 S1_PNPase S1_PNPase: P 99.5 2.8E-13 6E-18 104.0 8.3 65 275-342 1-68 (68)
54 cd05688 S1_RPS1_repeat_ec3 S1_ 99.5 2.5E-13 5.4E-18 103.9 7.9 65 274-341 1-68 (68)
55 cd04471 S1_RNase_R S1_RNase_R: 99.5 3.2E-13 6.8E-18 107.8 8.8 68 274-343 1-83 (83)
56 cd05695 S1_Rrp5_repeat_hs3 S1_ 99.4 5E-13 1.1E-17 106.8 7.6 65 275-341 1-66 (66)
57 PRK03987 translation initiatio 99.4 8.1E-13 1.8E-17 131.7 9.4 77 271-349 5-86 (262)
58 smart00316 S1 Ribosomal protei 99.4 2.8E-12 6.1E-17 96.3 8.7 69 273-343 1-72 (72)
59 cd04465 S1_RPS1_repeat_ec2_hs2 99.4 1.8E-12 3.9E-17 102.0 8.0 66 275-343 1-67 (67)
60 cd04473 S1_RecJ_like S1_RecJ_l 99.4 3.4E-12 7.3E-17 104.3 9.1 69 266-342 8-76 (77)
61 PHA02945 interferon resistance 99.3 4.2E-12 9.1E-17 111.0 8.8 71 273-348 10-87 (88)
62 cd04460 S1_RpoE S1_RpoE: RpoE, 99.3 5.7E-12 1.2E-16 106.7 8.1 78 276-355 1-96 (99)
63 COG1093 SUI2 Translation initi 99.3 2.6E-12 5.7E-17 129.6 5.8 75 272-349 9-89 (269)
64 cd05702 S1_Rrp5_repeat_hs11_sc 99.3 1.7E-11 3.6E-16 97.7 7.4 58 275-333 1-63 (70)
65 COG1185 Pnp Polyribonucleotide 99.3 6.7E-12 1.5E-16 138.6 6.8 74 270-346 615-691 (692)
66 cd04454 S1_Rrp4_like S1_Rrp4_l 99.2 3.3E-11 7.2E-16 98.3 8.4 70 273-345 5-77 (82)
67 TIGR03591 polynuc_phos polyrib 99.2 1.6E-11 3.4E-16 135.4 7.7 67 271-340 615-684 (684)
68 cd00164 S1_like S1_like: Ribos 99.2 6.2E-11 1.3E-15 87.7 6.8 62 278-341 1-65 (65)
69 cd04455 S1_NusA S1_NusA: N-uti 99.2 1.4E-10 3E-15 92.7 8.2 64 273-341 2-66 (67)
70 PRK09521 exosome complex RNA-b 99.1 8.9E-11 1.9E-15 110.5 7.7 70 270-344 60-142 (189)
71 PRK04163 exosome complex RNA-b 99.0 4.7E-10 1E-14 109.7 8.4 70 272-344 61-137 (235)
72 TIGR00448 rpoE DNA-directed RN 99.0 1E-09 2.2E-14 102.7 9.2 80 273-354 80-177 (179)
73 TIGR02063 RNase_R ribonuclease 98.9 2.6E-09 5.7E-14 117.5 9.0 68 273-342 626-708 (709)
74 PRK11642 exoribonuclease R; Pr 98.8 1.8E-08 3.8E-13 113.8 11.5 69 273-343 642-725 (813)
75 TIGR00358 3_prime_RNase VacB a 98.7 2.7E-08 5.9E-13 109.3 8.9 68 273-342 571-653 (654)
76 PRK08563 DNA-directed RNA poly 98.7 4.3E-08 9.3E-13 91.7 8.8 76 272-349 79-172 (187)
77 COG1095 RPB7 DNA-directed RNA 98.7 5.3E-08 1.1E-12 94.6 7.4 73 274-348 81-171 (183)
78 PRK09202 nusA transcription el 98.6 5.4E-08 1.2E-12 104.5 8.0 64 274-343 134-199 (470)
79 TIGR00757 RNaseEG ribonuclease 98.5 1.7E-07 3.6E-12 99.2 7.5 71 272-343 23-109 (414)
80 KOG1067 Predicted RNA-binding 98.5 1E-07 2.2E-12 105.0 5.3 84 269-355 663-749 (760)
81 KOG1070 rRNA processing protei 98.3 1.5E-06 3.2E-11 102.6 8.5 134 262-415 1150-1288(1710)
82 cd05791 S1_CSL4 S1_CSL4: CSL4, 98.3 3.3E-06 7.1E-11 72.7 7.6 69 273-344 5-86 (92)
83 PRK12327 nusA transcription el 98.2 2E-06 4.3E-11 90.2 7.3 98 273-379 133-230 (362)
84 TIGR01953 NusA transcription t 98.2 4.3E-06 9.2E-11 87.0 8.3 66 273-343 130-197 (341)
85 cd04462 S1_RNAPII_Rpb7 S1_RNAP 98.1 1.3E-05 2.9E-10 68.7 8.4 57 274-332 1-71 (88)
86 KOG1070 rRNA processing protei 97.9 9.9E-06 2.1E-10 96.0 5.3 81 265-347 590-673 (1710)
87 PTZ00162 DNA-directed RNA poly 97.9 4.5E-05 9.7E-10 72.9 7.9 71 273-345 80-166 (176)
88 PRK05054 exoribonuclease II; P 97.8 5.6E-05 1.2E-09 83.9 8.7 66 275-342 562-643 (644)
89 COG0557 VacB Exoribonuclease R 97.6 0.00015 3.2E-09 81.0 8.1 68 273-342 621-703 (706)
90 PRK11712 ribonuclease G; Provi 97.5 0.00016 3.4E-09 78.8 7.1 59 272-330 36-110 (489)
91 COG1107 Archaea-specific RecJ- 97.5 8.8E-05 1.9E-09 82.8 4.4 82 267-355 115-196 (715)
92 PF13509 S1_2: S1 domain; PDB: 97.5 0.00039 8.6E-09 56.0 6.6 61 274-343 1-61 (61)
93 PRK10811 rne ribonuclease E; R 97.5 0.00023 4.9E-09 82.9 7.1 58 273-330 37-107 (1068)
94 TIGR02062 RNase_B exoribonucle 97.4 0.0004 8.7E-09 77.2 8.0 64 275-340 558-637 (639)
95 COG1097 RRP4 RNA-binding prote 97.3 0.00064 1.4E-08 69.0 8.0 70 273-345 63-139 (239)
96 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.1 0.0023 5E-08 55.9 8.2 69 273-344 5-75 (86)
97 COG1530 CafA Ribonucleases G a 97.0 0.0011 2.4E-08 72.0 6.5 79 271-350 34-120 (487)
98 PF10447 EXOSC1: Exosome compo 96.8 0.0029 6.3E-08 55.0 5.8 57 273-330 3-82 (82)
99 PRK12328 nusA transcription el 96.8 0.0038 8.3E-08 66.7 8.0 99 273-380 137-237 (374)
100 KOG2916 Translation initiation 96.8 0.0013 2.7E-08 68.3 4.1 97 266-364 8-109 (304)
101 PHA02858 EIF2a-like PKR inhibi 96.4 0.0087 1.9E-07 53.3 6.5 66 273-342 15-85 (86)
102 KOG1856 Transcription elongati 96.2 0.0055 1.2E-07 72.7 5.1 74 270-344 981-1059(1299)
103 COG1096 Predicted RNA-binding 96.2 0.015 3.2E-07 57.7 7.2 74 265-343 55-141 (188)
104 cd05699 S1_Rrp5_repeat_hs7 S1_ 96.1 0.017 3.6E-07 49.8 6.2 64 275-343 1-72 (72)
105 COG2996 Predicted RNA-bindinin 96.1 0.014 3.1E-07 60.8 6.9 62 275-344 156-217 (287)
106 COG2996 Predicted RNA-bindinin 95.5 0.035 7.7E-07 57.9 7.1 166 268-467 67-278 (287)
107 cd05705 S1_Rrp5_repeat_hs14 S1 95.0 0.0079 1.7E-07 49.8 0.6 36 357-413 1-36 (74)
108 PRK12329 nusA transcription el 94.8 0.077 1.7E-06 58.3 7.4 66 273-342 151-223 (449)
109 TIGR02696 pppGpp_PNP guanosine 93.8 0.008 1.7E-07 68.7 -2.7 36 356-412 644-679 (719)
110 COG1098 VacB Predicted RNA bin 93.5 0.026 5.6E-07 53.4 0.5 38 356-414 2-39 (129)
111 cd04453 S1_RNase_E S1_RNase_E: 93.4 0.03 6.4E-07 48.1 0.8 39 355-414 3-43 (88)
112 cd05689 S1_RPS1_repeat_ec4 S1_ 92.9 0.03 6.4E-07 44.5 0.0 36 357-413 1-36 (72)
113 PRK09521 exosome complex RNA-b 92.9 0.07 1.5E-06 51.0 2.5 68 319-414 29-108 (189)
114 PLN00207 polyribonucleotide nu 92.9 0.019 4.1E-07 67.1 -1.6 69 317-413 719-787 (891)
115 cd05704 S1_Rrp5_repeat_hs13 S1 92.7 0.041 8.8E-07 45.0 0.5 35 358-413 2-37 (72)
116 PTZ00248 eukaryotic translatio 92.1 0.045 9.8E-07 57.6 0.1 40 353-413 10-52 (319)
117 PRK08582 hypothetical protein; 91.6 0.059 1.3E-06 50.1 0.4 37 357-414 3-39 (139)
118 cd05686 S1_pNO40 S1_pNO40: pNO 90.8 0.068 1.5E-06 43.4 -0.1 34 358-413 2-37 (73)
119 cd05690 S1_RPS1_repeat_ec5 S1_ 90.6 0.064 1.4E-06 41.9 -0.4 24 391-414 11-34 (69)
120 cd05706 S1_Rrp5_repeat_sc10 S1 89.9 0.11 2.3E-06 41.5 0.3 36 358-414 2-37 (73)
121 PF00313 CSD: 'Cold-shock' DNA 89.8 3.4 7.5E-05 33.0 8.8 50 278-329 1-53 (66)
122 cd05696 S1_Rrp5_repeat_hs4 S1_ 89.8 0.095 2.1E-06 42.7 -0.0 23 391-413 12-35 (71)
123 cd05707 S1_Rrp5_repeat_sc11 S1 89.6 0.11 2.3E-06 41.2 0.1 23 391-413 11-33 (68)
124 KOG3298 DNA-directed RNA polym 89.4 1.1 2.5E-05 44.3 6.9 61 274-336 81-155 (170)
125 COG1185 Pnp Polyribonucleotide 88.8 0.12 2.6E-06 59.3 -0.2 40 352-412 612-651 (692)
126 cd05703 S1_Rrp5_repeat_hs12_sc 88.4 0.13 2.9E-06 42.3 -0.1 23 391-413 11-33 (73)
127 cd05698 S1_Rrp5_repeat_hs6_sc5 88.2 0.15 3.3E-06 40.2 0.1 23 391-413 11-33 (70)
128 cd04461 S1_Rrp5_repeat_hs8_sc7 88.1 0.16 3.6E-06 41.8 0.2 38 356-414 11-48 (83)
129 cd04473 S1_RecJ_like S1_RecJ_l 87.3 0.21 4.5E-06 41.2 0.4 40 353-413 10-49 (77)
130 cd05697 S1_Rrp5_repeat_hs5 S1_ 86.6 0.19 4.2E-06 39.9 -0.1 23 391-413 11-33 (69)
131 PRK08059 general stress protei 86.1 0.27 5.8E-06 44.4 0.5 41 353-414 1-41 (123)
132 PF08292 RNA_pol_Rbc25: RNA po 85.7 3.3 7.1E-05 38.5 7.3 56 274-330 3-74 (122)
133 PF10246 MRP-S35: Mitochondria 85.6 2.4 5.3E-05 39.3 6.3 53 273-330 22-74 (104)
134 TIGR03591 polynuc_phos polyrib 85.5 0.25 5.4E-06 56.2 -0.0 38 355-413 614-651 (684)
135 PRK05807 hypothetical protein; 84.9 0.29 6.3E-06 45.4 0.1 37 357-415 3-39 (136)
136 PRK12442 translation initiatio 83.9 3.4 7.4E-05 37.3 6.3 61 277-343 8-72 (87)
137 PRK11824 polynucleotide phosph 82.7 0.41 9E-06 54.5 0.2 38 355-413 617-654 (693)
138 cd05695 S1_Rrp5_repeat_hs3 S1_ 81.7 0.45 9.9E-06 38.4 0.0 23 391-413 11-33 (66)
139 cd04452 S1_IF2_alpha S1_IF2_al 81.4 0.45 9.8E-06 37.9 -0.1 35 359-414 3-39 (76)
140 PRK09937 stationary phase/star 81.3 7.5 0.00016 33.3 7.2 63 279-345 3-67 (74)
141 COG4044 Uncharacterized protei 81.3 2 4.4E-05 44.3 4.4 71 266-338 67-152 (247)
142 PF00575 S1: S1 RNA binding do 80.7 0.54 1.2E-05 37.3 0.2 38 356-414 1-38 (74)
143 cd04465 S1_RPS1_repeat_ec2_hs2 79.9 0.5 1.1E-05 37.4 -0.3 41 391-436 11-51 (67)
144 PRK07252 hypothetical protein; 79.8 0.62 1.4E-05 42.6 0.3 34 359-413 3-36 (120)
145 PRK15464 cold shock-like prote 79.7 4.7 0.0001 34.3 5.4 52 278-330 5-58 (70)
146 PRK10943 cold shock-like prote 79.6 6.1 0.00013 33.1 6.0 54 276-330 2-57 (69)
147 cd05692 S1_RPS1_repeat_hs4 S1_ 79.1 0.52 1.1E-05 35.9 -0.4 23 391-413 11-33 (69)
148 cd05691 S1_RPS1_repeat_ec6 S1_ 79.0 0.62 1.3E-05 36.6 -0.0 24 391-414 11-34 (73)
149 KOG3409 Exosomal 3'-5' exoribo 78.1 4.8 0.0001 40.6 5.7 67 273-342 67-146 (193)
150 PRK15463 cold shock-like prote 77.8 6.9 0.00015 33.1 5.8 52 278-330 5-58 (70)
151 cd04471 S1_RNase_R S1_RNase_R: 77.7 0.64 1.4E-05 37.3 -0.3 23 391-413 12-35 (83)
152 COG1093 SUI2 Translation initi 76.6 1 2.2E-05 47.1 0.7 39 355-414 6-47 (269)
153 TIGR00008 infA translation ini 76.2 9.3 0.0002 32.9 6.2 57 277-339 6-66 (68)
154 COG1545 Predicted nucleic-acid 75.8 9.8 0.00021 35.8 6.8 76 251-331 39-124 (140)
155 cd05685 S1_Tex S1_Tex: The C-t 75.5 0.91 2E-05 34.6 0.0 24 391-414 11-34 (68)
156 PRK09507 cspE cold shock prote 75.2 10 0.00022 31.8 6.1 53 277-330 3-57 (69)
157 cd05684 S1_DHX8_helicase S1_DH 74.5 0.8 1.7E-05 37.4 -0.5 24 391-414 11-37 (79)
158 cd04458 CSP_CDS Cold-Shock Pro 73.6 15 0.00033 29.3 6.5 58 279-342 2-63 (65)
159 cd05702 S1_Rrp5_repeat_hs11_sc 72.5 1.2 2.7E-05 35.7 0.1 23 391-413 11-33 (70)
160 PRK09890 cold shock protein Cs 71.9 14 0.0003 31.1 6.1 52 278-330 5-58 (70)
161 COG2106 Uncharacterized conser 70.1 6.7 0.00015 41.3 4.8 48 272-330 103-150 (272)
162 PRK10354 RNA chaperone/anti-te 69.9 13 0.00028 31.1 5.6 52 278-330 5-58 (70)
163 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 68.7 1.9 4.1E-05 35.6 0.4 35 358-413 5-39 (86)
164 cd05694 S1_Rrp5_repeat_hs2_sc2 67.2 1.9 4.2E-05 35.9 0.2 38 357-415 2-40 (74)
165 TIGR02381 cspD cold shock doma 66.9 12 0.00027 31.1 4.8 51 279-330 3-55 (68)
166 PRK14998 cold shock-like prote 66.0 18 0.00038 31.0 5.7 51 279-330 3-55 (73)
167 KOG1857 Transcription accessor 65.5 2.1 4.6E-05 48.5 0.1 77 262-340 533-617 (623)
168 cd04472 S1_PNPase S1_PNPase: P 62.8 1.9 4.1E-05 33.2 -0.6 23 391-413 11-33 (68)
169 cd05693 S1_Rrp5_repeat_hs1_sc1 62.0 3.4 7.4E-05 36.5 0.8 35 358-413 2-36 (100)
170 PRK09202 nusA transcription el 61.4 1 2.2E-05 49.8 -3.2 86 300-412 72-165 (470)
171 cd05708 S1_Rrp5_repeat_sc12 S1 60.8 2.8 6E-05 33.1 -0.0 23 391-413 13-36 (77)
172 cd05687 S1_RPS1_repeat_ec1_hs1 59.9 2.9 6.3E-05 33.1 -0.0 23 391-413 11-33 (70)
173 smart00357 CSP Cold shock prot 59.0 52 0.0011 24.8 6.7 48 280-330 2-50 (64)
174 PF01336 tRNA_anti-codon: OB-f 58.6 16 0.00035 28.3 4.0 62 277-344 2-71 (75)
175 TIGR00638 Mop molybdenum-pteri 57.7 19 0.00041 28.3 4.2 51 276-330 7-62 (69)
176 PRK04012 translation initiatio 57.0 34 0.00074 31.2 6.2 72 264-340 10-82 (100)
177 PF02598 Methyltrn_RNA_3: Puta 56.6 29 0.00064 36.3 6.5 47 273-329 113-162 (291)
178 PRK00484 lysS lysyl-tRNA synth 55.1 69 0.0015 35.7 9.3 63 277-342 58-128 (491)
179 cd04322 LysRS_N LysRS_N: N-ter 53.8 27 0.00058 30.5 4.9 53 277-330 3-63 (108)
180 COG1095 RPB7 DNA-directed RNA 53.7 6.3 0.00014 39.5 1.1 74 323-427 44-122 (183)
181 COG4148 ModC ABC-type molybdat 53.6 20 0.00044 39.0 4.9 45 276-330 294-348 (352)
182 PF13742 tRNA_anti_2: OB-fold 53.2 42 0.00091 29.6 6.0 67 277-347 25-99 (99)
183 cd04489 ExoVII_LU_OBF ExoVII_L 51.4 96 0.0021 24.8 7.4 67 277-345 3-74 (78)
184 TIGR02063 RNase_R ribonuclease 49.5 4.8 0.0001 45.8 -0.4 45 348-413 616-661 (709)
185 PTZ00417 lysine-tRNA ligase; P 49.4 40 0.00087 38.7 6.6 51 277-328 136-197 (585)
186 PF08402 TOBE_2: TOBE domain; 48.5 92 0.002 24.0 6.6 49 276-328 16-68 (75)
187 cd04318 EcAsnRS_like_N EcAsnRS 48.1 56 0.0012 27.0 5.7 50 277-328 3-59 (82)
188 PF07076 DUF1344: Protein of u 47.8 60 0.0013 27.9 5.8 53 277-342 4-60 (61)
189 PRK14600 ruvA Holliday junctio 47.6 33 0.00071 33.9 4.9 47 277-329 4-50 (186)
190 TIGR00074 hypC_hupF hydrogenas 45.6 30 0.00066 30.2 3.9 42 278-327 5-46 (76)
191 TIGR00499 lysS_bact lysyl-tRNA 45.6 1.1E+02 0.0024 34.2 9.1 64 277-342 57-128 (496)
192 smart00316 S1 Ribosomal protei 45.3 7 0.00015 29.3 -0.0 24 391-414 13-36 (72)
193 PF03459 TOBE: TOBE domain; I 45.3 67 0.0014 25.1 5.5 49 277-329 6-59 (64)
194 PRK03987 translation initiatio 45.1 6.9 0.00015 40.3 -0.1 34 359-413 8-43 (262)
195 PF09883 DUF2110: Uncharacteri 45.1 36 0.00079 35.4 4.9 68 262-332 63-138 (225)
196 PF10446 DUF2457: Protein of u 45.1 15 0.00033 41.2 2.4 11 602-612 26-36 (458)
197 cd05700 S1_Rrp5_repeat_hs9 S1_ 43.8 70 0.0015 28.0 5.6 55 275-331 1-55 (65)
198 COG2183 Tex Transcriptional ac 42.6 10 0.00022 44.8 0.7 43 356-419 655-697 (780)
199 COG0298 HypC Hydrogenase matur 41.7 36 0.00078 30.8 3.8 44 278-327 5-49 (82)
200 PRK11642 exoribonuclease R; Pr 41.3 10 0.00023 44.5 0.6 34 358-412 642-676 (813)
201 PF01455 HupF_HypC: HupF/HypC 40.5 54 0.0012 27.9 4.5 41 278-326 5-47 (68)
202 COG3269 Predicted RNA-binding 40.4 87 0.0019 27.8 5.8 50 270-331 11-60 (73)
203 KOG1004 Exosomal 3'-5' exoribo 39.9 95 0.002 32.5 6.9 55 273-330 64-122 (230)
204 PLN00208 translation initiatio 39.7 93 0.002 30.5 6.5 73 263-340 20-93 (145)
205 PRK10409 hydrogenase assembly 39.2 42 0.00091 30.4 3.9 43 278-327 5-52 (90)
206 cd04323 AsnRS_cyto_like_N AsnR 39.2 75 0.0016 26.6 5.2 48 277-327 3-57 (84)
207 PLN02502 lysyl-tRNA synthetase 38.9 1.5E+02 0.0033 33.9 9.1 63 277-342 112-185 (553)
208 PF13437 HlyD_3: HlyD family s 37.6 99 0.0021 26.1 5.7 66 278-349 6-80 (105)
209 PTZ00329 eukaryotic translatio 36.2 1.3E+02 0.0027 29.9 6.9 78 256-338 12-91 (155)
210 cd04320 AspRS_cyto_N AspRS_cyt 35.5 74 0.0016 27.4 4.7 49 277-327 3-62 (102)
211 PRK06461 single-stranded DNA-b 35.5 91 0.002 28.8 5.6 74 266-343 4-90 (129)
212 PF12869 tRNA_anti-like: tRNA_ 34.9 54 0.0012 29.3 3.9 50 277-327 71-127 (144)
213 PRK03932 asnC asparaginyl-tRNA 34.6 47 0.001 36.4 4.2 48 277-327 20-75 (450)
214 cd05793 S1_IF1A S1_IF1A: Trans 33.9 1E+02 0.0023 26.7 5.3 59 278-340 2-61 (77)
215 cd04317 EcAspRS_like_N EcAspRS 33.7 70 0.0015 28.9 4.5 49 277-327 18-72 (135)
216 TIGR00084 ruvA Holliday juncti 32.3 79 0.0017 31.2 4.9 48 277-330 4-51 (191)
217 TIGR00458 aspS_arch aspartyl-t 31.8 88 0.0019 34.1 5.6 68 274-343 11-89 (428)
218 PF14444 S1-like: S1-like 31.2 1.1E+02 0.0025 26.1 5.0 44 277-329 3-46 (58)
219 PRK05159 aspC aspartyl-tRNA sy 31.0 1.7E+02 0.0036 32.1 7.5 66 274-342 15-91 (437)
220 KOG2830 Protein phosphatase 2A 30.9 86 0.0019 34.2 5.2 35 584-618 240-275 (324)
221 KOG1067 Predicted RNA-binding 30.6 16 0.00034 42.5 -0.2 31 391-421 679-709 (760)
222 TIGR00999 8a0102 Membrane Fusi 30.6 1E+02 0.0022 29.7 5.3 63 278-348 95-165 (265)
223 TIGR00523 eIF-1A eukaryotic/ar 30.5 1.8E+02 0.004 26.5 6.5 65 268-338 12-79 (99)
224 KOG0343 RNA Helicase [RNA proc 30.3 43 0.00093 39.3 3.1 127 392-544 372-510 (758)
225 PRK14603 ruvA Holliday junctio 30.1 93 0.002 31.0 5.0 48 277-330 4-51 (197)
226 cd04485 DnaE_OBF DnaE_OBF: A s 29.6 1.7E+02 0.0037 22.7 5.5 64 278-345 2-74 (84)
227 PRK14605 ruvA Holliday junctio 29.1 97 0.0021 30.7 4.9 49 277-330 4-52 (194)
228 PHA02945 interferon resistance 28.8 23 0.00051 32.2 0.6 39 392-432 22-62 (88)
229 PRK14601 ruvA Holliday junctio 28.5 1E+02 0.0022 30.7 4.9 48 277-330 4-52 (183)
230 KOG1857 Transcription accessor 28.4 27 0.00059 40.1 1.1 45 264-309 565-609 (623)
231 TIGR01843 type_I_hlyD type I s 27.9 1.1E+02 0.0023 31.4 5.2 70 277-349 277-356 (423)
232 PRK13901 ruvA Holliday junctio 27.6 1E+02 0.0023 31.1 4.9 48 277-330 4-51 (196)
233 PRK12336 translation initiatio 27.6 1.6E+02 0.0034 29.4 6.1 48 271-330 144-191 (201)
234 KOG3013 Exosomal 3'-5' exoribo 27.2 51 0.0011 35.4 2.8 67 273-342 84-163 (301)
235 PF02237 BPL_C: Biotin protein 27.1 79 0.0017 24.6 3.2 19 274-293 11-29 (48)
236 cd04454 S1_Rrp4_like S1_Rrp4_l 27.1 88 0.0019 25.8 3.7 44 318-364 5-58 (82)
237 PRK00116 ruvA Holliday junctio 26.8 1.4E+02 0.0031 29.2 5.6 49 277-330 4-52 (192)
238 COG0361 InfA Translation initi 26.7 3.4E+02 0.0074 24.2 7.3 63 277-343 8-72 (75)
239 PRK14602 ruvA Holliday junctio 26.1 1.1E+02 0.0025 30.5 4.8 50 277-330 4-53 (203)
240 TIGR00358 3_prime_RNase VacB a 25.9 23 0.0005 40.4 0.1 35 358-413 571-606 (654)
241 cd04319 PhAsnRS_like_N PhAsnRS 25.4 1.1E+02 0.0025 26.5 4.2 48 277-327 3-58 (103)
242 PRK00276 infA translation init 25.3 3.4E+02 0.0075 22.9 6.9 58 277-339 8-68 (72)
243 TIGR00998 8a0101 efflux pump m 25.2 1.5E+02 0.0033 29.8 5.6 67 277-348 210-284 (334)
244 PF07405 DUF1506: Protein of u 24.8 64 0.0014 31.1 2.7 58 286-344 51-122 (127)
245 PRK10413 hydrogenase 2 accesso 24.1 1.1E+02 0.0023 27.3 3.8 43 278-327 5-53 (82)
246 PRK08402 replication factor A; 24.0 2E+02 0.0044 31.3 6.5 76 265-343 61-154 (355)
247 CHL00010 infA translation init 23.6 4.7E+02 0.01 22.6 7.5 65 278-345 9-74 (78)
248 PRK14604 ruvA Holliday junctio 23.4 1.7E+02 0.0038 29.1 5.5 49 277-330 4-52 (195)
249 TIGR01953 NusA transcription t 23.2 9.7 0.00021 40.7 -3.3 94 312-438 79-181 (341)
250 cd04100 Asp_Lys_Asn_RS_N Asp_L 22.9 1.7E+02 0.0037 24.4 4.6 49 277-327 3-58 (85)
251 PF07757 AdoMet_MTase: Predict 22.9 22 0.00048 33.5 -0.6 22 286-308 57-78 (112)
252 PLN02856 fumarylacetoacetase 22.7 1.1E+02 0.0024 34.3 4.4 69 268-341 343-413 (424)
253 PF03293 Pox_RNA_pol: Poxvirus 22.6 1.7E+02 0.0036 29.3 5.1 59 268-330 75-144 (160)
254 PRK11578 macrolide transporter 22.5 1.9E+02 0.0041 30.1 5.8 69 278-349 190-266 (370)
255 cd00592 HTH_MerR-like Helix-Tu 22.4 3.2E+02 0.0069 23.3 6.3 61 170-230 26-86 (100)
256 TIGR02142 modC_ABC molybdenum 22.1 2E+02 0.0044 30.1 6.0 50 277-330 297-351 (354)
257 smart00652 eIF1a eukaryotic tr 22.0 3.1E+02 0.0066 24.2 6.1 61 273-340 3-66 (83)
258 PRK12445 lysyl-tRNA synthetase 21.8 3.2E+02 0.007 30.9 7.8 64 277-342 69-140 (505)
259 TIGR03794 NHPM_micro_HlyD NHPM 21.7 1.7E+02 0.0038 31.0 5.5 70 278-350 260-341 (421)
260 TIGR01000 bacteriocin_acc bact 21.1 1.8E+02 0.0039 31.5 5.6 72 278-350 323-404 (457)
261 cd00210 PTS_IIA_glc PTS_IIA, P 20.8 1.3E+02 0.0028 28.3 3.8 53 278-330 42-101 (124)
262 cd03524 RPA2_OBF_family RPA2_O 20.6 2.8E+02 0.006 20.4 4.9 62 278-343 2-71 (75)
263 COG2421 Predicted acetamidase/ 20.5 1.7E+02 0.0036 31.9 5.0 65 261-331 12-84 (305)
No 1
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=1.8e-32 Score=293.10 Aligned_cols=120 Identities=25% Similarity=0.400 Sum_probs=116.5
Q ss_pred CCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccccc---ccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 269 LPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRH---HIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 269 L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~d---VLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
|+.|++||+|+|+|++||+| |||||||| +|||||||||||.++.+ ++++||+|+|+||++ |.+|+|||||||++
T Consensus 187 ~~~l~~G~vV~G~V~~It~~-GafVdigG-vdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~-D~e~~RVsLSlK~l 263 (541)
T COG0539 187 LNKLEVGEVVEGVVKNITDY-GAFVDIGG-VDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISL-DEERGRVSLSLKQL 263 (541)
T ss_pred HhcCCCCceEEEEEEEeecC-cEEEEecC-eeeEEehhhccccccCCHHHhcccCCEEEEEEEEE-ccCCCeEEEEehhc
Confidence 68999999999999999999 99999999 59999999999999865 999999999999999 89999999999999
Q ss_pred CCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehh
Q 005716 346 QPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHN 412 (681)
Q Consensus 346 ~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~ 412 (681)
.++||..|.++|++|..+. |.|.+ ++.|||||++.|||+||+|||.
T Consensus 264 ~~dPw~~i~~~~~~g~~v~-------G~Vt~--------------i~~~GafVei~~GvEGlvhvSE 309 (541)
T COG0539 264 EEDPWEGIEKKYPVGDKVE-------GKVTN--------------LTDYGAFVEIEEGVEGLVHVSE 309 (541)
T ss_pred ccCcHHHHhhhcCCCCEEE-------EEEEE--------------eecCcEEEEecCCccceeechh
Confidence 9999999999999999999 99999 9999999999999999999994
No 2
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=1.6e-25 Score=240.02 Aligned_cols=121 Identities=24% Similarity=0.355 Sum_probs=115.0
Q ss_pred CCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc---ccccccCCEEEEEEEEeeCCCCCeeeeeeeccC
Q 005716 270 PFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI---RHHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQ 346 (681)
Q Consensus 270 ~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI---~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~ 346 (681)
..+.+|++++|+|++|++| ||||+|+.+..||||||||||.++ .++|++||+|+|+||+| |+++.|||||||++.
T Consensus 273 ~~~~~g~~v~G~Vt~i~~~-GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~i-d~e~rRIsL~iKq~~ 350 (541)
T COG0539 273 KKYPVGDKVEGKVTNLTDY-GAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDI-DPERRRISLGLKQLK 350 (541)
T ss_pred hhcCCCCEEEEEEEEeecC-cEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEee-CchhceEEeeehhhh
Confidence 5678999999999999999 999999888899999999999765 46999999999999999 899999999999999
Q ss_pred CCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 347 PNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 347 pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
+|||..+..+|++|.++. |.|.. +++||+|+.+..+|+||+|+|..
T Consensus 351 ~~pw~~~~~~~~~g~~v~-------g~v~~--------------~t~~g~fv~le~gidG~vh~~d~ 396 (541)
T COG0539 351 ENPWEEFADKHPVGDVVE-------GKVKS--------------ITDFGAFVELEGGIDGLVHLSDL 396 (541)
T ss_pred cChhhhhhhhcCCCCeEE-------EEEee--------------ecccceEEccCCCccceEEHHhc
Confidence 999999999999999999 99999 99999999999999999999853
No 3
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.90 E-value=1.2e-24 Score=221.39 Aligned_cols=124 Identities=19% Similarity=0.206 Sum_probs=113.6
Q ss_pred CCCCEEEEEEEEeeecceeEEEcC--CceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeeccCC
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIG--GVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQP 347 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIG--Gv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~p 347 (681)
.+|++|.|+|++|++| ||||+|+ ++.+||||+|||||.+++ ++|++||+|.|+||.| |+++++|+||+|.+.+
T Consensus 16 ~~GdvV~g~V~~I~d~-GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~V-D~ekg~IdLS~K~v~~ 93 (319)
T PTZ00248 16 EEDDLVMVKVVRITEM-GAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRV-DKEKGYIDLSKKRVSP 93 (319)
T ss_pred CCCCEEEEEEEEEeCC-eEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEE-eCCCCEEEEEeeeccc
Confidence 3799999999999999 9999995 456999999999998875 4999999999999999 8889999999999999
Q ss_pred CccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCC-CCCcccc------cCccccceeeehhh-hhhhcc
Q 005716 348 NIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKP-EEEGLLS------THPYVDKLWQIHNA-EQLILD 419 (681)
Q Consensus 348 nPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~-efgafve------~hP~VegL~hIs~a-EQmiLd 419 (681)
+||..+..+|+.|.+++ +.|++ +. .||+|++ ..|.++++.|++.| ++.|.+
T Consensus 94 ~pw~~~~e~~~~g~~v~-------~~V~~--------------ia~~~g~~~eely~~i~~pl~~~~gh~y~af~~~v~~ 152 (319)
T PTZ00248 94 EDIEACEEKFSKSKKVH-------SIMRH--------------IAQKHGMSVEELYTKIIWPLYKKYGHALDALKEALTN 152 (319)
T ss_pred chHHHHHHhCcCCCEEE-------EEEEE--------------chhhcCCCHHHHHHHHHHHHHHhcCCHHHHHHHHhcC
Confidence 99999999999999999 99999 64 4999999 79999999999988 555553
No 4
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.90 E-value=3e-24 Score=227.42 Aligned_cols=121 Identities=26% Similarity=0.391 Sum_probs=113.9
Q ss_pred CCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccccc---ccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 269 LPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRH---HIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 269 L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~d---VLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
+..|++|++++|+|++|++| |||||||| .+||||+|+|||.++.+ ++++||.|+|+|+++ |++++||+||+|.+
T Consensus 203 ~~~lk~G~iv~G~V~~i~~~-G~FVdlgg-v~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~i-D~e~~rI~LSlK~~ 279 (486)
T PRK07899 203 LNQLQKGQVRKGVVSSIVNF-GAFVDLGG-VDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDV-DMDRERVSLSLKAT 279 (486)
T ss_pred HHhccCCCEEEEEEEEEECC-eEEEEECC-EEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEE-ECCCCEEEEEEeec
Confidence 35789999999999999999 99999987 59999999999988764 899999999999999 78899999999999
Q ss_pred CCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 346 QPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 346 ~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
.++||..+..++++|.++. |+|.+ +..||+||++.++|+||+|+|..
T Consensus 280 ~~dPw~~~~~~~~vG~vv~-------G~V~~--------------I~~fGvFVeL~~gieGLvh~SeL 326 (486)
T PRK07899 280 QEDPWQQFARTHAIGQIVP-------GKVTK--------------LVPFGAFVRVEEGIEGLVHISEL 326 (486)
T ss_pred cccchhhhHHhcCCCCEEE-------EEEEE--------------EeccEEEEEeCCCcEEEEEHHHc
Confidence 9999999999999999999 99999 99999999999999999999754
No 5
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.89 E-value=1.4e-23 Score=220.61 Aligned_cols=121 Identities=21% Similarity=0.266 Sum_probs=113.5
Q ss_pred CCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccc-ccc---ccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 270 PFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDW-YWI---RHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 270 ~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW-~rI---~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
..+++|++++|+|++|++| ||||+|+.+.+||||+|+|+| .++ .+++++||+|+|+|+++ |+++.||+||+|.+
T Consensus 288 ~~~~~G~~v~G~V~~v~~~-G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~i-D~e~~ri~Ls~K~~ 365 (491)
T PRK13806 288 DRLKAGDKVTGKVVRLAPF-GAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDI-DPAKRRISLSLRDA 365 (491)
T ss_pred ccCCCCCEEEEEEEEEeCc-eEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEE-EccCCEEEEEEeec
Confidence 5789999999999999999 999999866799999999999 444 45999999999999999 78889999999999
Q ss_pred CCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 346 QPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 346 ~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
.++||..+..+|++|.+++ |+|.+ +..||+||++.|+|+||+|+|..
T Consensus 366 ~~~p~~~~~~~~~vG~~v~-------G~V~~--------------i~~~G~FV~l~~gv~Gli~~se~ 412 (491)
T PRK13806 366 EGDPWADVAERFAPGTTVT-------GTVEK--------------RAQFGLFVNLAPGVTGLLPASVI 412 (491)
T ss_pred ccChhHHhhhhCCCCCEEE-------EEEEE--------------EecCceEEEcCCCcEEEEEHHHc
Confidence 9999999999999999999 99999 99999999999999999999864
No 6
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.89 E-value=1.1e-23 Score=235.27 Aligned_cols=121 Identities=18% Similarity=0.294 Sum_probs=113.5
Q ss_pred CCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccc-ccc---ccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 270 PFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDW-YWI---RHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 270 ~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW-~rI---~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
+.+++|++++|+|++|++| ||||+|+.+.+|||||||+|| .++ .+++++||+|+|+||++ |+++.||+||+|.+
T Consensus 574 ~~~~vG~iV~G~V~~I~~f-G~fVeL~~gveGLvhiSEls~~~~~~~p~~~~kvGd~V~vkVl~i-D~e~~rIsLS~K~l 651 (863)
T PRK12269 574 NKFGVNDVVKGRVTKIADF-GAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGY-DIQAGRVSLGLKQV 651 (863)
T ss_pred ccCCCCCEEEEEEEEEeCC-eEEEEecCCceeeeEHHHhcCccccCCHHHcCCCCCEEEEEEEEE-ecccCceEEEehhc
Confidence 4589999999999999999 999999866799999999999 454 45899999999999999 88899999999999
Q ss_pred CCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 346 QPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 346 ~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
.+|||+.+.++|++|.+++ +.|.+ .+.||+||++.|+|+||+|+|..
T Consensus 652 ~~~Pw~~~~~~~~vG~~v~-------G~V~~--------------i~~~G~fV~l~~gV~GlIh~sel 698 (863)
T PRK12269 652 TANPWEEIEARYPVGARFT-------RRIVK--------------VTNAGAFIEMEEGIDGFLHVDDL 698 (863)
T ss_pred ccCchHHHHHhCCCCCEEE-------EEEEE--------------EecceEEEEeCCCcEEEEEhHHh
Confidence 9999999999999999999 99999 99999999999999999998764
No 7
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=99.87 E-value=9.9e-23 Score=227.77 Aligned_cols=122 Identities=17% Similarity=0.345 Sum_probs=115.2
Q ss_pred CCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 269 LPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 269 L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
++.+++|++|+|+|++|++| |||||+|| .+||||+|+|||.++. +++++||+|+|+||++ |++++||.||+|.+
T Consensus 488 ~~~l~~G~~V~G~Vk~i~~~-G~fVdl~G-v~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~i-D~e~~rI~LSlK~l 564 (863)
T PRK12269 488 FNSVHIEDSVSGVVKSFTSF-GAFIDLGG-FDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRL-DQAEKRINLSLKHF 564 (863)
T ss_pred HhcCCCCCEEEEEEEEEeCC-cEEEEECC-EEEEEEchhccccccCCHHHhccCCCEEEEEEEEE-ecCCCeEEEEEecc
Confidence 56899999999999999999 99999987 4999999999998875 5889999999999999 78899999999999
Q ss_pred CCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 346 QPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 346 ~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
.++||..+.++|++|.|+. |+|.+ +.+||+||++.|+|+||+|||...
T Consensus 565 ~~~p~~~~~~~~~vG~iV~-------G~V~~--------------I~~fG~fVeL~~gveGLvhiSEls 612 (863)
T PRK12269 565 QPDPWLEFENKFGVNDVVK-------GRVTK--------------IADFGAFIELAEGIEGLAHISEFS 612 (863)
T ss_pred ccchhhhhhccCCCCCEEE-------EEEEE--------------EeCCeEEEEecCCceeeeEHHHhc
Confidence 9999999999999999999 99999 899999999999999999998763
No 8
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=99.87 E-value=1.3e-22 Score=213.18 Aligned_cols=124 Identities=19% Similarity=0.315 Sum_probs=113.0
Q ss_pred CCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCC---Ceeeeee
Q 005716 269 LPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYR---FRFPIEM 342 (681)
Q Consensus 269 L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR---~RISLSL 342 (681)
+..+++|++++|+|++|++| |||||||++.+||||+|++||.++. +++++||+|+|+|++++...+ .||+||+
T Consensus 197 ~~~l~~G~iv~G~V~~v~~~-G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~ 275 (491)
T PRK13806 197 METVKEGDVVEGTVTRLAPF-GAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSI 275 (491)
T ss_pred HhhCCCCCEEEEEEEEEeCC-eEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEe
Confidence 34689999999999999999 9999997667999999999998764 589999999999999943332 5899999
Q ss_pred eccCCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 343 RFVQPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 343 K~~~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
|.+.++||..+..++++|.++. |+|.+ ...||+||++.|+|+||+|+|..-
T Consensus 276 K~~~~~p~~~~~~~~~~G~~v~-------G~V~~--------------v~~~G~fV~l~~gv~Glvh~sels 326 (491)
T PRK13806 276 KQAGGDPWDTVGDRLKAGDKVT-------GKVVR--------------LAPFGAFVEILPGIEGLVHVSEMS 326 (491)
T ss_pred hhhhcccchhhhccCCCCCEEE-------EEEEE--------------EeCceEEEEeCCCcEEEEEHHHcC
Confidence 9999999999999999999999 99999 999999999999999999998754
No 9
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.86 E-value=4.6e-22 Score=209.30 Aligned_cols=122 Identities=23% Similarity=0.389 Sum_probs=114.2
Q ss_pred CCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccccc---ccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 269 LPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRH---HIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 269 L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~d---VLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
+.+|++|++++|+|++|++| |||||||| .+||||+||+||.++.+ ++++||+|+|+|+++ |++++||+||+|.+
T Consensus 196 ~~~l~~G~iv~g~V~~v~~~-G~~V~i~g-~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~-d~~~~~i~lS~k~~ 272 (565)
T PRK06299 196 LENLEEGQVVEGVVKNITDY-GAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKF-DKEKKRVSLGLKQL 272 (565)
T ss_pred HhcCCCCCEEEEEEEEEeCC-eEEEEECC-EEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEE-eCCCCeEEEEEEec
Confidence 46789999999999999999 99999995 69999999999987654 799999999999999 78889999999999
Q ss_pred CCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 346 QPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 346 ~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
.+|||..+...|++|.|+. +.|.+ ...+|+||++.|+|+||+|++...
T Consensus 273 ~~~p~~~~~~~~~~G~~v~-------g~V~~--------------i~~~G~fV~l~~~v~Glv~~sel~ 320 (565)
T PRK06299 273 GEDPWEAIEKKYPVGSKVK-------GKVTN--------------ITDYGAFVELEEGIEGLVHVSEMS 320 (565)
T ss_pred ccChhHHHHhhCCCCCEEE-------EEEEE--------------EeCCeEEEEeCCCCEEEEEHHHcC
Confidence 9999999999999999999 99999 889999999999999999998763
No 10
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=1.5e-21 Score=178.70 Aligned_cols=80 Identities=28% Similarity=0.358 Sum_probs=72.4
Q ss_pred CCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccc---ccccccccCCEEEEEEEEeeCCCCCeeeeeeeccCC
Q 005716 271 FYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWY---WIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQP 347 (681)
Q Consensus 271 ~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~---rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~p 347 (681)
.+++|++|+|+||+|++| ||||+|.++.+||||||||+.. +|.++|+|||+|+|+||+||+ +++||||||.+..
T Consensus 2 ~~kvG~~l~GkItgI~~y-GAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide--~GKisLSIr~~~e 78 (129)
T COG1098 2 SMKVGSKLKGKITGITPY-GAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE--NGKISLSIRKLEE 78 (129)
T ss_pred CccccceEEEEEEeeEec-ceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc--CCCcceehHHhhh
Confidence 478999999999999999 9999998878999999999885 556799999999999999954 8999999999999
Q ss_pred Cccccc
Q 005716 348 NIDHLI 353 (681)
Q Consensus 348 nPW~~I 353 (681)
.|-..-
T Consensus 79 ~pe~~~ 84 (129)
T COG1098 79 EPEKQH 84 (129)
T ss_pred Cccccc
Confidence 886543
No 11
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.83 E-value=9e-21 Score=191.15 Aligned_cols=121 Identities=24% Similarity=0.338 Sum_probs=113.1
Q ss_pred CCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeeccC
Q 005716 270 PFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQ 346 (681)
Q Consensus 270 ~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~ 346 (681)
..+++|++|+|+|++|++| |+||+||+ .+|+||+|+++|.++. +++++||.|+|+|+++ |+.+.||.||+|.+.
T Consensus 188 ~~~~~G~~v~g~V~~v~~~-G~fV~l~~-v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~v-d~~~~~i~lS~k~~~ 264 (390)
T PRK06676 188 SSLKEGDVVEGTVARLTDF-GAFVDIGG-VDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSI-DWETERISLSLKDTL 264 (390)
T ss_pred hhCCCCCEEEEEEEEEecc-eEEEEeCC-eEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEE-eCCCCEEEEEEeecc
Confidence 5678999999999999999 99999987 5999999999998765 4899999999999999 788899999999999
Q ss_pred CCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 347 PNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 347 pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
++||+.+...+..|.+++ +.|.+ ...+|.||++.++++||+|+|...
T Consensus 265 ~~~~~~~~~~~~~G~~v~-------g~V~~--------------i~~~G~fV~l~~gi~Glv~~se~~ 311 (390)
T PRK06676 265 PGPWEGVEEKLPEGDVIE-------GTVKR--------------LTDFGAFVEVLPGVEGLVHISQIS 311 (390)
T ss_pred cCccccchhhhcCCcEEE-------EEEEE--------------EeCceEEEEECCCCeEEEEhHHcC
Confidence 999999999999999999 99999 899999999999999999999654
No 12
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=99.82 E-value=7e-21 Score=210.36 Aligned_cols=97 Identities=35% Similarity=0.471 Sum_probs=89.5
Q ss_pred CCCCCCCCCcc----hhhhcccCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEE
Q 005716 251 YYPGRRKRGKD----YEEGMYELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHV 323 (681)
Q Consensus 251 ~~PGRDPR~~~----f~egv~~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeV 323 (681)
.=||||||++. |++|+.+|.+|++||+++|+|+|+++| |||||||.++|||||||++|-..|+ ++|++||.|
T Consensus 631 ~kp~rdpR~~f~~~~~~~~v~~i~dLk~Gm~leg~Vrnv~~f-gafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV 709 (780)
T COG2183 631 EKPGRDPRDEFHTPTLDEGVESITDLKPGMILEGTVRNVVDF-GAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIV 709 (780)
T ss_pred hcCCCCCcccccccchhhhhhhHhhccCCCEEEEEEEEeeec-cceEEeccccceeeeHHHhhhhhcCChHHhcccCCEE
Confidence 34899999994 999999999999999999999999999 9999999999999999999987665 599999999
Q ss_pred EEEEEEeeCCCCCeeeeeeeccCCCc
Q 005716 324 IVEILAKRDPYRFRFPIEMRFVQPNI 349 (681)
Q Consensus 324 kVKVLsIdD~eR~RISLSLK~~~pnP 349 (681)
+|+|++| |..|+||+|||+......
T Consensus 710 ~v~V~~v-D~~r~rI~Lsmr~~~~~~ 734 (780)
T COG2183 710 KVKVIEV-DTARKRIALSMRLDEEEG 734 (780)
T ss_pred EEEEEEE-ecccCeeeeEeeccCCcc
Confidence 9999999 899999999998765443
No 13
>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=99.82 E-value=1.6e-20 Score=194.82 Aligned_cols=121 Identities=21% Similarity=0.382 Sum_probs=113.3
Q ss_pred CCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccccc---ccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 269 LPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRH---HIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 269 L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~d---VLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
++.|++|++++|+|++|++| |+|||+|| .+||||+|++||.++.+ ++++||+|.|+|+++ |+++++|.||+|.+
T Consensus 182 ~~~l~~G~~v~g~V~~i~~~-G~~V~l~g-~~g~lp~~e~s~~~~~~~~~~~~vG~~v~v~Vl~~-d~~~~~i~lS~k~~ 258 (516)
T TIGR00717 182 LENLKEGDVVKGVVKNITDF-GAFVDLGG-VDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKF-DKEKGRISLSLKQL 258 (516)
T ss_pred HHhccCCCEEEEEEEEEECC-eEEEEECC-EEEEEEHHHcCCCCCCCHHHhccCCCEEEEEEEEE-ECCCCcEEEEEEec
Confidence 45689999999999999999 99999987 59999999999988764 799999999999999 77889999999999
Q ss_pred CCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 346 QPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 346 ~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
.++||..+...++.|.|+. +.|.+ ...+|+||++.++|+||+|++..
T Consensus 259 ~~~p~~~~~~~~~~G~i~~-------g~V~~--------------v~~~G~fV~l~~~v~g~v~~sel 305 (516)
T TIGR00717 259 GEDPWEAIEKKFPVGDKIT-------GRVTN--------------LTDYGVFVEIEEGIEGLVHVSEM 305 (516)
T ss_pred chhHHHHHHhhccCCCEEE-------EEEEE--------------eeCCcEEEEeCCCCEEEEEHHHc
Confidence 9999999999999999999 99999 88999999999999999999964
No 14
>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=99.81 E-value=3.7e-20 Score=192.09 Aligned_cols=121 Identities=17% Similarity=0.247 Sum_probs=112.8
Q ss_pred CCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc----ccccccCCEEEEEEEEeeCCCCCeeeeeeeccC
Q 005716 271 FYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI----RHHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQ 346 (681)
Q Consensus 271 ~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI----~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~ 346 (681)
.+.+|++++|+|++|++| ||||+||.+.+||||+|+++|.+. ...+++||.|.|+|+++ |+.++||.||+|.+.
T Consensus 356 ~~~~G~~v~g~V~~v~~~-G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~v-d~~~~~i~ls~K~~~ 433 (516)
T TIGR00717 356 KHPVGDRVTGKIKKITDF-GAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAV-DKEKKRISLGVKQLT 433 (516)
T ss_pred hCCCCCEEEEEEEEEecc-eEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEE-eCcCCEEEEeecccc
Confidence 478999999999999999 999999977799999999999653 35899999999999999 788899999999999
Q ss_pred CCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 347 PNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 347 pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
+|||..+...++.|.+++ |.|.+ ..++|+||++.++++||+|++..-
T Consensus 434 ~~p~~~~~~~~~~G~~v~-------g~V~~--------------v~~~G~fV~l~~~~~Glv~~s~l~ 480 (516)
T TIGR00717 434 ENPWEKFAAKYKVGSVVK-------GKVTE--------------IKDFGAFVELPGGVEGLIRNSELS 480 (516)
T ss_pred CCchhhhhhccCcceEEE-------EEEEE--------------EecceEEEEcCCCeEEEEEHHHcC
Confidence 999999999999999999 99999 999999999999999999999753
No 15
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.79 E-value=1.3e-19 Score=190.91 Aligned_cols=123 Identities=20% Similarity=0.272 Sum_probs=114.2
Q ss_pred CCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc----ccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 270 PFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI----RHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 270 ~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI----~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
..+++|++|+|+|++|++| ||||+||.+.+||||+|+++|.++ .+.+++||.|+|+|+++ |..++||.||+|.+
T Consensus 369 ~~~~~G~~v~g~V~~v~~~-G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~v-d~~~~~i~ls~k~~ 446 (565)
T PRK06299 369 EKYPVGDVVEGKVKNITDF-GAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKV-DVEKERISLGIKQL 446 (565)
T ss_pred HhCCCCCEEEEEEEEEecc-eEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEE-eCCCCEEEEEEehh
Confidence 3578999999999999999 999999966799999999999654 45899999999999999 78889999999999
Q ss_pred CCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhhh
Q 005716 346 QPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAEQ 415 (681)
Q Consensus 346 ~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aEQ 415 (681)
.++||..+...++.|.+++ |.|.+ ...+|+||.+.++|.||+|+|.+..
T Consensus 447 ~~~p~~~~~~~~~~G~vV~-------G~V~~--------------v~~~G~fV~l~~gi~g~i~~se~s~ 495 (565)
T PRK06299 447 EEDPFEEFAKKHKKGSIVT-------GTVTE--------------VKDKGAFVELEDGVEGLIRASELSR 495 (565)
T ss_pred hcCchhHHHhhcCCCCEEE-------EEEEE--------------EecCceEEecCCCcEEEEEHHHhcc
Confidence 9999999999999999999 99999 9999999999999999999998743
No 16
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.78 E-value=2.8e-19 Score=193.48 Aligned_cols=122 Identities=25% Similarity=0.387 Sum_probs=113.7
Q ss_pred CCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 269 LPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 269 L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
+.++++|+++.|+|++|++| |+||+|+| .+||||+|+++|.++. +.+++||.|+|+|+++ |+.+++|.||+|.+
T Consensus 472 ~~~l~~G~iV~g~V~~v~~~-G~fV~l~g-v~Gll~~sels~~~~~~~~~~~~vGd~V~vkV~~i-d~~~~~I~lS~K~~ 548 (647)
T PRK00087 472 WNSLEEGDVVEGEVKRLTDF-GAFVDIGG-VDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDI-DKENKKLSLSLKKL 548 (647)
T ss_pred HHhCCCCCEEEEEEEEEeCC-cEEEEECC-EEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEE-ECCCCEEEEEeecc
Confidence 45688999999999999999 99999965 5999999999998765 4899999999999999 78889999999999
Q ss_pred CCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 346 QPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 346 ~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
.++||..+..++++|.++. +.|.+ ..+||+||++.++++||+|++...
T Consensus 549 ~~~p~~~~~~~~~~G~~v~-------g~V~~--------------i~~~G~fV~l~~~i~Gli~~sel~ 596 (647)
T PRK00087 549 LPDPWENVEEKYPVGSIVL-------GKVVR--------------IAPFGAFVELEPGVDGLVHISQIS 596 (647)
T ss_pred ccChhhhhhhhccCCeEEE-------EEEEE--------------EECCeEEEEECCCCEEEEEhhhcC
Confidence 9999999999999999999 99999 999999999999999999998754
No 17
>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=99.74 E-value=4.1e-18 Score=139.36 Aligned_cols=68 Identities=18% Similarity=0.290 Sum_probs=62.7
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc------cccccCCEEEEEEEEeeCCCCCeeeee
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR------HHIKVGMHVIVEILAKRDPYRFRFPIE 341 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~------dVLKVGDeVkVKVLsIdD~eR~RISLS 341 (681)
|++|++|+|+|++|++| ||||+|+.+.+|+||+|+|||.+++ +++++||.|+|+|+++ |+++.||.||
T Consensus 1 ~k~G~~V~g~V~~i~~~-G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~i-d~~~~~i~LS 74 (74)
T cd05705 1 IKEGQLLRGYVSSVTKQ-GVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSV-NSEKNLVELS 74 (74)
T ss_pred CCCCCEEEEEEEEEeCC-cEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEE-ECCCCEEecC
Confidence 58999999999999999 9999998778999999999997743 5899999999999999 7888999987
No 18
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.74 E-value=2.8e-18 Score=173.08 Aligned_cols=119 Identities=14% Similarity=0.171 Sum_probs=109.7
Q ss_pred CCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeeccC-
Q 005716 271 FYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQ- 346 (681)
Q Consensus 271 ~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~- 346 (681)
.+++|++|+|+|++|+++ |||||||+..+|+||+||++|..+. +++++||+|+|+|+++ +..+.+|.||+|.+.
T Consensus 28 ~~~~G~iv~G~V~~i~~~-g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~-~~~~~~i~lS~k~~~~ 105 (318)
T PRK07400 28 HFKPGDIVNGTVFSLEPR-GALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSD-ENEDGQLTLSIRRIEY 105 (318)
T ss_pred hcCCCCEEEEEEEEEECC-EEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEE-eCCCCeEEEehhhhhh
Confidence 489999999999999999 9999999989999999999998764 5899999999999999 566789999999886
Q ss_pred CCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 347 PNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 347 pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
.++|+.+...+..+.++. +.|.. ...+|+||.+ .||+||+|+|..
T Consensus 106 ~~~w~~l~~~~~~~~~V~-------g~V~~--------------~~~~G~~V~l-~Gv~gfip~s~l 150 (318)
T PRK07400 106 MRAWERVRQLQKEDATVR-------SEVFA--------------TNRGGALVRI-EGLRGFIPGSHI 150 (318)
T ss_pred hhHHHHHHHhccCCCEEE-------EEEEE--------------EECCeEEEEE-CCEEEEEEHHHc
Confidence 499999999999999999 99999 8899999999 699999999974
No 19
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=99.73 E-value=5.1e-18 Score=171.22 Aligned_cols=114 Identities=18% Similarity=0.218 Sum_probs=101.5
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeeeeeccCCCcccc
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQPNIDHL 352 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~pnPW~~ 352 (681)
..|++|+|+|++++++ |+||||+|. .||||+|++||...++.+ +|+.|+|+||++ |+++.||.||+|..... .
T Consensus 117 ~~~~~V~g~V~~~~~~-G~~V~l~Gv-~gfip~s~ls~~~~~~~~-vG~~i~~kVl~i-d~~~~~i~lS~K~~~~~---~ 189 (318)
T PRK07400 117 KEDATVRSEVFATNRG-GALVRIEGL-RGFIPGSHISTRKPKEEL-VGEELPLKFLEV-DEERNRLVLSHRRALVE---R 189 (318)
T ss_pred cCCCEEEEEEEEEECC-eEEEEECCE-EEEEEHHHcCccCCcccc-CCCEEEEEEEEE-EcccCEEEEEhhHhhhh---h
Confidence 3589999999999999 999999865 999999999998777765 999999999999 78889999999976543 3
Q ss_pred ccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhhh
Q 005716 353 IFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAEQ 415 (681)
Q Consensus 353 I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aEQ 415 (681)
...++++|.|+. |.|.+ .+.||+||.+ .+|+||+|++.+-.
T Consensus 190 ~~~~~k~G~vv~-------G~V~~--------------I~~~G~fV~i-~gv~Gllhisels~ 230 (318)
T PRK07400 190 KMNRLEVGEVVV-------GTVRG--------------IKPYGAFIDI-GGVSGLLHISEISH 230 (318)
T ss_pred hhccCCCCCEEE-------EEEEE--------------EECCeEEEEE-CCEEEEEEHHHccc
Confidence 567899999999 99999 9999999998 58999999997643
No 20
>PRK08582 hypothetical protein; Provisional
Probab=99.72 E-value=1.6e-17 Score=151.26 Aligned_cols=78 Identities=24% Similarity=0.335 Sum_probs=72.0
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeeccCCC
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQPN 348 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~pn 348 (681)
+++|++|+|+|++|++| ||||+|+++.+||||||+++|..+. ++|++||+|+|+|++|+ . ..+|.||||.+.++
T Consensus 3 ~kvG~iv~G~V~~I~~f-G~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id-~-~gkI~LSlk~~~~~ 79 (139)
T PRK08582 3 IEVGSKLQGKVTGITNF-GAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE-D-DGKIGLSIKKAKDR 79 (139)
T ss_pred CcCCCEEEEEEEEEECC-eEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEEC-C-CCcEEEEEEecccC
Confidence 78999999999999999 9999998888999999999997764 58999999999999994 4 48999999999999
Q ss_pred cccc
Q 005716 349 IDHL 352 (681)
Q Consensus 349 PW~~ 352 (681)
||..
T Consensus 80 ~~~~ 83 (139)
T PRK08582 80 PKRQ 83 (139)
T ss_pred chhh
Confidence 9975
No 21
>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=99.71 E-value=3.2e-17 Score=134.61 Aligned_cols=72 Identities=19% Similarity=0.231 Sum_probs=67.4
Q ss_pred CCCCCCEEEEEEEEeeecceeEEEcC-CceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeeeeeccCC
Q 005716 271 FYYPGQICEGKVTTVHLYQGAFVDIG-GVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQP 347 (681)
Q Consensus 271 ~LkeGqIVEGkVtnItdF~GAFVDIG-Gv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~p 347 (681)
+|++|++|.|+|++|++| |+|||+| ++.+||||+|+++|. ..+++||.|.|+|+++ |+++++|.||+|.+.+
T Consensus 1 dl~~G~~v~g~V~si~d~-G~~v~~g~~gv~Gfl~~~~~~~~---~~~~~Gq~v~~~V~~v-d~~~~~v~ls~k~~~~ 73 (74)
T cd05694 1 DLVEGMVLSGCVSSVEDH-GYILDIGIPGTTGFLPKKDAGNF---SKLKVGQLLLCVVEKV-KDDGRVVSLSADPSKV 73 (74)
T ss_pred CCCCCCEEEEEEEEEeCC-EEEEEeCCCCcEEEEEHHHCCcc---cccCCCCEEEEEEEEE-ECCCCEEEEEEeeccc
Confidence 589999999999999999 9999998 456999999999998 9999999999999999 7899999999998865
No 22
>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=99.69 E-value=6.6e-17 Score=130.64 Aligned_cols=68 Identities=25% Similarity=0.211 Sum_probs=62.2
Q ss_pred CCCCCEEEEEEEEeee-cceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 272 YYPGQICEGKVTTVHL-YQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 272 LkeGqIVEGkVtnItd-F~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
|++|+++.|+|++|.+ | ||||+|+.+.+||||||++||.++. +++++||.|+|+|++++ ++||.||+|
T Consensus 1 l~~G~iv~G~V~~i~~~~-g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~---~~~i~LSl~ 72 (72)
T cd05704 1 LEEGAVTLGMVTKVIPHS-GLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKK---DGKYQLSLR 72 (72)
T ss_pred CCCCCEEEEEEEEeeCCc-EEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEec---CCEEEEEeC
Confidence 5799999999999996 7 9999999888999999999998775 58999999999999994 389999986
No 23
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.68 E-value=3.2e-17 Score=165.56 Aligned_cols=149 Identities=17% Similarity=0.193 Sum_probs=126.6
Q ss_pred chhhhcccCCCCCCCCEEEEEEEEeeecceeEEEc-CCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCC
Q 005716 261 DYEEGMYELPFYYPGQICEGKVTTVHLYQGAFVDI-GGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRF 336 (681)
Q Consensus 261 ~f~egv~~L~~LkeGqIVEGkVtnItdF~GAFVDI-GGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~ 336 (681)
.|.+-+..+.++++|++|+|+|++|+++ |+|||| |++.+|+||.+|++|.++. ..+++||+|+|+|+++ +..++
T Consensus 4 ~~~~~~~~~~~~~~G~iv~G~V~~i~~~-g~~V~i~~~~~~g~lp~~e~~~~~~~~~~~~~~vGd~v~~~V~~v-~~~~~ 81 (390)
T PRK06676 4 EFEESLNSVKEVEVGDVVTGEVLKVEDK-QVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKV-EDGEG 81 (390)
T ss_pred HHHHHhhhhhcccCCCEEEEEEEEEECC-eEEEEEecCCcEEEEEHHHhccccccCcccccCCCCEEEEEEEEE-ECCCC
Confidence 4677788899999999999999999998 999999 7678999999999996554 4899999999999999 56667
Q ss_pred eeeeeeeccCC-CccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhhh
Q 005716 337 RFPIEMRFVQP-NIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAEQ 415 (681)
Q Consensus 337 RISLSLK~~~p-nPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aEQ 415 (681)
++.||+|.+.. .+|+.+...+..|.|++ +.|.+ ...+|.||.+ .|++|++|++.+-.
T Consensus 82 ~i~lS~k~~~~~~~~~~~~~~~~~G~~v~-------g~V~~--------------v~~~G~~V~~-~G~~gflp~~el~~ 139 (390)
T PRK06676 82 NLLLSKRRLEAEKAWDKLEEKFEEGEVVE-------VKVTE--------------VVKGGLVVDV-EGVRGFIPASLIST 139 (390)
T ss_pred CEEEEHHHhhhhhhHHHHHHhccCCCEEE-------EEEEE--------------EECCeEEEEE-CCEEEEEEHHHcCC
Confidence 99999998765 78999999999999999 99999 7788999999 69999999985432
Q ss_pred hhccccccCccccCCccccccC
Q 005716 416 LILDDMEANPDKYKGKKLSELT 437 (681)
Q Consensus 416 miLdd~e~npdky~~~~~~~l~ 437 (681)
+...++.+|.|+.+.-..
T Consensus 140 ----~~~~~~~~~vG~~v~~~V 157 (390)
T PRK06676 140 ----RFVEDFSDFKGKTLEVKI 157 (390)
T ss_pred ----ccCCChHHcCCCEEEEEE
Confidence 334456677887765433
No 24
>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=99.68 E-value=9.3e-17 Score=131.06 Aligned_cols=74 Identities=23% Similarity=0.362 Sum_probs=67.6
Q ss_pred ccCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 267 YELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 267 ~~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
.++.++++|+++.|+|++|++| |+||+|+++.+|+||+|+++|.++. +++++||+|+|+|+++ |.++.+|.|||
T Consensus 7 ~~~~~~~~G~i~~g~V~~v~~~-G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~i-d~~~~~i~lsl 83 (83)
T cd04461 7 TNFSDLKPGMVVHGYVRNITPY-GVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSV-DEEKQRFLLSL 83 (83)
T ss_pred hhHHhCCCCCEEEEEEEEEeec-eEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEE-cCCCCEEEEeC
Confidence 3567799999999999999999 9999998778999999999998764 4999999999999999 78889999996
No 25
>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=99.67 E-value=2.1e-16 Score=127.23 Aligned_cols=67 Identities=27% Similarity=0.407 Sum_probs=59.9
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCc-eeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGV-YDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv-~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
+.|++++|+|++|++| |+||+|.+. .+||||+|+++|.++. +++++||+|+|+|+++ |..+ |++|||
T Consensus 2 ~~g~~~~g~V~~i~~f-G~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~v-d~~~-ki~ls~ 72 (73)
T cd05686 2 ALYQIFKGEVASVTEY-GAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGR-EMKD-KMKLSL 72 (73)
T ss_pred cCCCEEEEEEEEEEee-eEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEE-CCCC-cEEEEe
Confidence 5899999999999999 999999653 6999999999998775 4899999999999999 5555 999987
No 26
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=99.67 E-value=6.4e-17 Score=172.11 Aligned_cols=142 Identities=16% Similarity=0.153 Sum_probs=122.1
Q ss_pred CCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc---ccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 269 LPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI---RHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 269 L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI---~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
+..+++|++|+|+|++|+++ |+|||||...+|+||++|+||.+. .+++++||+|+|+|+++ +..++++.||+|.+
T Consensus 30 ~~~~~~GdiV~G~V~~v~~~-gv~VdIg~k~eG~Ip~~Els~~~~~~~~~~~~vGd~Ie~~V~~~-~~~~g~liLS~k~~ 107 (486)
T PRK07899 30 IKYFNDGDIVEGTVVKVDRD-EVLLDIGYKTEGVIPSRELSIKHDVDPNEVVEVGDEVEALVLQK-EDKEGRLILSKKRA 107 (486)
T ss_pred HhcCCCCCEEEEEEEEEECC-cEEEEECCCcEEEEEHHHhcccccCChhhcCCCCCEEEEEEEEE-ECCCCeEEEEehhh
Confidence 56789999999999999999 999999988899999999999765 45899999999999999 55668999999988
Q ss_pred C-CCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhhhhhccccccC
Q 005716 346 Q-PNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAEQLILDDMEAN 424 (681)
Q Consensus 346 ~-pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aEQmiLdd~e~n 424 (681)
. .++|..+.+.+..|.++. ++|.+ ....|.||.+ |+.|++|+|..+. ..-.+
T Consensus 108 ~~~~~w~~ie~~~e~g~~V~-------G~V~~--------------v~k~G~~Vdl--Gi~gflP~Sel~~----~~~~~ 160 (486)
T PRK07899 108 QYERAWGTIEKIKEKDGVVT-------GTVIE--------------VVKGGLILDI--GLRGFLPASLVEM----RRVRD 160 (486)
T ss_pred cccchHHHHHHHhcCCCEEE-------EEEEE--------------EECCeEEEEE--CCEEEEEhhHhcc----cccCC
Confidence 7 899999999999999999 99999 8889999999 8999999986542 11235
Q ss_pred ccccCCccccccCCC
Q 005716 425 PDKYKGKKLSELTDD 439 (681)
Q Consensus 425 pdky~~~~~~~l~d~ 439 (681)
+.+|.|+.+.-..-+
T Consensus 161 ~~~~vGq~V~vkVle 175 (486)
T PRK07899 161 LQPYIGQEIEAKIIE 175 (486)
T ss_pred hhhcCCCEEEEEEEE
Confidence 667888887655543
No 27
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=99.65 E-value=1.1e-16 Score=180.07 Aligned_cols=82 Identities=21% Similarity=0.348 Sum_probs=74.1
Q ss_pred CCCCCEEE-EEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeeccCC
Q 005716 272 YYPGQICE-GKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQP 347 (681)
Q Consensus 272 LkeGqIVE-GkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~p 347 (681)
.++|++++ |+|++|++| ||||+|+.+.+||||||+|+|.++. +++++||+|+|+|++| |. ++||+||+|.+.+
T Consensus 751 ~~vG~iy~~g~V~~I~~F-GaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~I-D~-~grI~LSlK~l~~ 827 (891)
T PLN00207 751 PTVGDIYRNCEIKSIAPY-GAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEV-ND-KGQLRLSRRALLP 827 (891)
T ss_pred cCCCcEEECcEEEEEecc-EEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEE-CC-CCcEEEEEecccc
Confidence 46999995 699999999 9999997667999999999998765 4999999999999999 55 7899999999999
Q ss_pred Ccccccccc
Q 005716 348 NIDHLIFNR 356 (681)
Q Consensus 348 nPW~~I~er 356 (681)
|||....++
T Consensus 828 ~Pw~~~~~~ 836 (891)
T PLN00207 828 EANSEKSSQ 836 (891)
T ss_pred Cchhhhhhh
Confidence 999987663
No 28
>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=99.64 E-value=7.2e-16 Score=121.65 Aligned_cols=70 Identities=31% Similarity=0.501 Sum_probs=65.0
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccc---cccccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYW---IRHHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~r---I~dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
+++|+++.|+|++|++| |+||+||++.+|+||+|++++.. ....+++||+|+|+|+++ |.+++||.||+|
T Consensus 2 ~~~G~iv~g~V~~v~~~-g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~v-d~~~~~i~lS~k 74 (74)
T PF00575_consen 2 LKEGDIVEGKVTSVEDF-GVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKV-DKEKGRIRLSLK 74 (74)
T ss_dssp SSTTSEEEEEEEEEETT-EEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEE-ETTTTEEEEEST
T ss_pred CCCCCEEEEEEEEEECC-EEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEE-ECCCCeEEEEEC
Confidence 68999999999999999 99999997779999999999964 456999999999999999 788999999987
No 29
>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=99.62 E-value=1.2e-15 Score=119.54 Aligned_cols=67 Identities=25% Similarity=0.418 Sum_probs=61.9
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
|+++.|+|++|++| |+||+|+++.+||||+|++++.++. +.+++||+|+|+|+++ |++++||.||+|
T Consensus 1 g~~~~g~V~~v~~~-G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~-d~~~~~i~ls~k 70 (70)
T cd05698 1 GLKTHGTIVKVKPN-GCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSC-DPEQQRLLLSCK 70 (70)
T ss_pred CCEEEEEEEEEecC-cEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEE-cCCCCEEEEEeC
Confidence 89999999999999 9999998778999999999987654 4899999999999999 788899999986
No 30
>PRK07252 hypothetical protein; Provisional
Probab=99.62 E-value=1.9e-15 Score=135.18 Aligned_cols=86 Identities=24% Similarity=0.359 Sum_probs=75.1
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeeccCC-
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQP- 347 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~p- 347 (681)
+++|+++.|+|++|++| ||||+|+++.+||||+|+++|.++. +++++||.|+|+|+++ |.++.||.||+|.+.+
T Consensus 1 ~kvG~iv~G~V~~V~~~-G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~i-D~~~~ri~lSlk~~~~~ 78 (120)
T PRK07252 1 MKIGDKLKGTITGIKPY-GAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDF-DEYTGKASLSLRTLEEE 78 (120)
T ss_pred CCCCCEEEEEEEEEeCc-EEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEE-eCCCCEEEEEEeecccC
Confidence 46899999999999999 9999998778999999999997764 5899999999999999 7888999999999988
Q ss_pred CccccccccCCC
Q 005716 348 NIDHLIFNRFDF 359 (681)
Q Consensus 348 nPW~~I~erf~v 359 (681)
..|..-.++|+-
T Consensus 79 ~~~~~~~~~~~~ 90 (120)
T PRK07252 79 KQHFPHRHRFSN 90 (120)
T ss_pred ccccCccccccc
Confidence 566655555543
No 31
>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=99.61 E-value=2.7e-15 Score=118.61 Aligned_cols=71 Identities=18% Similarity=0.235 Sum_probs=63.4
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCC--ceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeec
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGG--VYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRF 344 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGG--v~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~ 344 (681)
+++|+++.|+|++|.+| |+||+|.+ +.+||||+|+++|.++. +++++||.|+|+|+++ |..+.+|.||+|.
T Consensus 1 ~~~G~~~~g~V~~v~~~-g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~-d~~~~~i~ls~k~ 76 (76)
T cd04452 1 PEEGELVVVTVKSIADM-GAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRV-DKEKGYIDLSKKR 76 (76)
T ss_pred CCCCCEEEEEEEEEEcc-EEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEE-ECCCCEEEEEEcC
Confidence 36899999999999999 99999953 36999999999998764 5899999999999999 6778999999984
No 32
>PRK05807 hypothetical protein; Provisional
Probab=99.61 E-value=2.7e-15 Score=136.23 Aligned_cols=71 Identities=27% Similarity=0.448 Sum_probs=64.6
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc---ccccccCCEEEEEEEEeeCCCCCeeeeeeeccC
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI---RHHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQ 346 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI---~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~ 346 (681)
+++|++|+|+|++|++| ||||+|++ .+||||||++++..+ .+++++||+|+|+|+++ |. ..+|+||||.+.
T Consensus 3 ~~vG~vv~G~Vt~i~~~-GafV~L~~-~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~i-d~-~gkI~LSlk~~~ 76 (136)
T PRK05807 3 LKAGSILEGTVVNITNF-GAFVEVEG-KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISI-DD-NGKISLSIKQAM 76 (136)
T ss_pred ccCCCEEEEEEEEEECC-eEEEEECC-EEEEEEhhhcccccccCccccCCCCCEEEEEEEEE-CC-CCcEEEEEEecc
Confidence 67999999999999999 99999965 599999999998776 45899999999999999 44 699999999987
No 33
>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=99.60 E-value=2.1e-15 Score=117.33 Aligned_cols=65 Identities=29% Similarity=0.495 Sum_probs=59.0
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccc-ccc---ccccccCCEEEEEEEEeeCCCCCeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDW-YWI---RHHIKVGMHVIVEILAKRDPYRFRFPIE 341 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW-~rI---~dVLKVGDeVkVKVLsIdD~eR~RISLS 341 (681)
|+++.|+|++|++| |+||+|+++.+||||+|+++| .++ .+++++||+|+|+|+++ |.++.||+||
T Consensus 1 G~~~~g~V~~i~~~-G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~i-d~~~~~i~l~ 69 (69)
T cd05690 1 GTVVSGKIKSITDF-GIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNI-DVERERISLG 69 (69)
T ss_pred CCEEEEEEEEEEee-eEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEE-ECCcCEEeCC
Confidence 78999999999999 999999877899999999998 344 45899999999999999 7888999886
No 34
>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=99.60 E-value=2.4e-15 Score=122.37 Aligned_cols=67 Identities=16% Similarity=0.189 Sum_probs=61.8
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccc--cc---cccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYW--IR---HHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~r--I~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
|++|+|+|++|++| |+||.|+.+.+|+||+|++||.. ++ +.+++||.|+++|+++ |+++.||.||+|
T Consensus 1 G~~V~g~V~~i~~~-g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~i-d~~~~~i~Ls~k 72 (73)
T cd05703 1 GQEVTGFVNNVSKE-FVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGV-DKEHKLLRLSAR 72 (73)
T ss_pred CCEEEEEEEEEeCC-EEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEE-eCCCCEEEEEec
Confidence 89999999999999 99999987789999999999863 44 4999999999999999 888899999997
No 35
>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=99.60 E-value=3.9e-15 Score=117.81 Aligned_cols=70 Identities=21% Similarity=0.151 Sum_probs=64.0
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc---ccccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI---RHHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI---~dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
|++|+++.|+|++|++| |+||+|+.+.+|+||+|+++|... .+++++||.|+|+|+++ |..+++|.||+|
T Consensus 1 ~~~G~iv~g~V~~v~~~-gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~-d~~~~~i~ls~~ 73 (73)
T cd05706 1 LKVGDILPGRVTKVNDR-YVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSV-DVPNKKIALSLR 73 (73)
T ss_pred CCCCCEEEEEEEEEeCC-eEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEE-eCCCCEEEEEEC
Confidence 57999999999999999 999999977899999999998654 45899999999999999 777899999985
No 36
>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=99.59 E-value=4.9e-15 Score=119.74 Aligned_cols=70 Identities=27% Similarity=0.446 Sum_probs=63.3
Q ss_pred CCEEEEEEEEeeecceeEEEcC---CceeeeeEccccccccc-c---cccccCCEEEEEEEEeeCCCCCeeeeeeeccCC
Q 005716 275 GQICEGKVTTVHLYQGAFVDIG---GVYDGWVPIKGNDWYWI-R---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQP 347 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIG---Gv~DGLVHISEISW~rI-~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~p 347 (681)
|+++.|+|++|++| |+||+|+ .+.+||||+|+++|.++ . +++++||+|+|+|++++ +.|+.||+|.+++
T Consensus 1 G~~~~g~V~~v~~~-G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd---~~~i~~s~k~~~~ 76 (79)
T cd05684 1 GKIYKGKVTSIMDF-GCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ---NGKISLSMKDVDQ 76 (79)
T ss_pred CCEEEEEEEEEEee-eEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe---CCEEEEEEEeccc
Confidence 78999999999999 9999998 24699999999999764 4 38999999999999994 7999999999988
Q ss_pred C
Q 005716 348 N 348 (681)
Q Consensus 348 n 348 (681)
+
T Consensus 77 ~ 77 (79)
T cd05684 77 D 77 (79)
T ss_pred C
Confidence 6
No 37
>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=99.57 E-value=1e-14 Score=114.56 Aligned_cols=71 Identities=25% Similarity=0.351 Sum_probs=64.1
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCC-ceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGG-VYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGG-v~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
++|+++.|+|++|++| |+||+|++ ..+||||+|+++|.++. +.+++||.|+|+|+++ |.++.||.||+|..
T Consensus 1 ~~g~~v~g~V~~i~~~-g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~v-d~~~~~i~ls~k~~ 75 (77)
T cd05708 1 KVGQKIDGTVRRVEDY-GVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKI-DAEKKRISLGLKAS 75 (77)
T ss_pred CCCCEEEEEEEEEEcc-eEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEE-eCCCCEEEEEEEee
Confidence 4799999999999999 99999974 57999999999997764 5899999999999999 78889999999864
No 38
>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=99.57 E-value=5.7e-15 Score=119.16 Aligned_cols=66 Identities=21% Similarity=0.220 Sum_probs=59.9
Q ss_pred CCEEE-EEEEEe-eecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 275 GQICE-GKVTTV-HLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 275 GqIVE-GkVtnI-tdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
|++++ |+|++| .+| ||||+|+.+.+||||+|++++.++. +.+++||+|+|+|+++ |+.++||+|||
T Consensus 1 G~v~~~g~V~~v~~~~-G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~i-d~~~~~i~lS~ 71 (71)
T cd05696 1 GAVVDSVKVTKVEPDL-GAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGY-SPMDGLLQLSL 71 (71)
T ss_pred CcEeeeeEEEEEccCc-eEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEE-eCCCCEEEEeC
Confidence 78999 999999 699 9999997667999999999997754 5899999999999999 78889999996
No 39
>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=99.57 E-value=7.5e-15 Score=115.71 Aligned_cols=66 Identities=24% Similarity=0.437 Sum_probs=60.6
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
|++++|+|++|.+| |+||+|+.+.+|+||+|+++|.++. +.+++||+|+|+|+++ |+.++||.|||
T Consensus 1 G~~v~g~V~~v~~~-Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~i-d~~~~~i~ls~ 69 (69)
T cd05697 1 GQVVKGTIRKLRPS-GIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSV-EPERKRLVLTL 69 (69)
T ss_pred CCEEEEEEEEEecc-EEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEE-ECCCCEEEEEC
Confidence 89999999999999 9999997668999999999987654 4899999999999999 78889999985
No 40
>PRK08059 general stress protein 13; Validated
Probab=99.57 E-value=1.1e-14 Score=129.10 Aligned_cols=80 Identities=26% Similarity=0.437 Sum_probs=73.4
Q ss_pred CCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 269 LPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 269 L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
+..+++|+++.|+|++|++| |+||+|+.+.+||||+|++++.++. +++++||+|+|+|+++ |.++.+|.||+|.+
T Consensus 2 ~~~~k~G~iv~G~V~~i~~~-G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~i-d~~~~~i~lslk~~ 79 (123)
T PRK08059 2 MSQYEVGSVVTGKVTGIQPY-GAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSV-DEEKGKISLSIRAT 79 (123)
T ss_pred cccCCCCCEEEEEEEEEecc-eEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEE-ECCCCeEEEEEEEc
Confidence 46689999999999999999 9999998778999999999998774 4899999999999999 67889999999999
Q ss_pred CCCcc
Q 005716 346 QPNID 350 (681)
Q Consensus 346 ~pnPW 350 (681)
.++|-
T Consensus 80 ~~~~~ 84 (123)
T PRK08059 80 EEAPE 84 (123)
T ss_pred ccCcc
Confidence 99884
No 41
>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=99.56 E-value=8.5e-15 Score=115.12 Aligned_cols=65 Identities=26% Similarity=0.383 Sum_probs=59.6
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIE 341 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLS 341 (681)
|+++.|+|++|++| ||||+|+++.+||||+|++++.++. +.+++||.|+|+|+++ |+++.||.||
T Consensus 1 G~~v~g~V~~v~~~-Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~-d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANN-GVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSI-DPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECc-cEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEE-eCCCCEEecC
Confidence 78999999999999 9999998778999999999987654 5899999999999999 7888999886
No 42
>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=99.55 E-value=2.1e-14 Score=109.13 Aligned_cols=66 Identities=33% Similarity=0.570 Sum_probs=60.4
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
|+++.|+|++|++| |+||+|+.+.+||||+|+++|.++. +.+++||.|+|+|+++ |. +.++.||+|
T Consensus 1 G~~~~g~V~~i~~~-g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~-~~-~~~i~ls~k 69 (69)
T cd05692 1 GSVVEGTVTRLKPF-GAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSI-DA-RGRISLSIK 69 (69)
T ss_pred CCEEEEEEEEEEee-eEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEE-CC-CCcEEEEEC
Confidence 78999999999999 9999999778999999999997764 4899999999999999 55 789999986
No 43
>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=99.55 E-value=1.9e-14 Score=112.33 Aligned_cols=69 Identities=26% Similarity=0.345 Sum_probs=63.4
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc---ccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI---RHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI---~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
|+++.|+|++|+++ |+||+|++..+|+||+|++++..+ .+++++||.|+|+|+++ |..+.++.||+|.+
T Consensus 1 G~~v~g~V~~v~~~-g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~-d~~~~~i~ls~k~~ 72 (73)
T cd05691 1 GSIVTGKVTEVDAK-GATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNV-DRKNRKISLSIKAK 72 (73)
T ss_pred CCEEEEEEEEEECC-eEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEE-eCCCCEEEEEEEEc
Confidence 88999999999999 999999877899999999998766 45899999999999999 78889999999875
No 44
>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=99.54 E-value=9.6e-15 Score=126.36 Aligned_cols=72 Identities=15% Similarity=0.263 Sum_probs=64.2
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccc----------------------cccccccCCEEEEEEEE
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYW----------------------IRHHIKVGMHVIVEILA 329 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~r----------------------I~dVLKVGDeVkVKVLs 329 (681)
|++|++|.|+|++|+++ |+||+|+++.+|+||+|+|+|.. +.+.+++||.|+++|++
T Consensus 1 L~~G~vV~G~V~~v~~~-gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~ 79 (100)
T cd05693 1 LSEGMLVLGQVKEITKL-DLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVS 79 (100)
T ss_pred CCCCCEEEEEEEEEcCC-CEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEE
Confidence 68999999999999999 99999988889999999999953 45689999999999999
Q ss_pred eeCC--CCCeeeeeeec
Q 005716 330 KRDP--YRFRFPIEMRF 344 (681)
Q Consensus 330 IdD~--eR~RISLSLK~ 344 (681)
+++. .++||.||||-
T Consensus 80 ~d~~~~~~~~i~LSlr~ 96 (100)
T cd05693 80 LDKSKSGKKRIELSLEP 96 (100)
T ss_pred ccCCcCCCcEEEEEecH
Confidence 9543 28999999974
No 45
>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=99.52 E-value=3.5e-14 Score=111.60 Aligned_cols=67 Identities=30% Similarity=0.320 Sum_probs=61.2
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
|++|.|+|++|.++ |||||||+..+|+||++|++|.++. +++++||.|+|+|+++ ++.+.+|-||+|
T Consensus 1 G~iv~g~V~~i~~~-~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~-~~~~~~i~lS~~ 70 (70)
T cd05687 1 GDIVKGTVVSVDDD-EVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRV-EDEEGNVVLSKR 70 (70)
T ss_pred CCEEEEEEEEEeCC-EEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEE-ECCCCeEEEEeC
Confidence 89999999999999 9999999888999999999998754 5899999999999999 556789999986
No 46
>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=99.52 E-value=4e-14 Score=111.84 Aligned_cols=68 Identities=31% Similarity=0.435 Sum_probs=60.3
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccc-cc---ccccccCCEEEEEEEEeeCCCCCeeeee
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWY-WI---RHHIKVGMHVIVEILAKRDPYRFRFPIE 341 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~-rI---~dVLKVGDeVkVKVLsIdD~eR~RISLS 341 (681)
+.+|+++.|+|++|++| |+||.|+.+.+||||+|+++|. +. ..++++||.|+|+|+++ |.++.||.|+
T Consensus 1 ~~~g~~~~g~V~~i~~~-G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~i-d~~~~~i~~~ 72 (72)
T cd05689 1 YPEGTRLFGKVTNLTDY-GCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDI-DEERRRISLG 72 (72)
T ss_pred CcCCCEEEEEEEEEEee-EEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEe-eCCcCEEeCC
Confidence 46899999999999999 9999997668999999999985 32 35899999999999999 7888899875
No 47
>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=99.52 E-value=4.1e-14 Score=115.71 Aligned_cols=72 Identities=22% Similarity=0.284 Sum_probs=63.7
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccc-------cccccccCCEEEEEEEEeeCCCCCeeeeeeec
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYW-------IRHHIKVGMHVIVEILAKRDPYRFRFPIEMRF 344 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~r-------I~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~ 344 (681)
.++|++|+|+|++|+++ |+||+||...+|+||+|+++|.+ +.+++++||.|+++|+++ ++. .++.||+|.
T Consensus 4 p~~GdiV~g~V~~i~~~-g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~-~~~-~~i~LS~~~ 80 (86)
T cd05789 4 PEVGDVVIGRVTEVGFK-RWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSV-DSD-GSVSLHTRS 80 (86)
T ss_pred CCCCCEEEEEEEEECCC-EEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEE-CCC-CCEEEEeCc
Confidence 47999999999999999 99999998899999999999832 345899999999999999 555 899999987
Q ss_pred cC
Q 005716 345 VQ 346 (681)
Q Consensus 345 ~~ 346 (681)
..
T Consensus 81 ~~ 82 (86)
T cd05789 81 LK 82 (86)
T ss_pred cc
Confidence 53
No 48
>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=99.51 E-value=5.4e-14 Score=119.15 Aligned_cols=75 Identities=20% Similarity=0.150 Sum_probs=63.3
Q ss_pred CCCCCCEEEEEEEEeeec-ceeEEEcCCceeeeeEcccccc---ccc---ccccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 271 FYYPGQICEGKVTTVHLY-QGAFVDIGGVYDGWVPIKGNDW---YWI---RHHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 271 ~LkeGqIVEGkVtnItdF-~GAFVDIGGv~DGLVHISEISW---~rI---~dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
.+++|+++.|+|++|++| +||||||+.+.+||||+||||| .++ .+++++||+|.|+|+.. ....+--.|+.+
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~-~~~~K~~~lt~~ 82 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKE-PIGTKGPRLTTN 82 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEe-cCCCCCceEEEE
Confidence 467999999999999996 5999999977899999999999 444 45999999999999998 666666667665
Q ss_pred ccC
Q 005716 344 FVQ 346 (681)
Q Consensus 344 ~~~ 346 (681)
.+-
T Consensus 83 ~~~ 85 (88)
T cd04453 83 ISL 85 (88)
T ss_pred EEc
Confidence 543
No 49
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=99.49 E-value=6.6e-14 Score=154.01 Aligned_cols=89 Identities=26% Similarity=0.179 Sum_probs=76.3
Q ss_pred CCCCCCc----chhhhcccC-----------CCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---c
Q 005716 254 GRRKRGK----DYEEGMYEL-----------PFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---H 315 (681)
Q Consensus 254 GRDPR~~----~f~egv~~L-----------~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---d 315 (681)
++|++.+ .|..|...+ ..+++|+++.|+|++|++| ||||+|+.+.+||||||+++|.+++ +
T Consensus 586 ~idi~d~G~v~i~~~~~~~~~~a~~~I~~~~~~~~vG~v~~G~V~~I~~f-GafVei~~~~~GllhiSels~~~v~~~~~ 664 (693)
T PRK11824 586 KIDIEDDGTVKIAATDGEAAEAAKERIEGITAEPEVGEIYEGKVVRIVDF-GAFVEILPGKDGLVHISEIADERVEKVED 664 (693)
T ss_pred ccccCCCceEEEEcccHHHHHHHHHHHHHhcccCcCCeEEEEEEEEEECC-eEEEEECCCCEEEEEeeeccCccccCccc
Confidence 3666655 255565555 6789999999999999999 9999998778999999999998775 5
Q ss_pred ccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 316 HIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 316 VLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
++++||+|+|+|+++ |.. +||+||+|.+
T Consensus 665 v~kvGD~V~VkV~~i-D~~-grI~LS~k~~ 692 (693)
T PRK11824 665 VLKEGDEVKVKVLEI-DKR-GRIRLSRKAV 692 (693)
T ss_pred eeCCCCEEEEEEEEE-CCC-CcEEEEEEec
Confidence 899999999999999 555 9999999976
No 50
>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=99.47 E-value=8.4e-14 Score=154.49 Aligned_cols=68 Identities=24% Similarity=0.259 Sum_probs=60.2
Q ss_pred CCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccc---c-ccc---ccccccCCEEEEEEEEeeCCCCCeeeee
Q 005716 271 FYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGND---W-YWI---RHHIKVGMHVIVEILAKRDPYRFRFPIE 341 (681)
Q Consensus 271 ~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEIS---W-~rI---~dVLKVGDeVkVKVLsIdD~eR~RISLS 341 (681)
.+++|++++|+|++|++| ||||+|+.+.+||||||||| | .++ .+++++||+|+|||++|| . ++||+|+
T Consensus 644 ~~~vG~i~~GkV~~I~df-GaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID-~-~gKI~L~ 718 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAF-GAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADID-D-RGKLSLV 718 (719)
T ss_pred cCCCCCEEEEEEEEEECc-eEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEEC-C-CCCeeec
Confidence 478999999999999999 99999976679999999996 4 555 459999999999999994 3 7899986
No 51
>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=99.46 E-value=2e-13 Score=103.87 Aligned_cols=65 Identities=35% Similarity=0.481 Sum_probs=59.1
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIE 341 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLS 341 (681)
|+++.|+|++|++| |+||+|+....||+|++++++.++. ..+++||.|+|+|+++ |..+.+|.||
T Consensus 1 g~~~~g~V~~i~~~-G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~v-d~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDF-GAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISI-DEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecc-cEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEE-ECCCCEEecC
Confidence 78999999999999 9999999888999999999987664 4899999999999999 6777899876
No 52
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=99.46 E-value=6.4e-14 Score=152.19 Aligned_cols=141 Identities=18% Similarity=0.170 Sum_probs=119.4
Q ss_pred ccCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 267 YELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 267 ~~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
..+..+++|++|+|+|+++++. |+|||+|+..+|+||+++++|.... +.+++||.|+|+|++++ ...++|.||+|
T Consensus 295 ~~~~~l~~G~iV~G~V~~v~~~-gv~Vdig~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd-~~~g~i~LS~k 372 (647)
T PRK00087 295 ELEKQIRRGDIVKGTVVSVNEN-EVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLE-DEDGYVVLSKK 372 (647)
T ss_pred HHHhhccCCCEEEEEEEEEECC-EEEEEECCCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEE-CCCCcEEEEee
Confidence 3567899999999999999998 9999999888999999999997654 58999999999999994 45579999999
Q ss_pred ccC-CCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhhhhhccccc
Q 005716 344 FVQ-PNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAEQLILDDME 422 (681)
Q Consensus 344 ~~~-pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aEQmiLdd~e 422 (681)
... ..+|+.+...+..|.|+. ++|.+ ....|.||.+. +++|++|++..-.- .-
T Consensus 373 ~~~~~~~~~~l~~~~~~G~iv~-------g~V~~--------------v~~~G~~V~lg-gi~gfiP~sel~~~----~~ 426 (647)
T PRK00087 373 EADREKAWKELEEAFENGEPVK-------GKVKE--------------VVKGGLLVDYG-GVRAFLPASHVELG----YV 426 (647)
T ss_pred hhcchhHHHHHHHHhhCCCEEE-------EEEEE--------------EECCeEEEEEC-CEEEEEEHHHhCcc----cc
Confidence 886 678999999999999999 99998 78889999885 69999998865332 22
Q ss_pred cCccccCCccccc
Q 005716 423 ANPDKYKGKKLSE 435 (681)
Q Consensus 423 ~npdky~~~~~~~ 435 (681)
.+|.+|.|+.+.=
T Consensus 427 ~d~~~~vG~~v~v 439 (647)
T PRK00087 427 EDLSEYKGQELEV 439 (647)
T ss_pred CCHHHhCCCEEEE
Confidence 3566677766643
No 53
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=99.46 E-value=2.8e-13 Score=103.98 Aligned_cols=65 Identities=35% Similarity=0.455 Sum_probs=59.1
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
|+++.|+|++|++| |+||+|+...+||+|+++++|.++. +++++||.|+|+|+++ |. +.++.||+
T Consensus 1 g~~~~g~V~~v~~~-G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~-d~-~~~i~ls~ 68 (68)
T cd04472 1 GKIYEGKVVKIKDF-GAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEV-DD-RGRISLSR 68 (68)
T ss_pred CCEEEEEEEEEEEe-EEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEE-CC-CCcEEeeC
Confidence 78999999999999 9999998778999999999997664 4899999999999999 66 78999885
No 54
>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=99.45 E-value=2.5e-13 Score=103.92 Aligned_cols=65 Identities=35% Similarity=0.652 Sum_probs=59.2
Q ss_pred CCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeee
Q 005716 274 PGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIE 341 (681)
Q Consensus 274 eGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLS 341 (681)
+|+++.|+|+++++| |+||+|++ .+|+||+++++|.++. +++++||.|+|+|+++ |..++++.||
T Consensus 1 ~g~~~~g~V~~v~~~-g~~v~l~~-~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~v-d~~~~~i~ls 68 (68)
T cd05688 1 EGDVVEGTVKSITDF-GAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKI-DKERKRISLG 68 (68)
T ss_pred CCCEEEEEEEEEEee-eEEEEECC-eEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEE-ECCCCEEecC
Confidence 589999999999999 99999996 6999999999997764 4899999999999999 7788999886
No 55
>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=99.45 E-value=3.2e-13 Score=107.82 Aligned_cols=68 Identities=21% Similarity=0.349 Sum_probs=60.2
Q ss_pred CCCEEEEEEEEeeecceeEEEcCC-ceeeeeEccccccccc--------------ccccccCCEEEEEEEEeeCCCCCee
Q 005716 274 PGQICEGKVTTVHLYQGAFVDIGG-VYDGWVPIKGNDWYWI--------------RHHIKVGMHVIVEILAKRDPYRFRF 338 (681)
Q Consensus 274 eGqIVEGkVtnItdF~GAFVDIGG-v~DGLVHISEISW~rI--------------~dVLKVGDeVkVKVLsIdD~eR~RI 338 (681)
+|++++|+|++|++| |+||+|+. +.+||||+|+++|.++ ...+++||.|+|+|+++ |.++.+|
T Consensus 1 ~g~~~~g~V~~v~~~-G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~v-d~~~~~i 78 (83)
T cd04471 1 VGEEFDGVISGVTSF-GLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRV-DLDRRKI 78 (83)
T ss_pred CCCEEEEEEEeEEee-eEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEe-ccccCEE
Confidence 489999999999999 99999996 5799999999998542 25899999999999999 7788999
Q ss_pred eeeee
Q 005716 339 PIEMR 343 (681)
Q Consensus 339 SLSLK 343 (681)
.|+++
T Consensus 79 ~~~l~ 83 (83)
T cd04471 79 DFELV 83 (83)
T ss_pred EEEEC
Confidence 99863
No 56
>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=99.42 E-value=5e-13 Score=106.80 Aligned_cols=65 Identities=23% Similarity=0.213 Sum_probs=57.2
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc-ccccccCCEEEEEEEEeeCCCCCeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI-RHHIKVGMHVIVEILAKRDPYRFRFPIE 341 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI-~dVLKVGDeVkVKVLsIdD~eR~RISLS 341 (681)
|++|+|+|++|++| ||||+|.++.+|+||+|+++-.+. .+.+++||+|+++|+.+ |+.++||.||
T Consensus 1 G~~V~g~V~~i~~~-G~~v~l~~~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~i-d~~~~~i~LS 66 (66)
T cd05695 1 GMLVNARVKKVLSN-GLILDFLSSFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYV-DPSTKVVGLS 66 (66)
T ss_pred CCEEEEEEEEEeCC-cEEEEEcCCceEEEEHHHcCCccCcccCcCCCCEEEEEEEEE-eCCCCEEecC
Confidence 89999999999999 999999555799999999974222 57899999999999999 7888899987
No 57
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.40 E-value=8.1e-13 Score=131.68 Aligned_cols=77 Identities=23% Similarity=0.484 Sum_probs=68.9
Q ss_pred CCCCCCEEEEEEEEeeecceeEEEcCC--ceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 271 FYYPGQICEGKVTTVHLYQGAFVDIGG--VYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 271 ~LkeGqIVEGkVtnItdF~GAFVDIGG--v~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
..++|++|.|+|++|++| ||||+|.. +.+||||+|++++.+++ +++++||.|.|+|+++ |..+++|.||+|.+
T Consensus 5 ~P~~GdiV~G~V~~I~~~-G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~V-D~~k~~I~LSlK~v 82 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDF-GAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRV-DPRKGHIDLSLKRV 82 (262)
T ss_pred CCCCCCEEEEEEEEEECC-EEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEE-ecccCeEEEEEEec
Confidence 347899999999999999 99999963 46999999999987764 5999999999999999 78889999999998
Q ss_pred CCCc
Q 005716 346 QPNI 349 (681)
Q Consensus 346 ~pnP 349 (681)
.++-
T Consensus 83 ~~~e 86 (262)
T PRK03987 83 NEHQ 86 (262)
T ss_pred ccch
Confidence 8763
No 58
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=99.37 E-value=2.8e-12 Score=96.29 Aligned_cols=69 Identities=32% Similarity=0.517 Sum_probs=62.0
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc---ccccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI---RHHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI---~dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
++|+++.|+|++++++ |+||++|++..|+||+|++++... .+.+++||.|.|+|+++ +..+.++.||+|
T Consensus 1 ~~G~~v~g~V~~v~~~-g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~-~~~~~~i~ls~~ 72 (72)
T smart00316 1 EVGDVVEGTVTEITPF-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSV-DEEKGRIILSLK 72 (72)
T ss_pred CCCCEEEEEEEEEEcc-EEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEE-eCCCCEEEEEeC
Confidence 4799999999999998 999999966799999999998753 35899999999999999 677799999985
No 59
>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=99.37 E-value=1.8e-12 Score=101.97 Aligned_cols=66 Identities=30% Similarity=0.374 Sum_probs=58.4
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccccc-ccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRH-HIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~d-VLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
|++++|+|+++.++ |+||+++| .+||||+|++++.++.+ .-.+||.++|+|+++ |+.++||.||+|
T Consensus 1 G~iv~g~V~~v~~~-G~~v~l~g-~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~v-d~~~~~i~lS~k 67 (67)
T cd04465 1 GEIVEGKVTEKVKG-GLIVDIEG-VRAFLPASQVDLRPVEDLDEYVGKELKFKIIEI-DRERNNIVLSRR 67 (67)
T ss_pred CCEEEEEEEEEECC-eEEEEECC-EEEEEEHHHCCCcccCChHHhCCCEEEEEEEEE-eCCCCEEEEEcC
Confidence 78999999999999 99999965 69999999999988654 223899999999999 677889999986
No 60
>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=99.36 E-value=3.4e-12 Score=104.28 Aligned_cols=69 Identities=25% Similarity=0.321 Sum_probs=62.1
Q ss_pred cccCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 266 MYELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 266 v~~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
...++++++|++++|+|++|++| |+||++....+||||+|++ ...+++||+|+|+|+++ .++.||.||+
T Consensus 8 ~~~~~~~~~G~~~~g~V~~i~~~-G~fV~l~~~~~Glv~~se~-----~~~~~iGd~v~v~I~~i--~e~~~i~l~~ 76 (77)
T cd04473 8 ACTMEDLEVGKLYKGKVNGVAKY-GVFVDLNDHVRGLIHRSNL-----LRDYEVGDEVIVQVTDI--PENGNIDLIP 76 (77)
T ss_pred ccchhhCCCCCEEEEEEEeEecc-eEEEEECCCcEEEEEchhc-----cCcCCCCCEEEEEEEEE--CCCCcEEEEE
Confidence 35678899999999999999999 9999998778999999996 46799999999999999 4678999886
No 61
>PHA02945 interferon resistance protein; Provisional
Probab=99.33 E-value=4.2e-12 Score=111.00 Aligned_cols=71 Identities=17% Similarity=0.274 Sum_probs=63.5
Q ss_pred CCCCEEEEEEEEeeecceeEEEc---CCceeeeeEcccc--c--ccccccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDI---GGVYDGWVPIKGN--D--WYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDI---GGv~DGLVHISEI--S--W~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
.+|+++-|+|+. .+| ||||+| || ..|||||||+ + |-+.+++| +||+|.||||.+ |+.++-|-||||.+
T Consensus 10 ~~GelvigtV~~-~d~-ga~v~L~EY~g-~eg~i~~seveva~~wvK~rd~l-~GqkvV~KVirV-d~~kg~IDlSlK~V 84 (88)
T PHA02945 10 NVGDVLKGKVYE-NGY-ALYIDLFDYPH-SEAILAESVQMHMNRYFKYRDKL-VGKTVKVKVIRV-DYTKGYIDVNYKRM 84 (88)
T ss_pred CCCcEEEEEEEe-cCc-eEEEEecccCC-cEEEEEeehhhhccceEeeeeEe-cCCEEEEEEEEE-CCCCCEEEeEeeEc
Confidence 689999999999 999 999999 45 5999999966 5 65557899 999999999999 89999999999998
Q ss_pred CCC
Q 005716 346 QPN 348 (681)
Q Consensus 346 ~pn 348 (681)
..+
T Consensus 85 ~~~ 87 (88)
T PHA02945 85 CRH 87 (88)
T ss_pred ccC
Confidence 764
No 62
>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=99.31 E-value=5.7e-12 Score=106.71 Aligned_cols=78 Identities=29% Similarity=0.285 Sum_probs=67.7
Q ss_pred CEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc--------------cccccCCEEEEEEEEeeCCC----CCe
Q 005716 276 QICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR--------------HHIKVGMHVIVEILAKRDPY----RFR 337 (681)
Q Consensus 276 qIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~--------------dVLKVGDeVkVKVLsIdD~e----R~R 337 (681)
+++.|+|++|.+| |+||+|++ .+|+||++++++.++. .++++||.|+|+|++++-.. ..+
T Consensus 1 ~vv~g~V~~i~~~-GifV~l~~-v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~ 78 (99)
T cd04460 1 EVVEGEVVEVVDF-GAFVRIGP-VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESK 78 (99)
T ss_pred CEEEEEEEEEEec-cEEEEEcC-eEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCce
Confidence 4799999999999 99999986 6999999999986653 57899999999999994332 269
Q ss_pred eeeeeeccCCCccccccc
Q 005716 338 FPIEMRFVQPNIDHLIFN 355 (681)
Q Consensus 338 ISLSLK~~~pnPW~~I~e 355 (681)
|+||+|...-+||+-|.+
T Consensus 79 i~ls~k~~~~g~~~~~~~ 96 (99)
T cd04460 79 IGLTMRQPGLGKLEWIEE 96 (99)
T ss_pred EEEEEecCCCCcHHHhhh
Confidence 999999999999988765
No 63
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.29 E-value=2.6e-12 Score=129.56 Aligned_cols=75 Identities=29% Similarity=0.444 Sum_probs=68.2
Q ss_pred CCCCCEEEEEEEEeeecceeEEEc---CCceeeeeEccccccc---ccccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDI---GGVYDGWVPIKGNDWY---WIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDI---GGv~DGLVHISEISW~---rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
=.+|++|-|||+.|.+| ||||.| || ..|+|||||+|=. .|+++|++||+|-++||.| |+.|+-|-||||.+
T Consensus 9 PeeGEiVv~tV~~V~~~-GAyv~L~EY~g-~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrV-d~~rg~IDLSlkrV 85 (269)
T COG1093 9 PEEGEIVVGTVKQVADY-GAYVELDEYPG-KEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRV-DPKRGHIDLSLKRV 85 (269)
T ss_pred CCCCcEEEEEEEEeecc-ccEEEeeccCC-eeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEE-cCCCCeEeeehhhC
Confidence 36899999999999999 999999 55 4999999999744 4678999999999999999 89999999999999
Q ss_pred CCCc
Q 005716 346 QPNI 349 (681)
Q Consensus 346 ~pnP 349 (681)
+++-
T Consensus 86 ~~~q 89 (269)
T COG1093 86 TEHQ 89 (269)
T ss_pred CHHH
Confidence 9874
No 64
>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=99.25 E-value=1.7e-11 Score=97.72 Aligned_cols=58 Identities=17% Similarity=0.306 Sum_probs=52.0
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccc--cc---cccccCCEEEEEEEEeeCC
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYW--IR---HHIKVGMHVIVEILAKRDP 333 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~r--I~---dVLKVGDeVkVKVLsIdD~ 333 (681)
|++|.|+|++|.++ |+||.|+.+.+|+||++++++.. +. +++++||.|+++|+++++.
T Consensus 1 G~iV~g~V~~i~~~-gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~ 63 (70)
T cd05702 1 GDLVKAKVKSVKPT-QLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDA 63 (70)
T ss_pred CCEEEEEEEEEECC-cEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCc
Confidence 89999999999999 99999988889999999999863 43 5799999999999999543
No 65
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=99.25 E-value=6.7e-12 Score=138.61 Aligned_cols=74 Identities=24% Similarity=0.275 Sum_probs=66.5
Q ss_pred CCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeeccC
Q 005716 270 PFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQ 346 (681)
Q Consensus 270 ~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~ 346 (681)
..+++|++++|+|++|.+| ||||.|-.+.+||||||++++.|+. ++|++||+|.|||++|| .+.||.||+|.+.
T Consensus 615 ~e~evg~iy~G~V~ri~~f-GaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD--~~Gri~ls~~~~~ 691 (692)
T COG1185 615 REVEVGEVYEGTVVRIVDF-GAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEID--KQGRIRLSIKAVL 691 (692)
T ss_pred hhcccccEEEEEEEEEeec-ceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeec--ccCCccceehhcc
Confidence 6688999999999999999 9999996667999999999998764 69999999999999995 3589999998764
No 66
>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=99.23 E-value=3.3e-11 Score=98.35 Aligned_cols=70 Identities=17% Similarity=0.034 Sum_probs=62.7
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccc---cccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYW---IRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~r---I~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
++|++|.|+|++|++. |++||||+..+|+||+|+++-.. +.+.+++||.|.++|+++ ++. +++-||++..
T Consensus 5 ~~GdiV~G~V~~v~~~-~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~-~~~-~~i~LS~~~~ 77 (82)
T cd04454 5 DVGDIVIGIVTEVNSR-FWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISL-GDD-MNVLLTTADN 77 (82)
T ss_pred CCCCEEEEEEEEEcCC-EEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEe-CCC-CCEEEEECCC
Confidence 7899999999999998 99999998899999999998654 446899999999999999 555 8899999863
No 67
>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=99.22 E-value=1.6e-11 Score=135.45 Aligned_cols=67 Identities=33% Similarity=0.343 Sum_probs=60.0
Q ss_pred CCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeee
Q 005716 271 FYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPI 340 (681)
Q Consensus 271 ~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISL 340 (681)
.+++|+++.|+|++|++| ||||+|..+.+||||||+++|.++. +++++||+|+|+|+++ |. ++||+|
T Consensus 615 ~~~~G~i~~G~V~~I~~~-GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~i-d~-~gki~L 684 (684)
T TIGR03591 615 EPEVGKIYEGKVVRIMDF-GAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEI-DK-QGRIKL 684 (684)
T ss_pred ccccCcEEEEEEEEEeCC-EEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEE-CC-CCCccC
Confidence 468999999999999999 9999997667999999999998764 5999999999999999 44 678875
No 68
>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=99.18 E-value=6.2e-11 Score=87.74 Aligned_cols=62 Identities=29% Similarity=0.431 Sum_probs=55.1
Q ss_pred EEEEEEEeeecceeEEEcCCceeeeeEcccccccc---cccccccCCEEEEEEEEeeCCCCCeeeee
Q 005716 278 CEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYW---IRHHIKVGMHVIVEILAKRDPYRFRFPIE 341 (681)
Q Consensus 278 VEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~r---I~dVLKVGDeVkVKVLsIdD~eR~RISLS 341 (681)
+.|+|+++.++ |+||+++.+.+|++|+|++++.. +.+.+++||.|+|+|+++ |..++++.||
T Consensus 1 v~g~V~~v~~~-g~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~-d~~~~~i~ls 65 (65)
T cd00164 1 VTGKVVSITKF-GVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEV-DPEKGRISLS 65 (65)
T ss_pred CEEEEEEEEee-eEEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEE-cCCcCEEecC
Confidence 47999999999 99999997789999999999865 456899999999999999 6777888775
No 69
>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=99.16 E-value=1.4e-10 Score=92.66 Aligned_cols=64 Identities=20% Similarity=0.231 Sum_probs=54.9
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCC-CCeeeee
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPY-RFRFPIE 341 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~e-R~RISLS 341 (681)
.+|++|+|+|.+++++ |+|||+|+ .+|+||.||++. .+.+++||+|+|+|+++++.. +..|-||
T Consensus 2 ~~g~iV~G~V~~~~~~-~~~vdig~-~eg~lp~~e~~~---~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 2 REGEIVTGIVKRVDRG-NVIVDLGK-VEAILPKKEQIP---GESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCCCEEEEEEEEEcCC-CEEEEcCC-eEEEeeHHHCCC---CCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 4799999999999998 99999998 799999999984 457899999999999996532 3456666
No 70
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=99.14 E-value=8.9e-11 Score=110.52 Aligned_cols=70 Identities=19% Similarity=0.220 Sum_probs=61.8
Q ss_pred CCCCCCCEEEEEEEEeeecceeEEEcCC----------ceeeeeEccccccccc---ccccccCCEEEEEEEEeeCCCCC
Q 005716 270 PFYYPGQICEGKVTTVHLYQGAFVDIGG----------VYDGWVPIKGNDWYWI---RHHIKVGMHVIVEILAKRDPYRF 336 (681)
Q Consensus 270 ~~LkeGqIVEGkVtnItdF~GAFVDIGG----------v~DGLVHISEISW~rI---~dVLKVGDeVkVKVLsIdD~eR~ 336 (681)
..+++|++|.|+|++|+++ ||||||++ ..+|+||+|+++|..+ .+.+++||.|+++|++++ .
T Consensus 60 ~~~~~GdiV~GkV~~i~~~-g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~----~ 134 (189)
T PRK09521 60 PLLKKGDIVYGRVVDVKEQ-RALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT----D 134 (189)
T ss_pred CCCCCCCEEEEEEEEEcCC-eEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC----C
Confidence 5567999999999999998 99999974 3589999999999765 458999999999999993 6
Q ss_pred eeeeeeec
Q 005716 337 RFPIEMRF 344 (681)
Q Consensus 337 RISLSLK~ 344 (681)
++.||+|.
T Consensus 135 ~i~LS~k~ 142 (189)
T PRK09521 135 PLQLSTKG 142 (189)
T ss_pred cEEEEEec
Confidence 89999983
No 71
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=99.05 E-value=4.7e-10 Score=109.67 Aligned_cols=70 Identities=23% Similarity=0.280 Sum_probs=62.2
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc-------ccccccCCEEEEEEEEeeCCCCCeeeeeeec
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI-------RHHIKVGMHVIVEILAKRDPYRFRFPIEMRF 344 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI-------~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~ 344 (681)
-++|++|.|+|++|+.+ |+||||+...+|+||+|+++|.++ ++++++||.|.++|+++ ++. .++.||+|.
T Consensus 61 P~vGDiViG~V~~i~~~-~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i-~~~-~~~~LS~k~ 137 (235)
T PRK04163 61 PKVGDLVIGKVTDVTFS-GWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDV-DRT-RDVVLTLKG 137 (235)
T ss_pred CCCCCEEEEEEEEEeCc-eEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEE-CCC-CcEEEEEcC
Confidence 38999999999999999 999999988899999999999765 45899999999999999 444 359999975
No 72
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=99.02 E-value=1e-09 Score=102.72 Aligned_cols=80 Identities=25% Similarity=0.307 Sum_probs=67.7
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc--------------ccccccCCEEEEEEEEeeC----CC
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI--------------RHHIKVGMHVIVEILAKRD----PY 334 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI--------------~dVLKVGDeVkVKVLsIdD----~e 334 (681)
..|++++|+|+++++| |+||+||. .+|++|+|++..... ...+++||+|+|+|++++- +.
T Consensus 80 ~~gEvv~G~V~~v~~~-GifV~lg~-~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~~~~~ 157 (179)
T TIGR00448 80 ELGEIVEGEVIEIVEF-GAFVSLGP-FDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKDRRPE 157 (179)
T ss_pred cCCCEEEEEEEEEEee-EEEEEeCC-ceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccCCCCC
Confidence 3699999999999999 99999986 699999999974322 2489999999999999952 56
Q ss_pred CCeeeeeeeccCCCcccccc
Q 005716 335 RFRFPIEMRFVQPNIDHLIF 354 (681)
Q Consensus 335 R~RISLSLK~~~pnPW~~I~ 354 (681)
..||.||||+..-+|++-+.
T Consensus 158 ~~~I~lt~k~~~LG~~~w~~ 177 (179)
T TIGR00448 158 GSKIGLTMRQPLLGKLEWIE 177 (179)
T ss_pred cceEEEEeccCcCCcccccc
Confidence 77999999998888877553
No 73
>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=98.92 E-value=2.6e-09 Score=117.54 Aligned_cols=68 Identities=22% Similarity=0.327 Sum_probs=59.6
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCC-ceeeeeEcccccccc--------------cccccccCCEEEEEEEEeeCCCCCe
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGG-VYDGWVPIKGNDWYW--------------IRHHIKVGMHVIVEILAKRDPYRFR 337 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGG-v~DGLVHISEISW~r--------------I~dVLKVGDeVkVKVLsIdD~eR~R 337 (681)
++|++++|+|++|++| |+||.|++ +.+||||+|++++.. ....+++||+|+|+|+++ |..++|
T Consensus 626 ~iG~~~~g~V~~v~~f-GifV~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~v-d~~~~~ 703 (709)
T TIGR02063 626 KIGEEFEGVISGVTSF-GLFVELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKA-DLDTGK 703 (709)
T ss_pred cCCcEEEEEEEEEEeC-CEEEEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEE-ecccCe
Confidence 5799999999999999 99999975 469999999998532 124899999999999999 788899
Q ss_pred eeeee
Q 005716 338 FPIEM 342 (681)
Q Consensus 338 ISLSL 342 (681)
|.|++
T Consensus 704 I~~~l 708 (709)
T TIGR02063 704 IDFEL 708 (709)
T ss_pred EEEEE
Confidence 99986
No 74
>PRK11642 exoribonuclease R; Provisional
Probab=98.82 E-value=1.8e-08 Score=113.83 Aligned_cols=69 Identities=20% Similarity=0.302 Sum_probs=60.3
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCC-ceeeeeEccccccc--cc------------ccccccCCEEEEEEEEeeCCCCCe
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGG-VYDGWVPIKGNDWY--WI------------RHHIKVGMHVIVEILAKRDPYRFR 337 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGG-v~DGLVHISEISW~--rI------------~dVLKVGDeVkVKVLsIdD~eR~R 337 (681)
++|++++|+|++|++| |+||.|+. .++||||+|+++|. .. ...+++||+|+|+|+++ |..+.+
T Consensus 642 ~iGe~f~G~Is~V~~f-GifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~v-D~~~rk 719 (813)
T PRK11642 642 QVGNVFKGVISSVTGF-GFFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAV-NMDERK 719 (813)
T ss_pred cCCcEEEEEEEEeecC-ceEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEe-ecCCCe
Confidence 5899999999999999 99999964 37999999999763 21 24899999999999999 788899
Q ss_pred eeeeee
Q 005716 338 FPIEMR 343 (681)
Q Consensus 338 ISLSLK 343 (681)
|.|++-
T Consensus 720 I~f~l~ 725 (813)
T PRK11642 720 IDFSLI 725 (813)
T ss_pred EEEEEe
Confidence 999984
No 75
>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=98.73 E-value=2.7e-08 Score=109.26 Aligned_cols=68 Identities=19% Similarity=0.286 Sum_probs=60.0
Q ss_pred CCCCEEEEEEEEeeecceeEEEcC-CceeeeeEcccccccc--------------cccccccCCEEEEEEEEeeCCCCCe
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIG-GVYDGWVPIKGNDWYW--------------IRHHIKVGMHVIVEILAKRDPYRFR 337 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIG-Gv~DGLVHISEISW~r--------------I~dVLKVGDeVkVKVLsIdD~eR~R 337 (681)
++|++++|+|++|++| |+||.|. .+.+||||+|++.|.. ....+++||+|+|+|+++ |..+.+
T Consensus 571 ~iG~~~~g~I~~v~~~-GifV~L~~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~v-d~~~~~ 648 (654)
T TIGR00358 571 KVGTEFSGEISSVTRF-GMFVRLDDNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEV-NMETRS 648 (654)
T ss_pred CCCcEEEEEEEeEEcC-cEEEEecCCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEE-ecccCe
Confidence 4699999999999999 9999997 5579999999998852 124899999999999999 788899
Q ss_pred eeeee
Q 005716 338 FPIEM 342 (681)
Q Consensus 338 ISLSL 342 (681)
|.+++
T Consensus 649 I~f~l 653 (654)
T TIGR00358 649 IIFEL 653 (654)
T ss_pred EEEEE
Confidence 98886
No 76
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.72 E-value=4.3e-08 Score=91.73 Aligned_cols=76 Identities=30% Similarity=0.304 Sum_probs=63.1
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc--------------ccccccCCEEEEEEEEeeCCCC--
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI--------------RHHIKVGMHVIVEILAKRDPYR-- 335 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI--------------~dVLKVGDeVkVKVLsIdD~eR-- 335 (681)
-.+|+++.|+|+++.++ |+||+||. .+|++|++++.+..+ ..++++||.|+|+|++++-..+
T Consensus 79 P~~GEVv~g~V~~v~~~-Gi~V~lg~-~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~ 156 (187)
T PRK08563 79 PELQEVVEGEVVEVVEF-GAFVRIGP-VDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRP 156 (187)
T ss_pred ccCCCEEEEEEEEEEcc-EEEEEEeC-ceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCC
Confidence 34699999999999998 99999996 699999999986543 3489999999999999953332
Q ss_pred --CeeeeeeeccCCCc
Q 005716 336 --FRFPIEMRFVQPNI 349 (681)
Q Consensus 336 --~RISLSLK~~~pnP 349 (681)
.+|.||||...-++
T Consensus 157 ~~~~I~ls~~~~~LG~ 172 (187)
T PRK08563 157 RGSKIGLTMRQPGLGK 172 (187)
T ss_pred CCCEEEEEecCCCCCc
Confidence 58999999865554
No 77
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.66 E-value=5.3e-08 Score=94.60 Aligned_cols=73 Identities=32% Similarity=0.368 Sum_probs=61.3
Q ss_pred CCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccc----------cccc----ccccCCEEEEEEEEeeCCCC----
Q 005716 274 PGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWY----------WIRH----HIKVGMHVIVEILAKRDPYR---- 335 (681)
Q Consensus 274 eGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~----------rI~d----VLKVGDeVkVKVLsIdD~eR---- 335 (681)
.|.+|+|.|+++..| ||||-||- .|||||+|+|... .+-+ ++++|+.|.++|+++.-..+
T Consensus 81 ~gEVV~GeVv~~~~~-G~fV~igp-~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~~~~~~ 158 (183)
T COG1095 81 RGEVVEGEVVEVVEF-GAFVRIGP-LDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRE 158 (183)
T ss_pred cccEEEEEEEEEeec-ceEEEecc-ccccccHhhccCcccccCcccceeeecccceEEecCCEEEEEEEEEecccCcccc
Confidence 478999999999999 99999995 4999999999654 2222 99999999999999965555
Q ss_pred CeeeeeeeccCCC
Q 005716 336 FRFPIEMRFVQPN 348 (681)
Q Consensus 336 ~RISLSLK~~~pn 348 (681)
-+|.|+||+..-+
T Consensus 159 ~~I~lTmrq~~LG 171 (183)
T COG1095 159 SKIGLTMRQPGLG 171 (183)
T ss_pred ceEEEEeccccCC
Confidence 6899999986543
No 78
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=98.65 E-value=5.4e-08 Score=104.48 Aligned_cols=64 Identities=20% Similarity=0.227 Sum_probs=57.5
Q ss_pred CCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCC--eeeeeee
Q 005716 274 PGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRF--RFPIEMR 343 (681)
Q Consensus 274 eGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~--RISLSLK 343 (681)
+|++|+|+|++++++ |+||||||. +|++|.|+++ +.+.+++||.|+|+|++| ++.++ +|-||.+
T Consensus 134 ~GeIV~G~V~ri~~~-giiVDLggv-ea~LP~sE~i---p~E~~~~GdrIka~I~~V-d~~~kg~qIilSRt 199 (470)
T PRK09202 134 VGEIITGVVKRVERG-NIIVDLGRA-EAILPRKEQI---PRENFRPGDRVRAYVYEV-RKEARGPQIILSRT 199 (470)
T ss_pred cCCEEEEEEEEEecC-CEEEEECCe-EEEecHHHcC---CCccCCCCCEEEEEEEEE-ecCCCCCeEEEEeC
Confidence 799999999999998 999999875 9999999996 778999999999999999 55555 8888874
No 79
>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=98.53 E-value=1.7e-07 Score=99.25 Aligned_cols=71 Identities=24% Similarity=0.293 Sum_probs=56.7
Q ss_pred CCCCCEEEEEEEEeeec-ceeEEEcCCceeeeeEccccccc---------------ccccccccCCEEEEEEEEeeCCCC
Q 005716 272 YYPGQICEGKVTTVHLY-QGAFVDIGGVYDGWVPIKGNDWY---------------WIRHHIKVGMHVIVEILAKRDPYR 335 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF-~GAFVDIGGv~DGLVHISEISW~---------------rI~dVLKVGDeVkVKVLsIdD~eR 335 (681)
..+|+|+.|+|++|.++ +|||||||.+..|++|+|++++. .|.++|++||+|.|.|+.= ....
T Consensus 23 ~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~Ke-~~~~ 101 (414)
T TIGR00757 23 QLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECLAPAEAKREAGPSISELLRPGQSVLVQVVKE-PRGN 101 (414)
T ss_pred CCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhccccccccccccCCHHHhCcCCCEEEEEEeeC-CcCC
Confidence 45899999999999997 58999999999999999999873 2456899999999999983 3333
Q ss_pred Ceeeeeee
Q 005716 336 FRFPIEMR 343 (681)
Q Consensus 336 ~RISLSLK 343 (681)
+.-.|+.+
T Consensus 102 Kgp~lT~~ 109 (414)
T TIGR00757 102 KGARLTTD 109 (414)
T ss_pred CCCeEEEE
Confidence 43334443
No 80
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=98.51 E-value=1e-07 Score=105.01 Aligned_cols=84 Identities=15% Similarity=0.148 Sum_probs=73.0
Q ss_pred CCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 269 LPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 269 L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
..+|+.|-+++++||.|.+| ||||.|-.++.||+|+|+++-.+|. ++|+|||.+.||-+..|. +.-|-||.|.+
T Consensus 663 ~~~l~~g~vy~~tIt~~rd~-G~~V~l~p~~~~Llh~sqL~~e~iakpsd~levGq~I~vk~ie~d~--~g~~~ls~ral 739 (760)
T KOG1067|consen 663 VQDLEFGGVYTATITEIRDT-GVMVELYPMQQGLLHNSQLDQEKIAKPSDLLEVGQEIQVKYIERDP--RGGIMLSSRAL 739 (760)
T ss_pred ccceEeeeEEEEEEeeeccc-ceEEEecCCchhhccchhcccccccChHHHHhhcceeEEEEEeecC--ccceeehhhhh
Confidence 36888999999999999999 9999997788999999999988775 499999999999999953 56778899999
Q ss_pred CCCccccccc
Q 005716 346 QPNIDHLIFN 355 (681)
Q Consensus 346 ~pnPW~~I~e 355 (681)
.|+|=..+..
T Consensus 740 Lp~p~~~~~s 749 (760)
T KOG1067|consen 740 LPDPATKESS 749 (760)
T ss_pred cCCcccCCcc
Confidence 9988655443
No 81
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=98.30 E-value=1.5e-06 Score=102.65 Aligned_cols=134 Identities=16% Similarity=0.210 Sum_probs=104.8
Q ss_pred hhhhcccCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccc---ccccccCCEEEEEEEEeeCCCCCee
Q 005716 262 YEEGMYELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI---RHHIKVGMHVIVEILAKRDPYRFRF 338 (681)
Q Consensus 262 f~egv~~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI---~dVLKVGDeVkVKVLsIdD~eR~RI 338 (681)
-...+.++++|++||+|.|.|.++.+- |.||-||-.++++++||+++-.-. +.++.+|+-|.++|+++ +...+||
T Consensus 1150 kd~~iks~eDlk~g~iv~G~V~nv~~~-glfi~ls~~v~a~v~is~~~ds~~k~w~k~~~~gklv~~rv~~v-e~~s~ri 1227 (1710)
T KOG1070|consen 1150 KDGSIKSIEDLKIGDIVRGFVKNVETK-GLFIALSRKVEAFVPISGLSDSFEKEWEKHLPVGKLVTGRVLSV-EEDSKRI 1227 (1710)
T ss_pred cCCcccchhhcccCceeEEEEEEecCC-cEEEEEccceEEEEEccccccchhhhhhccCCccceeeeEEEEe-eccCceE
Confidence 344567799999999999999999996 999999988999999999987654 45999999999999999 6777899
Q ss_pred eeeeeccCCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccc--cceeeehhhhh
Q 005716 339 PIEMRFVQPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYV--DKLWQIHNAEQ 415 (681)
Q Consensus 339 SLSLK~~~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~V--egL~hIs~aEQ 415 (681)
.|+||.-.-+=-..+.. ....| ..||.-.|+|.+ ...||-|+.+-++| -||-||+.--+
T Consensus 1228 el~Lk~s~~~d~~~~~~--~~~~l--~~gd~~~g~v~~--------------~~~~G~fi~l~~tv~~~g~~~~~e~~d 1288 (1710)
T KOG1070|consen 1228 ELSLKNSDIKDTVKLLK--DSKDL--KKGDREDGTVEV--------------VDPFGLFIKLDVTVNMVGLCHISEEAD 1288 (1710)
T ss_pred EEEEeccccCCchhhhh--hhhhh--hccccccceEEE--------------ecCCceEEEecCcceecccccceeecc
Confidence 99999743221111111 11111 123444489999 88999999999999 99999986433
No 82
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.25 E-value=3.3e-06 Score=72.68 Aligned_cols=69 Identities=17% Similarity=0.123 Sum_probs=58.5
Q ss_pred CCCCEEEEEEEEeeecceeEEEc--------CCceeeeeEcccccccc-----cccccccCCEEEEEEEEeeCCCCCeee
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDI--------GGVYDGWVPIKGNDWYW-----IRHHIKVGMHVIVEILAKRDPYRFRFP 339 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDI--------GGv~DGLVHISEISW~r-----I~dVLKVGDeVkVKVLsIdD~eR~RIS 339 (681)
++|++|-|+|++|+.- .|+||| .....|++|+|++.-.. +.+.+++||.|+++|+++.+. ..+-
T Consensus 5 ~~GDiVig~V~~v~~~-~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~~--~~~~ 81 (92)
T cd05791 5 KVGSIVIARVTRINPR-FAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGDA--SSYY 81 (92)
T ss_pred CCCCEEEEEEEEEcCC-EEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCCC--CCcE
Confidence 8999999999999985 999999 88889999999996543 457999999999999999542 4477
Q ss_pred eeeec
Q 005716 340 IEMRF 344 (681)
Q Consensus 340 LSLK~ 344 (681)
||++.
T Consensus 82 Lst~~ 86 (92)
T cd05791 82 LSTAE 86 (92)
T ss_pred EEecC
Confidence 77764
No 83
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=98.24 E-value=2e-06 Score=90.20 Aligned_cols=98 Identities=16% Similarity=0.218 Sum_probs=68.3
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeeeeeccCCCcccc
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQPNIDHL 352 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~pnPW~~ 352 (681)
++|++|+|+|++++++ |+|||||+ .+|++|.+++.- .+.+++||.|+|+|++|+ ..+++..|.+-.+.|+-=..
T Consensus 133 k~GeiV~G~V~~~~~~-~~~Vdlg~-vEa~LP~~E~ip---~e~~~~Gd~Ika~V~~V~-~~~kgp~IivSRt~p~~v~~ 206 (362)
T PRK12327 133 REGDIVTGVVQRRDNR-FVYVNLGK-IEAVLPPAEQIP---GETYKHGDRIKVYVVKVE-KTTKGPQIFVSRTHPGLVKR 206 (362)
T ss_pred hcCCEEEEEEEEEeCC-cEEEEeCC-eEEEecHHHcCC---CCCCCCCCEEEEEEEEEe-cCCCCCeEEEEeCCHHHHHH
Confidence 7899999999999998 99999998 599999998853 678999999999999994 44444344444455543333
Q ss_pred ccccCCCCCccccCCCCCchhhhhccC
Q 005716 353 IFNRFDFAPIFHRDEDKNPDELRRDCG 379 (681)
Q Consensus 353 I~erf~vgpI~~r~~d~n~geV~Rd~G 379 (681)
+++ -.+|-|.. |-..---|+|+.|
T Consensus 207 Lfe-~EVPEI~~--G~VeIk~iaR~pG 230 (362)
T PRK12327 207 LFE-LEVPEIYD--GTVEIKSIAREAG 230 (362)
T ss_pred HHH-HhCccccC--CeEEEEEEeeCCc
Confidence 332 23455544 1111245677555
No 84
>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=4.3e-06 Score=87.02 Aligned_cols=66 Identities=20% Similarity=0.335 Sum_probs=56.2
Q ss_pred CCCCEEEEEEEEeeecce-eEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCC-CCCeeeeeee
Q 005716 273 YPGQICEGKVTTVHLYQG-AFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDP-YRFRFPIEMR 343 (681)
Q Consensus 273 keGqIVEGkVtnItdF~G-AFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~-eR~RISLSLK 343 (681)
++|++|+|+|.++++. | +|||||+. +|++|.+|.+ ..+.+++||.|+|+|+++++. .+..|-||.+
T Consensus 130 k~GeiV~G~V~~v~~~-g~v~VdiG~~-ea~LP~~E~i---p~E~~~~Gd~ik~~V~~V~~~~kg~qIivSRt 197 (341)
T TIGR01953 130 KEGEIISGTVKRVNRR-GNLYVELGKT-EGILPKKEQI---PGEKFRIGDRIKAYVYEVRKTAKGPQIILSRT 197 (341)
T ss_pred hcCCEEEEEEEEEecC-CcEEEEECCe-EEEecHHHcC---CCcCCCCCCEEEEEEEEEEcCCCCCeEEEEeC
Confidence 5899999999999998 8 69999864 9999999998 456799999999999999643 2346878875
No 85
>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=98.11 E-value=1.3e-05 Score=68.74 Aligned_cols=57 Identities=21% Similarity=0.288 Sum_probs=48.0
Q ss_pred CCCEEEEEEEEeeecceeEEEcCCceeeeeEccccc-----------ccccc---cccccCCEEEEEEEEeeC
Q 005716 274 PGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGND-----------WYWIR---HHIKVGMHVIVEILAKRD 332 (681)
Q Consensus 274 eGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEIS-----------W~rI~---dVLKVGDeVkVKVLsIdD 332 (681)
.|.||+|+|++++.+ |+||.+|.. +|++|.+.|- |.... .++++|+.|.++|+++.-
T Consensus 1 kgEVi~g~V~~v~~~-G~~v~~Gpl-~~f~~~~~ip~~~~~~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~ 71 (88)
T cd04462 1 KGEVVDAIVTSVNKT-GFFAEVGPL-SIFISRHLIPSDMEFDPNASPPCFTSNEDIVIKKDTEVRLKIIGTRV 71 (88)
T ss_pred CCcEEEEEEEEEecc-EEEEEEcCc-eEEEEeeecCccceECCcCCCCeEeCCCcEEECCCCEEEEEEEEEEE
Confidence 489999999999999 999999975 9999999882 22222 389999999999999953
No 86
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=97.91 E-value=9.9e-06 Score=95.99 Aligned_cols=81 Identities=25% Similarity=0.397 Sum_probs=71.4
Q ss_pred hcccCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeee
Q 005716 265 GMYELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIE 341 (681)
Q Consensus 265 gv~~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLS 341 (681)
..++.+.+.+|+++.|+|.+|..+ ||||-+-|+..|+.+.|+||...+. +++.+||+|.|+|.++ |.++.|+.|+
T Consensus 590 lp~d~~~~~pg~~~~G~l~~~~~~-g~~V~F~g~lsGf~p~s~~sd~~v~~~~ehf~vGqTv~~~i~nv-d~ek~rm~l~ 667 (1710)
T KOG1070|consen 590 LPSDFEQAIPGKITKGTLCAIKEN-GAFVTFTGGLSGFAPVSEMSDDFVLSDSEHFPVGQTVRAKIVNV-DDEKRRMPLG 667 (1710)
T ss_pred CccchhhcCCCceEEEEEeeeccC-CeEEEecCccccccchhhhhhhhhcChhhhcccccEEEEEEEec-Cchhceeehh
Confidence 345667788999999999999999 9999996666999999999987764 5999999999999999 7899999999
Q ss_pred eeccCC
Q 005716 342 MRFVQP 347 (681)
Q Consensus 342 LK~~~p 347 (681)
+|.-.-
T Consensus 668 ~r~s~~ 673 (1710)
T KOG1070|consen 668 LRASSC 673 (1710)
T ss_pred hhhhhh
Confidence 986543
No 87
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.87 E-value=4.5e-05 Score=72.87 Aligned_cols=71 Identities=17% Similarity=0.179 Sum_probs=54.7
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccc-----------cccc----ccccccCCEEEEEEEEeeCCCC-C
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGND-----------WYWI----RHHIKVGMHVIVEILAKRDPYR-F 336 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEIS-----------W~rI----~dVLKVGDeVkVKVLsIdD~eR-~ 336 (681)
-.|.+++|+|++++.+ |+||.+|= .+++||.|.|. |.++ ...++.|+.|+++|+++.-+.+ .
T Consensus 80 f~gEVv~g~V~~v~~~-G~~v~~Gp-~~ifI~~~~l~~~~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~~~~ 157 (176)
T PTZ00162 80 FKDEVLDAIVTDVNKL-GFFAQAGP-LKAFVSRSAIPPDFVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNL 157 (176)
T ss_pred CCCCEEEEEEEEEecc-eEEEEeeC-eEEEEcHHHCCCccEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecCCCc
Confidence 4689999999999998 99999985 58999999984 3223 1289999999999999854333 3
Q ss_pred eeeeeeecc
Q 005716 337 RFPIEMRFV 345 (681)
Q Consensus 337 RISLSLK~~ 345 (681)
++-.+||..
T Consensus 158 ~~i~T~~~~ 166 (176)
T PTZ00162 158 FAIATINSD 166 (176)
T ss_pred EEEEEecCC
Confidence 444466543
No 88
>PRK05054 exoribonuclease II; Provisional
Probab=97.81 E-value=5.6e-05 Score=83.88 Aligned_cols=66 Identities=9% Similarity=-0.080 Sum_probs=54.3
Q ss_pred CCEEEEEEEEeeecceeEEEcC-CceeeeeEccccc--ccc--c-----------ccccccCCEEEEEEEEeeCCCCCee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIG-GVYDGWVPIKGND--WYW--I-----------RHHIKVGMHVIVEILAKRDPYRFRF 338 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIG-Gv~DGLVHISEIS--W~r--I-----------~dVLKVGDeVkVKVLsIdD~eR~RI 338 (681)
|+.++|+|++|+.| |.||.|. .+..||||+|.+. |.. . +..+++||.|+|+|.++ |..+.+|
T Consensus 562 ~~~f~g~I~~v~~~-G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~v-d~~~~~i 639 (644)
T PRK05054 562 DTRFAAEIIDISRG-GMRVRLLENGAVAFIPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEV-RMETRSI 639 (644)
T ss_pred CeEEEEEEEeeecC-cEEEEEeCCceEEEEEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEE-ccccCeE
Confidence 56999999999999 9999993 3469999999983 211 1 13799999999999999 7888888
Q ss_pred eeee
Q 005716 339 PIEM 342 (681)
Q Consensus 339 SLSL 342 (681)
.+++
T Consensus 640 ~~~~ 643 (644)
T PRK05054 640 IARP 643 (644)
T ss_pred EEEE
Confidence 7764
No 89
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=97.60 E-value=0.00015 Score=80.99 Aligned_cols=68 Identities=25% Similarity=0.368 Sum_probs=56.7
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCC-ceeeeeEccccc--ccc------------cccccccCCEEEEEEEEeeCCCCCe
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGG-VYDGWVPIKGND--WYW------------IRHHIKVGMHVIVEILAKRDPYRFR 337 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGG-v~DGLVHISEIS--W~r------------I~dVLKVGDeVkVKVLsIdD~eR~R 337 (681)
++|++..|+|++++.| |+||-|.. +.+||||||.+. +.. ...++.+||.|+|+|+++ +....+
T Consensus 621 ~vg~~f~g~V~~v~~~-g~~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v-~~~~~~ 698 (706)
T COG0557 621 RVGEEFDGVVTGVTSF-GFFVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSV-DLDERK 698 (706)
T ss_pred hcCCEEEEEEEEEEec-cEEEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEE-cccccc
Confidence 6899999999999999 99999943 379999999997 221 123899999999999999 667778
Q ss_pred eeeee
Q 005716 338 FPIEM 342 (681)
Q Consensus 338 ISLSL 342 (681)
|-+++
T Consensus 699 i~~~~ 703 (706)
T COG0557 699 IDFEL 703 (706)
T ss_pred eEEEe
Confidence 87765
No 90
>PRK11712 ribonuclease G; Provisional
Probab=97.55 E-value=0.00016 Score=78.83 Aligned_cols=59 Identities=25% Similarity=0.312 Sum_probs=49.4
Q ss_pred CCCCCEEEEEEEEeee-cceeEEEcCCceeeeeEcccccc---------------cccccccccCCEEEEEEEEe
Q 005716 272 YYPGQICEGKVTTVHL-YQGAFVDIGGVYDGWVPIKGNDW---------------YWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 272 LkeGqIVEGkVtnItd-F~GAFVDIGGv~DGLVHISEISW---------------~rI~dVLKVGDeVkVKVLsI 330 (681)
-.+|.|+.|+|++|.+ -++||||||.+..|++|++++.- ..|.++|++||+|-|.|..=
T Consensus 36 ~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke 110 (489)
T PRK11712 36 GIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD 110 (489)
T ss_pred cccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence 3589999999999986 35799999999999999999831 12456799999999999874
No 91
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=97.49 E-value=8.8e-05 Score=82.78 Aligned_cols=82 Identities=21% Similarity=0.246 Sum_probs=66.6
Q ss_pred ccCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeeeeeccC
Q 005716 267 YELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQ 346 (681)
Q Consensus 267 ~~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~ 346 (681)
-++.+++.|..+.|+|++|..| ||||+|.....||+|-++++- ..-+++|++|.|.|.+++ +++..|++. +..
T Consensus 115 c~~~Dve~g~~Y~g~v~~v~~~-GvFv~Ln~~v~GL~~~~d~~~---~~~~~vgdeiiV~v~~vr-~~~geidf~--~~~ 187 (715)
T COG1107 115 CTMEDVEAGKYYKGIVSRVEKY-GVFVELNSHVRGLIHRRDLGG---DPDYAVGDEIIVQVSDVR-PEKGEIDFE--PVG 187 (715)
T ss_pred cchhhcccceeeeccccchhhh-cceeecChhhhccccccccCC---CCCCCCCCeEEEEeeccC-CCCCcccee--ecC
Confidence 4678999999999999999999 999999999999999999986 346889999999999994 555666554 444
Q ss_pred CCccccccc
Q 005716 347 PNIDHLIFN 355 (681)
Q Consensus 347 pnPW~~I~e 355 (681)
.++...+.-
T Consensus 188 ~~~Y~~~~~ 196 (715)
T COG1107 188 LDRYREVQV 196 (715)
T ss_pred Cccchhhhh
Confidence 455555433
No 92
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=97.46 E-value=0.00039 Score=56.01 Aligned_cols=61 Identities=26% Similarity=0.251 Sum_probs=36.0
Q ss_pred CCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 274 PGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 274 eGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
+|++.+.+|+.++++ |+|+|.|+..+=|+|.+|+. .-+++||+|.|.|--= . ..|+..++|
T Consensus 1 iG~~~~L~V~~~~~~-g~fL~~~~~~~vlLp~~e~~-----~~~~~Gd~v~VFvY~D--~-~~rl~AT~k 61 (61)
T PF13509_consen 1 IGQINTLKVVDKNEF-GYFLDDGEGKEVLLPKSEVP-----EPLKVGDEVEVFVYLD--K-EGRLVATTK 61 (61)
T ss_dssp --------EEEE-SS-EEEEEETT-EEEEEEGGG-----------TTSEEEEEEEE---T-TS-EEEE--
T ss_pred CCCCcceEEEEEeCC-EEEEECCCCCEEEechHHcC-----CCCCCCCEEEEEEEEC--C-CCCEEEecC
Confidence 589999999999999 99999998779999999885 4599999999998753 2 357777765
No 93
>PRK10811 rne ribonuclease E; Reviewed
Probab=97.45 E-value=0.00023 Score=82.94 Aligned_cols=58 Identities=31% Similarity=0.474 Sum_probs=49.6
Q ss_pred CCCCEEEEEEEEeeec-ceeEEEcCCceeeeeEccccccc------------ccccccccCCEEEEEEEEe
Q 005716 273 YPGQICEGKVTTVHLY-QGAFVDIGGVYDGWVPIKGNDWY------------WIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 273 keGqIVEGkVtnItdF-~GAFVDIGGv~DGLVHISEISW~------------rI~dVLKVGDeVkVKVLsI 330 (681)
.+|.|+.|+|++|.+= +|||||||.+..|++|++++... .|...|++||.|.|.|..-
T Consensus 37 ~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~f~~~~~~~~~~~i~~~Lk~GqeILVQV~KE 107 (1068)
T PRK10811 37 KKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKE 107 (1068)
T ss_pred CccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccccccccccccccccccccCCCCEEEEEEeec
Confidence 4899999999999763 47999999999999999999531 3456899999999999875
No 94
>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=97.39 E-value=0.0004 Score=77.24 Aligned_cols=64 Identities=11% Similarity=-0.020 Sum_probs=52.7
Q ss_pred CCEEEEEEEEeeecceeEEEc-CCceeeeeEcccccc----c---------cc--ccccccCCEEEEEEEEeeCCCCCee
Q 005716 275 GQICEGKVTTVHLYQGAFVDI-GGVYDGWVPIKGNDW----Y---------WI--RHHIKVGMHVIVEILAKRDPYRFRF 338 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDI-GGv~DGLVHISEISW----~---------rI--~dVLKVGDeVkVKVLsIdD~eR~RI 338 (681)
|+...|+|++|+.| |.||.| ..+.+||||++.+.- . .+ +..+++||.|+|+|.++ |..+.+|
T Consensus 558 ~~~f~g~I~~v~~~-g~~v~l~~~~~~g~v~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~v-d~~~~~i 635 (639)
T TIGR02062 558 NTRFAAEIVDISRG-GMRVRLLENGAIAFIPAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEV-RMETRSI 635 (639)
T ss_pred CcEEEEEEEeeeCC-cEEEEEecCceEEEEEhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEe-ccccCcE
Confidence 56999999999999 999999 556799999999942 1 11 12799999999999999 7777777
Q ss_pred ee
Q 005716 339 PI 340 (681)
Q Consensus 339 SL 340 (681)
.+
T Consensus 636 ~~ 637 (639)
T TIGR02062 636 IA 637 (639)
T ss_pred ee
Confidence 64
No 95
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.34 E-value=0.00064 Score=68.96 Aligned_cols=70 Identities=21% Similarity=0.230 Sum_probs=61.3
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccc-------cccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYW-------IRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~r-------I~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
++||+|=|+|+.+... |=.||||+.+.+++|+|++-|.. .+.+|++||-|.++|.++ |.. ....|++|..
T Consensus 63 ~~gD~VIG~I~~v~~~-~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~v-d~~-~~~~L~~k~~ 139 (239)
T COG1097 63 EVGDVVIGKIIEVGPS-GWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDV-DRD-GEVELTLKDE 139 (239)
T ss_pred CCCCEEEEEEEEEccc-ceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEc-cCC-CceEEEeecC
Confidence 5799999999999998 99999999999999999996644 345999999999999999 544 7889999544
No 96
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.13 E-value=0.0023 Score=55.92 Aligned_cols=69 Identities=17% Similarity=0.041 Sum_probs=58.4
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccc--ccccccccccCCEEEEEEEEeeCCCCCeeeeeeec
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGND--WYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRF 344 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEIS--W~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~ 344 (681)
++||+|=|+|+.++.- +-+||||+...|++|++..- -++.+..|++||-|-++|.++ ++. ...-||+..
T Consensus 5 ~~gD~VIG~V~~~~~~-~~~VdI~s~~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~-~~~-~~~eLtc~~ 75 (86)
T cd05790 5 AKGDHVIGIVVAKAGD-FFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKA-NRD-MEPELSCVD 75 (86)
T ss_pred CCCCEEEEEEEEEcCC-eEEEEcCCCcceEechHHcccccccccccCCCCCEEEEEEEec-CCC-CCeEEEEeC
Confidence 5899999999999875 88999999999999998873 345567999999999999999 544 457888865
No 97
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=97.04 E-value=0.0011 Score=72.02 Aligned_cols=79 Identities=22% Similarity=0.244 Sum_probs=61.1
Q ss_pred CCCCCCEEEEEEEEeee-cceeEEEcCCceeeeeEccccccc-------ccccccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 271 FYYPGQICEGKVTTVHL-YQGAFVDIGGVYDGWVPIKGNDWY-------WIRHHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 271 ~LkeGqIVEGkVtnItd-F~GAFVDIGGv~DGLVHISEISW~-------rI~dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
...+|.|+.|+|++|.+ .+.||||||....|++|.+++.+. +|+.+++.||.+-|.|+.- ....+=-.||-
T Consensus 34 ~~~~gniy~grv~~i~p~~~aafvdig~~r~gfl~~~~~~~~~~~~~~~~i~~~lr~~~~~~Vqv~ke-~~G~Kga~lT~ 112 (487)
T COG1530 34 EQIVGNIYKGRVTRVLPSLEAAFVDIGLERNGFLHLSEIVPYFRAVLEEKIKVRLRGGQATLVQVVKE-PRGTKGARLTT 112 (487)
T ss_pred EeeecCceEEEecccCccchhheeeccCCccceEEecccchhhhhcccccceeeecCCceEEEEEEee-cCcccccccee
Confidence 44589999999998864 578999999999999999999992 2567999999999999987 55544444444
Q ss_pred eccCCCcc
Q 005716 343 RFVQPNID 350 (681)
Q Consensus 343 K~~~pnPW 350 (681)
+...+...
T Consensus 113 ~Is~~gry 120 (487)
T COG1530 113 DISLAGRY 120 (487)
T ss_pred EEeeceeE
Confidence 44444333
No 98
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=96.79 E-value=0.0029 Score=54.97 Aligned_cols=57 Identities=19% Similarity=0.147 Sum_probs=40.9
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCC------------------ceeeeeEccccccc-----ccccccccCCEEEEEEEE
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGG------------------VYDGWVPIKGNDWY-----WIRHHIKVGMHVIVEILA 329 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGG------------------v~DGLVHISEISW~-----rI~dVLKVGDeVkVKVLs 329 (681)
++|++|.|+|++|+.= -|+|+|=. ...|+||++++.=. .+.+-+++||.|+++|||
T Consensus 3 ~vGdiV~~rVtrv~~~-~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~ViS 81 (82)
T PF10447_consen 3 KVGDIVIARVTRVNPR-QAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARVIS 81 (82)
T ss_dssp -TT-EEEEEEEEE-SS-EEEEEEEES----------SSS----SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEEEE
T ss_pred CCCCEEEEEEEEEecc-EEEEEEEEEEeccccccccCCcccccccEEEEEeeeecccccchhhHHhccCCCCEEEEEEee
Confidence 6899999999999985 89998722 46799999998542 245789999999999998
Q ss_pred e
Q 005716 330 K 330 (681)
Q Consensus 330 I 330 (681)
+
T Consensus 82 l 82 (82)
T PF10447_consen 82 L 82 (82)
T ss_dssp E
T ss_pred C
Confidence 6
No 99
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=96.79 E-value=0.0038 Score=66.68 Aligned_cols=99 Identities=17% Similarity=0.189 Sum_probs=66.8
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCC--CeeeeeeeccCCCcc
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYR--FRFPIEMRFVQPNID 350 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR--~RISLSLK~~~pnPW 350 (681)
++|++|.|+|.++....++|||||+. +|+++-+|.. ..+.+++||.|+|.|.+|+...+ -.|-||. +.|+-=
T Consensus 137 ~~Geiv~g~V~r~~~~~~i~vdlg~~-ea~LP~~eqi---p~E~~~~Gdrik~~i~~V~~~~k~gp~IilSR--t~p~~v 210 (374)
T PRK12328 137 KVGKIVFGTVVRVDNEENTFIEIDEI-RAVLPMKNRI---KGEKFKVGDVVKAVLKRVKIDKNNGILIELSR--TSPKFL 210 (374)
T ss_pred hcCcEEEEEEEEEecCCCEEEEcCCe-EEEeCHHHcC---CCCcCCCCCEEEEEEEEEecCCCCCCEEEEEc--CCHHHH
Confidence 57999999999999753599999974 9999988865 56789999999999999965444 2566665 333322
Q ss_pred ccccccCCCCCccccCCCCCchhhhhccCC
Q 005716 351 HLIFNRFDFAPIFHRDEDKNPDELRRDCGR 380 (681)
Q Consensus 351 ~~I~erf~vgpI~~r~~d~n~geV~Rd~GR 380 (681)
..+++ -.+|-|.. |...---|+|++|.
T Consensus 211 ~~Lfe-~EVPEI~d--G~VeIk~IARepG~ 237 (374)
T PRK12328 211 EALLE-LEVPEIKD--GEVIIIHSARIPGE 237 (374)
T ss_pred HHHHH-HhCccccC--CeEEEEEEeccCcc
Confidence 22222 23455554 21222446775553
No 100
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=96.76 E-value=0.0013 Score=68.31 Aligned_cols=97 Identities=22% Similarity=0.234 Sum_probs=83.4
Q ss_pred cccCCCCCCCCEEEEEEEEeeecceeEEEc--CCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeee
Q 005716 266 MYELPFYYPGQICEGKVTTVHLYQGAFVDI--GGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPI 340 (681)
Q Consensus 266 v~~L~~LkeGqIVEGkVtnItdF~GAFVDI--GGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISL 340 (681)
+|+=.+=.++++|-+.|++|..- ||+|-| =+.+.|+|-.||+|-.||+ .+++||-.=-|.||.| |++++=|-|
T Consensus 8 ~ye~kyPev~e~VmvnV~sIaem-Gayv~LlEYnniEGmiLlsELSrRRIRSI~klirVGr~E~vvVlrV-DkekGYIDL 85 (304)
T KOG2916|consen 8 FYENKYPEVEEIVMVNVRSIAEM-GAYVKLLEYNNIEGMILLSELSRRRIRSIQKLIRVGRNEPVVVLRV-DKEKGYIDL 85 (304)
T ss_pred hhhccCCCcccEEEEEeeEehhc-cceEeeeecCCcccchhhhHHHHHHHHHHHHHHhcCCcceEEEEEE-cCCCCceec
Confidence 34444557899999999999998 999998 2356999999999998876 4999999999999999 899999999
Q ss_pred eeeccCCCccccccccCCCCCccc
Q 005716 341 EMRFVQPNIDHLIFNRFDFAPIFH 364 (681)
Q Consensus 341 SLK~~~pnPW~~I~erf~vgpI~~ 364 (681)
|++.+.|+-=..-.++|.-.-.+|
T Consensus 86 SkrrVs~ed~~kC~Er~~ksK~v~ 109 (304)
T KOG2916|consen 86 SKRRVSPEDKEKCEERFAKSKLVY 109 (304)
T ss_pred hhccCCHHHHHHHHHHHHHhHHHH
Confidence 999999988777788887766555
No 101
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=96.43 E-value=0.0087 Score=53.28 Aligned_cols=66 Identities=9% Similarity=0.088 Sum_probs=56.5
Q ss_pred CCCCEEEEEEEEeeecceeEEEc-CCceeeeeE-cccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDI-GGVYDGWVP-IKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDI-GGv~DGLVH-ISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
++|+++. .|+.|.+. ||+|.| +=+..|+|- -||++-.+++ +.+ ||-.+.|.||.+ |+.++=|-||.
T Consensus 15 ~v~dvv~-~Vv~i~d~-~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRV-Dk~KGYIDLs~ 85 (86)
T PHA02858 15 NINEVTK-GIVFVKDN-IFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRT-DKLKGYIDVRH 85 (86)
T ss_pred CCCeEEE-EEEEEecc-EEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEE-CCCCCEEEeEc
Confidence 6799999 88899999 999998 322688888 9999987764 577 999999999999 88888888874
No 102
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=96.19 E-value=0.0055 Score=72.69 Aligned_cols=74 Identities=26% Similarity=0.344 Sum_probs=60.0
Q ss_pred CCCCCCCEEEEEEEEeeecceeE--EEcCCceeeeeEcccccccccc---cccccCCEEEEEEEEeeCCCCCeeeeeeec
Q 005716 270 PFYYPGQICEGKVTTVHLYQGAF--VDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEILAKRDPYRFRFPIEMRF 344 (681)
Q Consensus 270 ~~LkeGqIVEGkVtnItdF~GAF--VDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKVLsIdD~eR~RISLSLK~ 344 (681)
+.+.+|.+|.++|++|+.=.|+- |=+.++.+|.||++++|-..|+ +-|+|||+|.++|++| |.+|+-+-||+|.
T Consensus 981 et~~~g~iV~~~V~~vt~rr~~Cv~v~ld~G~~g~i~~~~~Sd~~v~~p~~~v~vgq~v~~kvi~i-d~e~f~v~Ls~r~ 1059 (1299)
T KOG1856|consen 981 ETFYEGAIVPVTVTKVTHRRGICVRVRLDCGVTGFILAKNLSDRDVRRPENRVKVGQTVYCKVIKI-DKERFSVELSCRT 1059 (1299)
T ss_pred hHhccCceEEEeeeEEEecccceeEEEecCCCceeeeccccChhhccCHHHhhccCceEEEEeeee-eHhhhhhhhhhhh
Confidence 44889999999999999754444 2234446999999999986554 5889999999999999 8888888888764
No 103
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=96.17 E-value=0.015 Score=57.67 Aligned_cols=74 Identities=22% Similarity=0.214 Sum_probs=57.9
Q ss_pred hcccCCCCCCCCEEEEEEEEeeecceeEEEcCCc----------eeeeeEccccccc---ccccccccCCEEEEEEEEee
Q 005716 265 GMYELPFYYPGQICEGKVTTVHLYQGAFVDIGGV----------YDGWVPIKGNDWY---WIRHHIKVGMHVIVEILAKR 331 (681)
Q Consensus 265 gv~~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv----------~DGLVHISEISW~---rI~dVLKVGDeVkVKVLsId 331 (681)
+..+.+-++.|++|-|.|+++.. |.|-|.|=++ ..|-||||+++-. .+++.+++||.|+++|++.-
T Consensus 55 ~~~~~~~~K~GdiV~grV~~v~~-~~a~V~i~~ve~~~r~~~~~~~~~ihvs~~~~~~~~~~~d~f~~GDivrA~Vis~~ 133 (188)
T COG1096 55 GKKTPPLPKGGDIVYGRVTDVRE-QRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEKLSDAFRIGDIVRARVISTG 133 (188)
T ss_pred CCCCCCCCCCCCEEEEEEeeccc-eEEEEEEEEEecccccCCCCceeeEEEEecccccccccccccccccEEEEEEEecC
Confidence 33346678899999999999999 4999887333 3468999999764 56789999999999999993
Q ss_pred CCCCCeeeeeee
Q 005716 332 DPYRFRFPIEMR 343 (681)
Q Consensus 332 D~eR~RISLSLK 343 (681)
..+.||.+
T Consensus 134 ----~~~~Lst~ 141 (188)
T COG1096 134 ----DPIQLSTK 141 (188)
T ss_pred ----CCeEEEec
Confidence 44555653
No 104
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.09 E-value=0.017 Score=49.78 Aligned_cols=64 Identities=19% Similarity=0.258 Sum_probs=53.3
Q ss_pred CCEEEEEEEEeeecceeEEEcCC-ceeeeeEcccccccccc------cccccCCEE-EEEEEEeeCCCCCeeeeeee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGG-VYDGWVPIKGNDWYWIR------HHIKVGMHV-IVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGG-v~DGLVHISEISW~rI~------dVLKVGDeV-kVKVLsIdD~eR~RISLSLK 343 (681)
|++|+|+|..=++- +++|+|++ +.-|.|+.-.+|. ++. +-+.+||++ .+-|| +..+..|-||.|
T Consensus 1 G~lV~~~V~EKt~D-~l~v~l~~~~l~a~l~~~HLsD-~~~k~~~~~~klrvG~~L~~~lvL---~~~~r~i~lt~K 72 (72)
T cd05699 1 GKLVDARVLKKTLN-GLEVAILPEEIRAFLPTMHLSD-HVSNCPLLWHCLQEGDTIPNLMCL---SNYKGRIILTKK 72 (72)
T ss_pred CceEEEEEEEEcCC-cEEEEecCCCcEEEEEccccCC-chhhCHHHHhhhhcCCCccceEEE---eccccEEEEecC
Confidence 78999999999996 99999964 6688888888877 554 389999999 99999 456777878765
No 105
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=96.08 E-value=0.014 Score=60.79 Aligned_cols=62 Identities=16% Similarity=0.239 Sum_probs=54.9
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeeeeec
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRF 344 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~ 344 (681)
+|.|.|+|-++..- |.||=+.+++-|+||-||.- ....+|+.|++.|+.++. .++|-||++-
T Consensus 156 nq~v~~tVYr~~~~-G~fv~~e~~~~GfIh~sEr~-----~~prlG~~l~~rVi~~re--Dg~lnLSl~p 217 (287)
T COG2996 156 NQEVDATVYRLLES-GTFVITENGYLGFIHKSERF-----AEPRLGERLTARVIGVRE--DGKLNLSLRP 217 (287)
T ss_pred cCeeeeEEEEEecc-ceEEEEcCCeEEEEcchhhc-----ccccCCceEEEEEEEEcc--CCeeeccccc
Confidence 78999999999998 99999988899999999963 356789999999999964 6899999953
No 106
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=95.51 E-value=0.035 Score=57.93 Aligned_cols=166 Identities=20% Similarity=0.123 Sum_probs=114.4
Q ss_pred cCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccccccc-ccccCCEEEEEEEEeeCCCCCeeeeeeeccC
Q 005716 268 ELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRH-HIKVGMHVIVEILAKRDPYRFRFPIEMRFVQ 346 (681)
Q Consensus 268 ~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~d-VLKVGDeVkVKVLsIdD~eR~RISLSLK~~~ 346 (681)
..+.+.+|.-=.|+|+.+.+-.|||||.|...|=||+++++.-. ++ -.++||++-|.+. + |+ +.||.=.++.
T Consensus 67 ~~p~~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~--~~~wpq~Gd~l~v~l~-~-Dk-k~Ri~g~~a~-- 139 (287)
T COG2996 67 REPKATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTL--KSLWPQKGDKLLVYLY-V-DK-KGRIWGTLAI-- 139 (287)
T ss_pred ecceEeecceeEEEEEEEcCCcceEEecCCCcceeeehhhcccc--cccCCCCCCEEEEEEE-E-cc-CCcEEEEecc--
Confidence 45788899999999999994459999999999999999988531 12 3789999988864 5 43 3588766642
Q ss_pred CCccccccccCCC---CCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh----------
Q 005716 347 PNIDHLIFNRFDF---APIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA---------- 413 (681)
Q Consensus 347 pnPW~~I~erf~v---gpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a---------- 413 (681)
..+-++++.++-. ...++ +.|-| +.+-|.||=+..+--|++|=|-|
T Consensus 140 ~~~l~~l~~~~~~~l~nq~v~-------~tVYr--------------~~~~G~fv~~e~~~~GfIh~sEr~~~prlG~~l 198 (287)
T COG2996 140 EKILENLATPAYNNLKNQEVD-------ATVYR--------------LLESGTFVITENGYLGFIHKSERFAEPRLGERL 198 (287)
T ss_pred hhHHHhcCCccchhhhcCeee-------eEEEE--------------EeccceEEEEcCCeEEEEcchhhcccccCCceE
Confidence 3334444544444 66666 88888 88999999988888899987654
Q ss_pred ----------------------------hhhhccccccCccccCCccccccCCCcccCccCCe-eehhhhhhhh---hhh
Q 005716 414 ----------------------------EQLILDDMEANPDKYKGKKLSELTDDEEFDDENSV-EYTKVNYKKA---LLA 461 (681)
Q Consensus 414 ----------------------------EQmiLdd~e~npdky~~~~~~~l~d~ed~de~n~v-~~t~~~~k~~---~lp 461 (681)
.||||+=++.|.-. -++.|-++=++=.+. -.+|++||++ |+.
T Consensus 199 ~~rVi~~reDg~lnLSl~p~~~E~l~~daq~Il~yL~~~gG~------mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K 272 (287)
T COG2996 199 TARVIGVREDGKLNLSLRPRAHEMLDEDAQMILTYLESNGGF------MPFNDKSSPEDIKATFGISKGQFKRAIGGLMK 272 (287)
T ss_pred EEEEEEEccCCeeecccccccHHhhhhhHHHHHHHHHHcCCc------cccCCCCCHHHHHHHhCcCHHHHHHHHHHHHh
Confidence 35666555544322 245555554443333 5668999987 555
Q ss_pred HHHHhc
Q 005716 462 KIILKT 467 (681)
Q Consensus 462 k~~~~~ 467 (681)
+-.+++
T Consensus 273 ~g~I~q 278 (287)
T COG2996 273 AGKIKQ 278 (287)
T ss_pred CCeEEE
Confidence 444444
No 107
>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=95.02 E-value=0.0079 Score=49.78 Aligned_cols=36 Identities=3% Similarity=-0.008 Sum_probs=32.4
Q ss_pred CCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 357 FDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 357 f~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
++.|+++. |.|.+ .++||+||++-|+|+||+|++..
T Consensus 1 ~k~G~~V~-------g~V~~--------------i~~~G~fV~l~~~v~G~v~~~~l 36 (74)
T cd05705 1 IKEGQLLR-------GYVSS--------------VTKQGVFFRLSSSIVGRVLFQNV 36 (74)
T ss_pred CCCCCEEE-------EEEEE--------------EeCCcEEEEeCCCCEEEEEHHHc
Confidence 46788888 99999 99999999999999999998875
No 108
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=94.80 E-value=0.077 Score=58.30 Aligned_cols=66 Identities=8% Similarity=0.070 Sum_probs=50.8
Q ss_pred CCCCEEEEEEEEeeecceeEEEcC---C--ceeeeeEcccccccccccccccCCEEEEEEEEeeCCC-CC-eeeeee
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIG---G--VYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPY-RF-RFPIEM 342 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIG---G--v~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~e-R~-RISLSL 342 (681)
++|++|.|+|.++..- +++|||| | ...|+++-++.. ..+.+++||.|+|.|++|.... ++ .|-||.
T Consensus 151 ~~GeIV~G~V~r~e~~-~viv~l~~~~g~~~~EaiLP~~Eqi---p~E~y~~Gdrika~i~~V~~~~~kGpqIilSR 223 (449)
T PRK12329 151 LEDTVLTARVLRFERQ-SVIMAVSSGFGQPEVEAELPKREQL---PNDNYRANATFKVFLKEVSEGPRRGPQLFVSR 223 (449)
T ss_pred hcCcEEEEEEEEEcCC-CEEEEecccCCCcceEEEecHHHcC---CCCcCCCCCEEEEEEEEeecCCCCCCEEEEEc
Confidence 4799999999999886 9999994 2 268999887742 4568999999999999995432 22 455554
No 109
>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=93.77 E-value=0.008 Score=68.69 Aligned_cols=36 Identities=17% Similarity=0.148 Sum_probs=33.5
Q ss_pred cCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehh
Q 005716 356 RFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHN 412 (681)
Q Consensus 356 rf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~ 412 (681)
..++|.|+. |+|++ +++||+||++.|+++||+|||.
T Consensus 644 ~~~vG~i~~-------GkV~~--------------I~dfGaFVel~~G~eGLvHISe 679 (719)
T TIGR02696 644 MPEVGERFL-------GTVVK--------------TTAFGAFVSLLPGKDGLLHISQ 679 (719)
T ss_pred cCCCCCEEE-------EEEEE--------------EECceEEEEecCCceEEEEhhh
Confidence 367899999 99999 9999999999999999999994
No 110
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=93.45 E-value=0.026 Score=53.35 Aligned_cols=38 Identities=5% Similarity=0.020 Sum_probs=34.2
Q ss_pred cCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 356 RFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 356 rf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
.+++|.+++ |+|.. ++.|||||++.-+=-||||||..-
T Consensus 2 ~~kvG~~l~-------GkItg--------------I~~yGAFV~l~~g~tGLVHISEIa 39 (129)
T COG1098 2 SMKVGSKLK-------GKITG--------------ITPYGAFVELEGGKTGLVHISEIA 39 (129)
T ss_pred CccccceEE-------EEEEe--------------eEecceEEEecCCCcceEEehHhh
Confidence 467899999 99999 999999999999999999999643
No 111
>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=93.43 E-value=0.03 Score=48.10 Aligned_cols=39 Identities=3% Similarity=0.020 Sum_probs=34.5
Q ss_pred ccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCC--CcccccCccccceeeehhhh
Q 005716 355 NRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEE--EGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 355 erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~ef--gafve~hP~VegL~hIs~aE 414 (681)
.++.+|.|+. ++|.+ +..+ ||||++.++++||+|+|...
T Consensus 3 ~~~~~G~iy~-------g~V~~--------------i~~~~~GaFV~l~~g~~Gllh~seis 43 (88)
T cd04453 3 REPIVGNIYL-------GRVKK--------------IVPGLQAAFVDIGLGKNGFLHLSDIL 43 (88)
T ss_pred CcCCCCCEEE-------EEEEE--------------eccCCcEEEEEeCCCCEEEEEhHHcC
Confidence 4577899999 99999 8886 99999999999999999663
No 112
>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=92.91 E-value=0.03 Score=44.54 Aligned_cols=36 Identities=6% Similarity=0.079 Sum_probs=32.3
Q ss_pred CCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 357 FDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 357 f~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
|++|.++. +.|.+ ...||.|+++.++++||+|++..
T Consensus 1 ~~~g~~~~-------g~V~~--------------i~~~G~fv~l~~~~~Gl~~~~~l 36 (72)
T cd05689 1 YPEGTRLF-------GKVTN--------------LTDYGCFVELEEGVEGLVHVSEM 36 (72)
T ss_pred CcCCCEEE-------EEEEE--------------EEeeEEEEEcCCCCEEEEEEEec
Confidence 56788888 89999 99999999999999999999865
No 113
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=92.88 E-value=0.07 Score=50.99 Aligned_cols=68 Identities=10% Similarity=-0.013 Sum_probs=53.0
Q ss_pred cCCEEEEEEEEee--CCCCCeeeeeeeccCCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCc
Q 005716 319 VGMHVIVEILAKR--DPYRFRFPIEMRFVQPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEG 396 (681)
Q Consensus 319 VGDeVkVKVLsId--D~eR~RISLSLK~~~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efga 396 (681)
.+..+.+.++.+- |..+.+|+| +||+.....+++|+|+. ++|.+ ...+|+
T Consensus 29 ~~~~i~as~~G~~~id~~~~~Isv-------~P~~~~~~~~~~GdiV~-------GkV~~--------------i~~~g~ 80 (189)
T PRK09521 29 DNGEVYASVVGKVFIDDINRKISV-------IPFKKTPPLLKKGDIVY-------GRVVD--------------VKEQRA 80 (189)
T ss_pred eCCEEEEEeeEEEEEcCCCCEEEE-------ecCcCCCCCCCCCCEEE-------EEEEE--------------EcCCeE
Confidence 3445555444331 566788888 59998888888999999 99999 899999
Q ss_pred ccccC----------ccccceeeehhhh
Q 005716 397 LLSTH----------PYVDKLWQIHNAE 414 (681)
Q Consensus 397 fve~h----------P~VegL~hIs~aE 414 (681)
||.+. ++++|++|++..-
T Consensus 81 ~V~I~~~~~~~~~l~~~~~G~l~~s~i~ 108 (189)
T PRK09521 81 LVRIVSIEGSERELATSKLAYIHISQVS 108 (189)
T ss_pred EEEEEEecccccccCCCceeeEEhhHcC
Confidence 99974 5799999999764
No 114
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=92.87 E-value=0.019 Score=67.09 Aligned_cols=69 Identities=17% Similarity=0.126 Sum_probs=47.7
Q ss_pred cccCCEEEEEEEEeeCCCCCeeeeeeeccCCCccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCc
Q 005716 317 IKVGMHVIVEILAKRDPYRFRFPIEMRFVQPNIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEG 396 (681)
Q Consensus 317 LKVGDeVkVKVLsIdD~eR~RISLSLK~~~pnPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efga 396 (681)
+.++|...|+|++. |.. .+...+.. . ..+....++|.|+. -++|.+ .+.||+
T Consensus 719 Idi~ddg~V~I~a~-d~~--~i~~A~~~----I-~~l~~~~~vG~iy~------~g~V~~--------------I~~FGa 770 (891)
T PLN00207 719 IDTQDDGTVKITAK-DLS--SLEKSKAI----I-SSLTMVPTVGDIYR------NCEIKS--------------IAPYGA 770 (891)
T ss_pred cCcCCCeeEEEEeC-CHH--HHHHHHHH----H-HHHhcCcCCCcEEE------CcEEEE--------------EeccEE
Confidence 66888888888888 322 22222100 0 11222356899995 158999 999999
Q ss_pred ccccCccccceeeehhh
Q 005716 397 LLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 397 fve~hP~VegL~hIs~a 413 (681)
||++.|+++||+|||..
T Consensus 771 FVeL~~g~EGLVHISeL 787 (891)
T PLN00207 771 FVEIAPGREGLCHISEL 787 (891)
T ss_pred EEEeCCCCEEEEEhhhc
Confidence 99999999999999954
No 115
>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=92.69 E-value=0.041 Score=44.97 Aligned_cols=35 Identities=6% Similarity=-0.146 Sum_probs=29.9
Q ss_pred CCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCC-CCcccccCccccceeeehhh
Q 005716 358 DFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPE-EEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 358 ~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~e-fgafve~hP~VegL~hIs~a 413 (681)
++|.|+. |.|.+ ..+ ||+|+++-|+++||+|||.+
T Consensus 2 ~~G~iv~-------G~V~~--------------i~~~~g~~v~l~~~~~Glvhis~~ 37 (72)
T cd05704 2 EEGAVTL-------GMVTK--------------VIPHSGLTVQLPFGKTGLVSIFHL 37 (72)
T ss_pred CCCCEEE-------EEEEE--------------eeCCcEEEEECCCCCEEEEEHHHh
Confidence 4577777 88888 665 89999999999999999965
No 116
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=92.09 E-value=0.045 Score=57.65 Aligned_cols=40 Identities=10% Similarity=0.063 Sum_probs=35.9
Q ss_pred ccccCC-CCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccC--ccccceeeehhh
Q 005716 353 IFNRFD-FAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTH--PYVDKLWQIHNA 413 (681)
Q Consensus 353 I~erf~-vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~h--P~VegL~hIs~a 413 (681)
..++|+ +|+++. |+|.+ +.+||+||++. ++|+||+|||..
T Consensus 10 ~~~~~P~~GdvV~-------g~V~~--------------I~d~GafV~L~EY~gvEGlIhiSEl 52 (319)
T PTZ00248 10 YEQKFPEEDDLVM-------VKVVR--------------ITEMGAYVSLLEYDDIEGMILMSEL 52 (319)
T ss_pred hhhhCCCCCCEEE-------EEEEE--------------EeCCeEEEEecCCCCcEEEEEHHHh
Confidence 456788 799999 99999 99999999997 889999999974
No 117
>PRK08582 hypothetical protein; Provisional
Probab=91.64 E-value=0.059 Score=50.07 Aligned_cols=37 Identities=5% Similarity=0.039 Sum_probs=33.9
Q ss_pred CCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 357 FDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 357 f~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
+.+|.|+. +.|.. ++.||+||++.++++||+|||.+-
T Consensus 3 ~kvG~iv~-------G~V~~--------------I~~fG~fV~L~~~~~GlVhiSels 39 (139)
T PRK08582 3 IEVGSKLQ-------GKVTG--------------ITNFGAFVELPEGKTGLVHISEVA 39 (139)
T ss_pred CcCCCEEE-------EEEEE--------------EECCeEEEEECCCCEEEEEeeccC
Confidence 56789998 99999 999999999999999999999764
No 118
>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=90.79 E-value=0.068 Score=43.43 Aligned_cols=34 Identities=18% Similarity=0.202 Sum_probs=29.1
Q ss_pred CCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCcc--ccceeeehhh
Q 005716 358 DFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPY--VDKLWQIHNA 413 (681)
Q Consensus 358 ~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~--VegL~hIs~a 413 (681)
.+|.|+. ++|.+ ..+||+||++ ++ ++||+|+|..
T Consensus 2 ~~g~~~~-------g~V~~--------------i~~fG~fv~l-~~~~~eGlvh~sel 37 (73)
T cd05686 2 ALYQIFK-------GEVAS--------------VTEYGAFVKI-PGCRKQGLVHKSHM 37 (73)
T ss_pred cCCCEEE-------EEEEE--------------EEeeeEEEEE-CCCCeEEEEEchhh
Confidence 3677888 89999 8999999999 66 6999999954
No 119
>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=90.55 E-value=0.064 Score=41.93 Aligned_cols=24 Identities=13% Similarity=0.057 Sum_probs=22.3
Q ss_pred CCCCCcccccCccccceeeehhhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~aE 414 (681)
...||.||++.++++||+|++...
T Consensus 11 i~~~G~fv~l~~~~~Glv~~~~l~ 34 (69)
T cd05690 11 ITDFGIFVGLDGGIDGLVHISDIS 34 (69)
T ss_pred EEeeeEEEEeCCCCEEEEEHHHCC
Confidence 889999999999999999999765
No 120
>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=89.92 E-value=0.11 Score=41.48 Aligned_cols=36 Identities=14% Similarity=0.044 Sum_probs=31.7
Q ss_pred CCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 358 DFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 358 ~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
+.|.|+. ++|.+ ..++|+|+++.++++|++|++.+-
T Consensus 2 ~~G~iv~-------g~V~~--------------v~~~gi~v~l~~~~~g~v~~s~l~ 37 (73)
T cd05706 2 KVGDILP-------GRVTK--------------VNDRYVLVQLGNKVTGPSFITDAL 37 (73)
T ss_pred CCCCEEE-------EEEEE--------------EeCCeEEEEeCCCcEEEEEhhhcc
Confidence 4677888 99999 899999999999999999998653
No 121
>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=89.85 E-value=3.4 Score=33.01 Aligned_cols=50 Identities=22% Similarity=0.122 Sum_probs=37.5
Q ss_pred EEEEEEEeee---cceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEE
Q 005716 278 CEGKVTTVHL---YQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILA 329 (681)
Q Consensus 278 VEGkVtnItd---F~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLs 329 (681)
++|+|+...+ | |--..-++..|=++|+|++.-.. -..|++|+.|+..|..
T Consensus 1 ~~G~V~~~~~~kgy-GFI~~~~~~~diFfh~s~~~~~~-~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGY-GFITSDDGGEDIFFHISDLSGNG-FRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTE-EEEEETTSSSEEEEEGGGBCSSS-STS--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCc-eEEEEcccceeEEeccccccccc-cccCCCCCEEEEEEEE
Confidence 4799999986 7 64444455558999999997655 5678999999999987
No 122
>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=89.80 E-value=0.095 Score=42.73 Aligned_cols=23 Identities=9% Similarity=0.078 Sum_probs=20.8
Q ss_pred C-CCCCcccccCccccceeeehhh
Q 005716 391 K-PEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 391 ~-~efgafve~hP~VegL~hIs~a 413 (681)
. .+||+||++.|+|+||+|+|..
T Consensus 12 v~~~~G~~V~l~~gv~G~i~~s~l 35 (71)
T cd05696 12 VEPDLGAVFELKDGLLGFVHISHL 35 (71)
T ss_pred EccCceEEEEeCCCCEEEEEHHHC
Confidence 5 5899999999999999999954
No 123
>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=89.60 E-value=0.11 Score=41.19 Aligned_cols=23 Identities=9% Similarity=0.011 Sum_probs=21.6
Q ss_pred CCCCCcccccCccccceeeehhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~a 413 (681)
..++|+||++.++++||+|++..
T Consensus 11 v~~~Gv~V~l~~~~~G~v~~s~l 33 (68)
T cd05707 11 IANNGVFVTLGRGVDARVRVSEL 33 (68)
T ss_pred EECccEEEEeCCCCEEEEEHHHC
Confidence 88999999999999999999965
No 124
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=89.37 E-value=1.1 Score=44.26 Aligned_cols=61 Identities=21% Similarity=0.303 Sum_probs=41.2
Q ss_pred CCCEEEEEEEEeeecceeEEEcCCceeeee--E--ccccccc---c-c----c--cccccCCEEEEEEEEeeCCCCC
Q 005716 274 PGQICEGKVTTVHLYQGAFVDIGGVYDGWV--P--IKGNDWY---W-I----R--HHIKVGMHVIVEILAKRDPYRF 336 (681)
Q Consensus 274 eGqIVEGkVtnItdF~GAFVDIGGv~DGLV--H--ISEISW~---r-I----~--dVLKVGDeVkVKVLsIdD~eR~ 336 (681)
.|+||.|+|+.+..- |+|+.+|=. .=++ | -.++-.. . + . .++.+|..|.+||+..+-.++.
T Consensus 81 KGEVvdgvV~~Vnk~-G~F~~~GPl-~~f~sshl~ppd~~f~p~~n~P~f~~~d~s~I~~~~~VR~kiigtr~~~~~ 155 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKM-GVFARSGPL-EVFYSSHLKPPDYEFDPGENPPNFQTEDESVIQKGVEVRLKIIGTRVDETE 155 (170)
T ss_pred CCcEEEEEEEEEeee-eEEEeccce-EeeeecccCCCCcccCCCCCCCcccccccceeeeCcEEEEEEEEEEEeeee
Confidence 599999999999997 999999843 1111 0 0111110 0 1 1 1899999999999999655444
No 125
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=88.84 E-value=0.12 Score=59.26 Aligned_cols=40 Identities=15% Similarity=0.213 Sum_probs=37.1
Q ss_pred cccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehh
Q 005716 352 LIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHN 412 (681)
Q Consensus 352 ~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~ 412 (681)
.+.+.+.+|-|+. |.|.| ...|||||++.||-+||+|||+
T Consensus 612 ~i~~e~evg~iy~-------G~V~r--------------i~~fGaFv~l~~gkdgl~hiS~ 651 (692)
T COG1185 612 AITREVEVGEVYE-------GTVVR--------------IVDFGAFVELLPGKDGLVHISQ 651 (692)
T ss_pred HHHhhcccccEEE-------EEEEE--------------EeecceEEEecCCcceeEEehh
Confidence 4668889999999 99999 8889999999999999999996
No 126
>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=88.40 E-value=0.13 Score=42.33 Aligned_cols=23 Identities=17% Similarity=0.084 Sum_probs=21.9
Q ss_pred CCCCCcccccCccccceeeehhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~a 413 (681)
..++|+||++.|+|+|++|++..
T Consensus 11 i~~~g~~V~l~~~i~G~i~~~~l 33 (73)
T cd05703 11 VSKEFVWLTISPDVKGRIPLLDL 33 (73)
T ss_pred EeCCEEEEEeCCCcEEEEEHHHc
Confidence 89999999999999999999876
No 127
>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=88.17 E-value=0.15 Score=40.17 Aligned_cols=23 Identities=9% Similarity=-0.045 Sum_probs=21.3
Q ss_pred CCCCCcccccCccccceeeehhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~a 413 (681)
...+|+||++.++++||+|+|..
T Consensus 11 v~~~G~~V~l~~~~~gli~~s~l 33 (70)
T cd05698 11 VKPNGCIVSFYNNVKGFLPKSEL 33 (70)
T ss_pred EecCcEEEEECCCCEEEEEHHHc
Confidence 88999999999999999999954
No 128
>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=88.06 E-value=0.16 Score=41.83 Aligned_cols=38 Identities=8% Similarity=-0.072 Sum_probs=34.4
Q ss_pred cCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 356 RFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 356 rf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
.++.|.|+. +.|.+ ..++|.|+++.++++||+|++.+-
T Consensus 11 ~~~~G~i~~-------g~V~~--------------v~~~G~fv~l~~~~~g~v~~~el~ 48 (83)
T cd04461 11 DLKPGMVVH-------GYVRN--------------ITPYGVFVEFLGGLTGLAPKSYIS 48 (83)
T ss_pred hCCCCCEEE-------EEEEE--------------EeeceEEEEcCCCCEEEEEHHHCC
Confidence 378899999 99999 999999999999999999998653
No 129
>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=87.26 E-value=0.21 Score=41.24 Aligned_cols=40 Identities=8% Similarity=0.143 Sum_probs=35.2
Q ss_pred ccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 353 IFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 353 I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
..+.+++|.++. +.|.+ ..+||.|+++.++++||+|+|..
T Consensus 10 ~~~~~~~G~~~~-------g~V~~--------------i~~~G~fV~l~~~~~Glv~~se~ 49 (77)
T cd04473 10 TMEDLEVGKLYK-------GKVNG--------------VAKYGVFVDLNDHVRGLIHRSNL 49 (77)
T ss_pred chhhCCCCCEEE-------EEEEe--------------EecceEEEEECCCcEEEEEchhc
Confidence 345578899999 99999 89999999999999999999963
No 130
>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=86.64 E-value=0.19 Score=39.85 Aligned_cols=23 Identities=4% Similarity=-0.132 Sum_probs=21.1
Q ss_pred CCCCCcccccCccccceeeehhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~a 413 (681)
..++|+||++.++|+||+|++..
T Consensus 11 v~~~Gv~V~l~~~v~g~i~~~~l 33 (69)
T cd05697 11 LRPSGIFVKLSDHIKGLVPPMHL 33 (69)
T ss_pred EeccEEEEEecCCcEEEEEHHHC
Confidence 88999999999999999998854
No 131
>PRK08059 general stress protein 13; Validated
Probab=86.06 E-value=0.27 Score=44.36 Aligned_cols=41 Identities=5% Similarity=0.175 Sum_probs=36.4
Q ss_pred ccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 353 IFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 353 I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
+++++++|.++. ++|.+ ...+|+||.+.++++||+|++...
T Consensus 1 ~~~~~k~G~iv~-------G~V~~--------------i~~~G~fV~i~~~~~Gli~~sel~ 41 (123)
T PRK08059 1 MMSQYEVGSVVT-------GKVTG--------------IQPYGAFVALDEETQGLVHISEIT 41 (123)
T ss_pred CcccCCCCCEEE-------EEEEE--------------EecceEEEEECCCCEEEEEHHHCC
Confidence 356688999999 99999 899999999999999999998653
No 132
>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=85.73 E-value=3.3 Score=38.48 Aligned_cols=56 Identities=20% Similarity=0.392 Sum_probs=42.8
Q ss_pred CCCEEEEEEEEeeecceeEEEcCCceeeeeEccccc-----------cccc--c---cccccCCEEEEEEEEe
Q 005716 274 PGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGND-----------WYWI--R---HHIKVGMHVIVEILAK 330 (681)
Q Consensus 274 eGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEIS-----------W~rI--~---dVLKVGDeVkVKVLsI 330 (681)
+|.|+.|+|++-+.= |+.|.||=-.|=+|+-+.|- |-+. . -++..|++|+++|.++
T Consensus 3 ~gEvl~g~I~~~~~~-Gi~vslgFFddI~IP~~~L~~ps~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~ 74 (122)
T PF08292_consen 3 VGEVLTGKIKSSTAE-GIRVSLGFFDDIFIPPSLLPEPSRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESE 74 (122)
T ss_dssp TT-EEEEEEEEEETT-EEEEEECCEEEEEEECCCC-TTEEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEE
T ss_pred CCCEEEEEEEecCCC-cEEEEecccccEEECHHHCCCCCccCccCCEEEEECCCCceeEccCCCEEEEEEeEE
Confidence 699999999999996 99999998778777777762 3222 1 1889999999999999
No 133
>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=85.61 E-value=2.4 Score=39.27 Aligned_cols=53 Identities=19% Similarity=0.208 Sum_probs=44.0
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
..|.+|.|+|..|.+= -.|||+|+.......-..... +.+..|..|.|.+.+.
T Consensus 22 ~~gk~V~G~I~hvv~d-dLYIDfG~KFhcVc~rp~~~~----~~y~~G~rV~lrLkdl 74 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDD-DLYIDFGGKFHCVCKRPAVNG----EKYVRGSRVRLRLKDL 74 (104)
T ss_pred ccCCEEEEEEEEEecC-ceEEEeCCceeEEEecccccc----cccccCCEEEEEECCH
Confidence 4788999999999997 999999999888877655533 3477799999999876
No 134
>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=85.53 E-value=0.25 Score=56.15 Aligned_cols=38 Identities=16% Similarity=0.193 Sum_probs=34.2
Q ss_pred ccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 355 NRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 355 erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
...++|.|+. |+|.+ ..+||+||++.|+++||+|||..
T Consensus 614 ~~~~~G~i~~-------G~V~~--------------I~~~GafVei~~g~~GllHiSei 651 (684)
T TIGR03591 614 AEPEVGKIYE-------GKVVR--------------IMDFGAFVEILPGKDGLVHISEI 651 (684)
T ss_pred cccccCcEEE-------EEEEE--------------EeCCEEEEEECCCcEEEEEHHHc
Confidence 3467799999 99999 99999999999999999999965
No 135
>PRK05807 hypothetical protein; Provisional
Probab=84.87 E-value=0.29 Score=45.36 Aligned_cols=37 Identities=8% Similarity=0.068 Sum_probs=33.1
Q ss_pred CCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhhh
Q 005716 357 FDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAEQ 415 (681)
Q Consensus 357 f~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aEQ 415 (681)
+.+|.|+. +.|.. ...+|+||.+ +++.||+|||.+..
T Consensus 3 ~~vG~vv~-------G~Vt~--------------i~~~GafV~L-~~~~Glvhiseis~ 39 (136)
T PRK05807 3 LKAGSILE-------GTVVN--------------ITNFGAFVEV-EGKTGLVHISEVAD 39 (136)
T ss_pred ccCCCEEE-------EEEEE--------------EECCeEEEEE-CCEEEEEEhhhccc
Confidence 67889999 99999 8999999999 88999999998754
No 136
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=83.94 E-value=3.4 Score=37.25 Aligned_cols=61 Identities=20% Similarity=0.163 Sum_probs=48.1
Q ss_pred EEEEEEEEeeecceeEE-EcCCceeeeeEccccccccccc---ccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 277 ICEGKVTTVHLYQGAFV-DIGGVYDGWVPIKGNDWYWIRH---HIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 277 IVEGkVtnItdF~GAFV-DIGGv~DGLVHISEISW~rI~d---VLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
.++|+|+.+-.- +-|. -|-.++.=|-|||. +++. -+-+||.|+|.+-.. |..+.||---.|
T Consensus 8 e~~G~V~e~Lp~-~~frV~LenG~~vla~isG----KmR~~rIrIl~GD~V~VE~spY-DltkGRIiyR~~ 72 (87)
T PRK12442 8 ELDGIVDEVLPD-SRFRVTLENGVEVGAYASG----RMRKHRIRILAGDRVTLELSPY-DLTKGRINFRHK 72 (87)
T ss_pred EEEEEEEEECCC-CEEEEEeCCCCEEEEEecc----ceeeeeEEecCCCEEEEEECcc-cCCceeEEEEec
Confidence 488999999776 6664 66655688889885 4443 567899999999999 789999977766
No 137
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=82.66 E-value=0.41 Score=54.46 Aligned_cols=38 Identities=16% Similarity=0.199 Sum_probs=33.9
Q ss_pred ccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 355 NRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 355 erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
...++|.++. |+|.+ ...||+||++.|+++||+|||..
T Consensus 617 ~~~~vG~v~~-------G~V~~--------------I~~fGafVei~~~~~GllhiSel 654 (693)
T PRK11824 617 AEPEVGEIYE-------GKVVR--------------IVDFGAFVEILPGKDGLVHISEI 654 (693)
T ss_pred ccCcCCeEEE-------EEEEE--------------EECCeEEEEECCCCEEEEEeeec
Confidence 3467788998 99999 99999999999999999999954
No 138
>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=81.69 E-value=0.45 Score=38.40 Aligned_cols=23 Identities=4% Similarity=-0.161 Sum_probs=21.3
Q ss_pred CCCCCcccccCccccceeeehhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~a 413 (681)
..++|+|+++.++|+||+|++..
T Consensus 11 i~~~G~~v~l~~~v~g~v~~~~l 33 (66)
T cd05695 11 VLSNGLILDFLSSFTGTVDFLHL 33 (66)
T ss_pred EeCCcEEEEEcCCceEEEEHHHc
Confidence 88999999999999999999864
No 139
>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=81.42 E-value=0.45 Score=37.86 Aligned_cols=35 Identities=3% Similarity=0.015 Sum_probs=28.8
Q ss_pred CCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccC--ccccceeeehhhh
Q 005716 359 FAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTH--PYVDKLWQIHNAE 414 (681)
Q Consensus 359 vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~h--P~VegL~hIs~aE 414 (681)
.|.++. +.|.+ ...+|.||++. ++++||+|++.+.
T Consensus 3 ~G~~~~-------g~V~~--------------v~~~g~~v~l~~~~~~~gll~~s~l~ 39 (76)
T cd04452 3 EGELVV-------VTVKS--------------IADMGAYVSLLEYGNIEGMILLSELS 39 (76)
T ss_pred CCCEEE-------EEEEE--------------EEccEEEEEEcCCCCeEEEEEhHHcC
Confidence 466677 88888 88999999997 4699999999653
No 140
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=81.31 E-value=7.5 Score=33.31 Aligned_cols=63 Identities=17% Similarity=0.111 Sum_probs=44.5
Q ss_pred EEEEEEeeeccee-EEEc-CCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 279 EGKVTTVHLYQGA-FVDI-GGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 279 EGkVtnItdF~GA-FVDI-GGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
+|+|+....-.|- ||-. +|+.|=+||||.|.-.- ...|.+||.|+..|..- . +.+-...+..+
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~g-~~~l~~G~~V~f~~~~~-~--~G~~A~~V~~~ 67 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG-YRTLKAGQSVQFDVHQG-P--KGNHASVIVPV 67 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeeccccC-CCCCCCCCEEEEEEEEC-C--CCceeeEEEEC
Confidence 5899988775454 7744 44569999999996332 35789999999998765 2 45555555544
No 141
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=81.28 E-value=2 Score=44.28 Aligned_cols=71 Identities=24% Similarity=0.293 Sum_probs=52.0
Q ss_pred cccCCCCCCCCEEEEEEEEeee--cceeEEEcCCc----eeeeeEcccccc----ccccc-----ccccCCEEEEEEEEe
Q 005716 266 MYELPFYYPGQICEGKVTTVHL--YQGAFVDIGGV----YDGWVPIKGNDW----YWIRH-----HIKVGMHVIVEILAK 330 (681)
Q Consensus 266 v~~L~~LkeGqIVEGkVtnItd--F~GAFVDIGGv----~DGLVHISEISW----~rI~d-----VLKVGDeVkVKVLsI 330 (681)
+.+|+++++|+++-|+...+.+ | ||+||||.. .|.||+.-++.= +.|++ -+=....|+|.|..+
T Consensus 67 i~sl~~~~~Gdv~vGrl~~l~~vgy-g~yvdigV~~p~~~dalvply~Lk~~~gekpvrqi~r~FG~V~~lPveV~V~ev 145 (247)
T COG4044 67 IPSLSKVEEGDVYVGRLIDLGKVGY-GAYVDIGVLGPRPKDALVPLYELKRTFGEKPVRQIIRRFGWVDHLPVEVEVNEV 145 (247)
T ss_pred CCccccCCCCcEEEEEEeeecccee-EEEccccccCCCcccccccHHHHHhccCCCcHHHHHHHcCCcccCceEEEEEec
Confidence 3478899999999999999875 7 999999865 689998877642 22333 223467799999999
Q ss_pred eCCCCCee
Q 005716 331 RDPYRFRF 338 (681)
Q Consensus 331 dD~eR~RI 338 (681)
++.+.-|
T Consensus 146 -nk~~~EI 152 (247)
T COG4044 146 -NKLAQEI 152 (247)
T ss_pred -cchhhhh
Confidence 4433333
No 142
>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=80.72 E-value=0.54 Score=37.34 Aligned_cols=38 Identities=5% Similarity=0.054 Sum_probs=33.6
Q ss_pred cCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhh
Q 005716 356 RFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 356 rf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aE 414 (681)
+++.|.|++ |.|.+ ...+|.||.+..+++|++|++..-
T Consensus 1 k~~~G~iv~-------g~V~~--------------v~~~g~~V~l~~~~~g~ip~~~l~ 38 (74)
T PF00575_consen 1 KLKEGDIVE-------GKVTS--------------VEDFGVFVDLGNGIEGFIPISELS 38 (74)
T ss_dssp -SSTTSEEE-------EEEEE--------------EETTEEEEEESTSSEEEEEGGGSS
T ss_pred CCCCCCEEE-------EEEEE--------------EECCEEEEEECCcEEEEEEeehhc
Confidence 467889999 99999 889999999999999999998754
No 143
>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=79.89 E-value=0.5 Score=37.43 Aligned_cols=41 Identities=17% Similarity=0.160 Sum_probs=28.4
Q ss_pred CCCCCcccccCccccceeeehhhhhhhccccccCccccCCcccccc
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNAEQLILDDMEANPDKYKGKKLSEL 436 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~aEQmiLdd~e~npdky~~~~~~~l 436 (681)
..++|+||+. ++++||+|.+.... .+ -.++.++.|+.+.-.
T Consensus 11 v~~~G~~v~l-~g~~gfip~s~~~~---~~-~~~~~~~vG~~i~~~ 51 (67)
T cd04465 11 KVKGGLIVDI-EGVRAFLPASQVDL---RP-VEDLDEYVGKELKFK 51 (67)
T ss_pred EECCeEEEEE-CCEEEEEEHHHCCC---cc-cCChHHhCCCEEEEE
Confidence 7889999999 89999999884432 22 124555667665433
No 144
>PRK07252 hypothetical protein; Provisional
Probab=79.82 E-value=0.62 Score=42.56 Aligned_cols=34 Identities=6% Similarity=0.022 Sum_probs=30.1
Q ss_pred CCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 359 FAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 359 vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
+|.|+. |.|.. ...+|+||++.++++||+|++..
T Consensus 3 vG~iv~-------G~V~~--------------V~~~G~fVei~~~~~GllhiseL 36 (120)
T PRK07252 3 IGDKLK-------GTITG--------------IKPYGAFVALENGTTGLIHISEI 36 (120)
T ss_pred CCCEEE-------EEEEE--------------EeCcEEEEEECCCCEEEEEHHHc
Confidence 567777 88888 89999999999999999999864
No 145
>PRK15464 cold shock-like protein CspH; Provisional
Probab=79.67 E-value=4.7 Score=34.26 Aligned_cols=52 Identities=19% Similarity=0.063 Sum_probs=39.5
Q ss_pred EEEEEEEeeeccee-EEEc-CCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 278 CEGKVTTVHLYQGA-FVDI-GGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 278 VEGkVtnItdF~GA-FVDI-GGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
+.|+|+...+=.|- ||.. +|+.|=+||||.+.-.. ...+.+||.|+..|..=
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~g-~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPRD-AEVLIPGLRVEFCRVNG 58 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhcC-CCCCCCCCEEEEEEEEC
Confidence 47999998885564 8865 34569999999995432 24699999999988764
No 146
>PRK10943 cold shock-like protein CspC; Provisional
Probab=79.58 E-value=6.1 Score=33.09 Aligned_cols=54 Identities=20% Similarity=0.167 Sum_probs=40.2
Q ss_pred CEEEEEEEEeeeccee-EEEc-CCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 276 QICEGKVTTVHLYQGA-FVDI-GGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 276 qIVEGkVtnItdF~GA-FVDI-GGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
+.++|+|+.-.+-.|- ||.- +|+.|=+||||.+.-.. ...+.+||.|...|..=
T Consensus 2 ~~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~g-~~~l~~G~~V~f~~~~~ 57 (69)
T PRK10943 2 AKIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGNG-FKTLAEGQNVEFEIQDG 57 (69)
T ss_pred CccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHccccC-CCCCCCCCEEEEEEEEC
Confidence 3578999998874453 7765 44569999999996432 25688999999987654
No 147
>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=79.11 E-value=0.52 Score=35.88 Aligned_cols=23 Identities=9% Similarity=-0.039 Sum_probs=21.1
Q ss_pred CCCCCcccccCccccceeeehhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~a 413 (681)
...+|+||.+.++++||+|++..
T Consensus 11 i~~~g~~v~i~~~~~g~l~~~~l 33 (69)
T cd05692 11 LKPFGAFVELGGGISGLVHISQI 33 (69)
T ss_pred EEeeeEEEEECCCCEEEEEhHHc
Confidence 78899999999999999999864
No 148
>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=78.95 E-value=0.62 Score=36.56 Aligned_cols=24 Identities=4% Similarity=-0.028 Sum_probs=21.9
Q ss_pred CCCCCcccccCccccceeeehhhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~aE 414 (681)
...+|.|+++.++++|++|++...
T Consensus 11 v~~~g~~v~l~~~~~g~i~~~~~~ 34 (73)
T cd05691 11 VDAKGATVKLGDGVEGFLRAAELS 34 (73)
T ss_pred EECCeEEEEeCCCCEEEEEHHHCC
Confidence 789999999999999999999654
No 149
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=78.07 E-value=4.8 Score=40.57 Aligned_cols=67 Identities=18% Similarity=0.261 Sum_probs=50.0
Q ss_pred CCCCEEEEEEEEeeecceeEEEcC--------CceeeeeEcccccc---cc--cccccccCCEEEEEEEEeeCCCCCeee
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIG--------GVYDGWVPIKGNDW---YW--IRHHIKVGMHVIVEILAKRDPYRFRFP 339 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIG--------Gv~DGLVHISEISW---~r--I~dVLKVGDeVkVKVLsIdD~eR~RIS 339 (681)
.+|+||..+|+.|..= =|=|||= .-..||||..++-= .+ |-+-+.+||.|.++||+..+.. .+-
T Consensus 67 ~~G~IVtarV~~i~~r-fAkv~I~~V~d~~lk~~FrglirkqdvR~tEkdrv~v~ksFrPgDiVlAkVis~~~~~--~y~ 143 (193)
T KOG3409|consen 67 FVGAIVTARVSRINLR-FAKVDILSVGDKPLKKSFRGLIRKQDVRATEKDRVKVYKSFRPGDIVLAKVISLGDGS--NYL 143 (193)
T ss_pred ccCcEEEEEEEeeccc-eeeEEEEEEcCEEhhhhhcceeehhhccccccchhhhhhccCCCcEEEEEEeecCCCC--cEE
Confidence 5799999999999985 7888872 23569999988842 22 3457779999999999986544 344
Q ss_pred eee
Q 005716 340 IEM 342 (681)
Q Consensus 340 LSL 342 (681)
|+.
T Consensus 144 LTt 146 (193)
T KOG3409|consen 144 LTT 146 (193)
T ss_pred EEE
Confidence 554
No 150
>PRK15463 cold shock-like protein CspF; Provisional
Probab=77.77 E-value=6.9 Score=33.06 Aligned_cols=52 Identities=19% Similarity=0.143 Sum_probs=39.1
Q ss_pred EEEEEEEeeeccee-EEEc-CCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 278 CEGKVTTVHLYQGA-FVDI-GGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 278 VEGkVtnItdF~GA-FVDI-GGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
+.|+|+.-..=.|- ||.. +|+.|=+||||.+.-.. ..-+++||.|...|..=
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~g-~~~l~~G~~V~f~v~~~ 58 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLRD-AEELTTGLRVEFCRING 58 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhcC-CCCCCCCCEEEEEEEEC
Confidence 47999998885453 8866 44569999999996432 24688999999977654
No 151
>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=77.71 E-value=0.64 Score=37.34 Aligned_cols=23 Identities=9% Similarity=-0.003 Sum_probs=20.7
Q ss_pred CCCCCcccccCc-cccceeeehhh
Q 005716 391 KPEEEGLLSTHP-YVDKLWQIHNA 413 (681)
Q Consensus 391 ~~efgafve~hP-~VegL~hIs~a 413 (681)
...+|.||.+.+ +++||+|++..
T Consensus 12 v~~~G~fv~l~~~~~~G~v~~~~l 35 (83)
T cd04471 12 VTSFGLFVELDNLTVEGLVHVSTL 35 (83)
T ss_pred EEeeeEEEEecCCCEEEEEEEEec
Confidence 788999999999 79999999843
No 152
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=76.58 E-value=1 Score=47.15 Aligned_cols=39 Identities=8% Similarity=0.137 Sum_probs=32.3
Q ss_pred ccCCC-CCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCccccc--Cccccceeeehhhh
Q 005716 355 NRFDF-APIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLST--HPYVDKLWQIHNAE 414 (681)
Q Consensus 355 erf~v-gpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~--hP~VegL~hIs~aE 414 (681)
++||- |.|+- ++|++ ..+|||||.+ +||++|++|||-.=
T Consensus 6 ~~~PeeGEiVv-------~tV~~--------------V~~~GAyv~L~EY~g~Eg~ihiSEva 47 (269)
T COG1093 6 REYPEEGEIVV-------GTVKQ--------------VADYGAYVELDEYPGKEGFIHISEVA 47 (269)
T ss_pred cCCCCCCcEEE-------EEEEE--------------eeccccEEEeeccCCeeeeEEHHHHH
Confidence 34554 88888 99999 9999999987 68899999999644
No 153
>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=76.21 E-value=9.3 Score=32.94 Aligned_cols=57 Identities=32% Similarity=0.257 Sum_probs=43.9
Q ss_pred EEEEEEEEeeecceeEE-EcCCceeeeeEccccccccccc---ccccCCEEEEEEEEeeCCCCCeee
Q 005716 277 ICEGKVTTVHLYQGAFV-DIGGVYDGWVPIKGNDWYWIRH---HIKVGMHVIVEILAKRDPYRFRFP 339 (681)
Q Consensus 277 IVEGkVtnItdF~GAFV-DIGGv~DGLVHISEISW~rI~d---VLKVGDeVkVKVLsIdD~eR~RIS 339 (681)
.++|+|+.+-.- |.|- -|-.++.=|-|||. +++. -+.+||.|+|.+-.. |..+.||-
T Consensus 6 e~~G~V~e~L~~-~~f~V~l~ng~~vla~i~G----Kmr~~rI~I~~GD~V~Ve~spy-d~tkgrIi 66 (68)
T TIGR00008 6 EMEGKVTESLPN-AMFRVELENGHEVLAHISG----KIRMHYIRILPGDKVKVELSPY-DLTRGRIT 66 (68)
T ss_pred EEEEEEEEECCC-CEEEEEECCCCEEEEEecC----cchhccEEECCCCEEEEEECcc-cCCcEeEE
Confidence 478999999775 6664 66555688888885 4432 577899999999988 78888873
No 154
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=75.78 E-value=9.8 Score=35.76 Aligned_cols=76 Identities=18% Similarity=0.125 Sum_probs=53.9
Q ss_pred CCCCCCCCCcchhh-hcccCCCCCCCCEEEEEEEEeeecce---------eEEEcCCceeeeeEcccccccccccccccC
Q 005716 251 YYPGRRKRGKDYEE-GMYELPFYYPGQICEGKVTTVHLYQG---------AFVDIGGVYDGWVPIKGNDWYWIRHHIKVG 320 (681)
Q Consensus 251 ~~PGRDPR~~~f~e-gv~~L~~LkeGqIVEGkVtnItdF~G---------AFVDIGGv~DGLVHISEISW~rI~dVLKVG 320 (681)
|||-|.-=..-+.+ .|...+.=..|-+++=||..+... | |.|.|+++.-+|.||.. .--+-+++|
T Consensus 39 ~~PPr~~Cp~C~~~~~~E~vels~~G~V~t~Tv~~~~~~-~~~~~~P~viaiV~l~~~~~i~~~i~~----~~p~~v~iG 113 (140)
T COG1545 39 YFPPRAYCPKCGSETELEWVELSGEGKVETYTVVYVKPP-GFSLEEPYVIAIVELEEGGRILGQLVD----VDPDDVEIG 113 (140)
T ss_pred EcCCcccCCCCCCCCceEEEEeCCCeEEEEEEEEeeCCC-CcccCCCEEEEEEEeCCCCceEEEEEe----cCcccccCC
Confidence 45444433344666 456666667888999999998875 5 77888655467778776 223578999
Q ss_pred CEEEEEEEEee
Q 005716 321 MHVIVEILAKR 331 (681)
Q Consensus 321 DeVkVKVLsId 331 (681)
++|++++..+.
T Consensus 114 m~V~~v~~~~~ 124 (140)
T COG1545 114 MKVEAVFRKRE 124 (140)
T ss_pred CEEEEEEEEcc
Confidence 99999999883
No 155
>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=75.49 E-value=0.91 Score=34.56 Aligned_cols=24 Identities=13% Similarity=0.068 Sum_probs=21.5
Q ss_pred CCCCCcccccCccccceeeehhhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~aE 414 (681)
...+|.||.+.++++||+|++...
T Consensus 11 i~~~G~fv~l~~~~~g~~~~~~l~ 34 (68)
T cd05685 11 VTDFGAFVDIGVKQDGLIHISKMA 34 (68)
T ss_pred EecccEEEEcCCCCEEEEEHHHCC
Confidence 788999999999999999997653
No 156
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=75.15 E-value=10 Score=31.76 Aligned_cols=53 Identities=21% Similarity=0.169 Sum_probs=39.1
Q ss_pred EEEEEEEEeeeccee-EEEc-CCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 277 ICEGKVTTVHLYQGA-FVDI-GGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 277 IVEGkVtnItdF~GA-FVDI-GGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
.++|+|+...+=.|- ||.. +|+.|=+||||.+.-.. ...+.+||.|...|..=
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~g-~~~l~~G~~V~f~~~~~ 57 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTNG-FKTLAEGQRVEFEITNG 57 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeecccccC-CCCCCCCCEEEEEEEEC
Confidence 467999998774343 7766 44569999999996432 24688999999977665
No 157
>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=74.52 E-value=0.8 Score=37.36 Aligned_cols=24 Identities=8% Similarity=-0.036 Sum_probs=20.8
Q ss_pred CCCCCcccccC---ccccceeeehhhh
Q 005716 391 KPEEEGLLSTH---PYVDKLWQIHNAE 414 (681)
Q Consensus 391 ~~efgafve~h---P~VegL~hIs~aE 414 (681)
...||+||++. ++++||+|++...
T Consensus 11 v~~~G~fv~l~~~~~~~~gll~~s~l~ 37 (79)
T cd05684 11 IMDFGCFVQLEGLKGRKEGLVHISQLS 37 (79)
T ss_pred EEeeeEEEEEeCCCCCcEEEEEhHhcc
Confidence 78899999998 4699999998654
No 158
>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=73.59 E-value=15 Score=29.28 Aligned_cols=58 Identities=21% Similarity=0.204 Sum_probs=40.8
Q ss_pred EEEEEEeee---cceeEEEc-CCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 279 EGKVTTVHL---YQGAFVDI-GGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 279 EGkVtnItd---F~GAFVDI-GGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
.|+|+...+ | | ||.. +++.|=++|+|.+.-.- ...+++||.|...+..- + ++..+..+
T Consensus 2 ~G~Vk~~~~~kGf-G-FI~~~~~g~diffh~~~~~~~~-~~~~~~G~~V~f~~~~~-~--~g~~A~~V 63 (65)
T cd04458 2 TGTVKWFDDEKGF-G-FITPDDGGEDVFVHISALEGDG-FRSLEEGDRVEFELEEG-D--KGPQAVNV 63 (65)
T ss_pred cEEEEEEECCCCe-E-EEecCCCCcCEEEEhhHhhccC-CCcCCCCCEEEEEEEEC-C--CCCeEEEe
Confidence 588988766 6 5 5544 44669999999997432 46789999999987765 2 34444443
No 159
>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=72.49 E-value=1.2 Score=35.69 Aligned_cols=23 Identities=4% Similarity=-0.099 Sum_probs=21.2
Q ss_pred CCCCCcccccCccccceeeehhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~a 413 (681)
..++|+||++.++++|++|++..
T Consensus 11 i~~~gi~v~l~~~i~g~i~~~~i 33 (70)
T cd05702 11 VKPTQLNVQLADNVHGRIHVSEV 33 (70)
T ss_pred EECCcEEEEeCCCcEEEEEHHHh
Confidence 78899999999999999999864
No 160
>PRK09890 cold shock protein CspG; Provisional
Probab=71.90 E-value=14 Score=31.09 Aligned_cols=52 Identities=17% Similarity=0.128 Sum_probs=38.4
Q ss_pred EEEEEEEeeeccee-EEEc-CCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 278 CEGKVTTVHLYQGA-FVDI-GGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 278 VEGkVtnItdF~GA-FVDI-GGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
+.|+|+...+-.|- ||-. +|+.|=+||||.+.-... ..+++||.|...|..-
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~~~-~~l~~G~~V~f~~~~~ 58 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSNEF-RTLNENQKVEFSIEQG 58 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccCCC-CCCCCCCEEEEEEEEC
Confidence 47999998764453 7765 344699999999975433 3689999999976554
No 161
>COG2106 Uncharacterized conserved protein [Function unknown]
Probab=70.11 E-value=6.7 Score=41.34 Aligned_cols=48 Identities=27% Similarity=0.322 Sum_probs=39.3
Q ss_pred CCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 272 YYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 272 LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
-.+|.+.+|.|+..... |.+||||.. .++-.+. -+++|..|+|.|.+.
T Consensus 103 ~~~Ge~ReG~v~~~~~~-~~~v~iG~~--~~~~l~~--------~~~~~~RvTvri~~~ 150 (272)
T COG2106 103 PKEGEYREGLVIRRGKK-GNLVDIGKD--KLAKLSS--------PAPPGARVTVRIISR 150 (272)
T ss_pred ccceeecceEEEEecCC-ceEEEecCC--cceeccC--------CCCCCceEEEEEEec
Confidence 46799999999999998 999999964 4433222 289999999999998
No 162
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=69.93 E-value=13 Score=31.10 Aligned_cols=52 Identities=19% Similarity=0.151 Sum_probs=38.0
Q ss_pred EEEEEEEeeeccee-EEEc-CCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 278 CEGKVTTVHLYQGA-FVDI-GGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 278 VEGkVtnItdF~GA-FVDI-GGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
+.|+|+...+-.|- ||.. +|+.|=+||||.+.-.. ..-|++||.|+..|..=
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~g-~~~l~~G~~V~f~~~~~ 58 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQNDG-YKSLDEGQKVSFTIESG 58 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeeccccC-CCCCCCCCEEEEEEEEC
Confidence 47999988664442 7766 44469999999996432 25689999999977654
No 163
>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=68.69 E-value=1.9 Score=35.65 Aligned_cols=35 Identities=3% Similarity=0.024 Sum_probs=31.4
Q ss_pred CCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 358 DFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 358 ~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
+.|+|+. ++|.+ ..++|+++.+.++++|++|++..
T Consensus 5 ~~GdiV~-------g~V~~--------------i~~~g~~v~i~~~~~G~l~~se~ 39 (86)
T cd05789 5 EVGDVVI-------GRVTE--------------VGFKRWKVDINSPYDAVLPLSEV 39 (86)
T ss_pred CCCCEEE-------EEEEE--------------ECCCEEEEECCCCeEEEEEHHHc
Confidence 4688888 99999 89999999999999999999965
No 164
>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=67.19 E-value=1.9 Score=35.95 Aligned_cols=38 Identities=8% Similarity=0.044 Sum_probs=32.1
Q ss_pred CCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccC-ccccceeeehhhhh
Q 005716 357 FDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTH-PYVDKLWQIHNAEQ 415 (681)
Q Consensus 357 f~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~h-P~VegL~hIs~aEQ 415 (681)
++.|.|++ +.|+. ..++|+|++.- .+|+||+|.+.+..
T Consensus 2 l~~G~~v~-------g~V~s--------------i~d~G~~v~~g~~gv~Gfl~~~~~~~ 40 (74)
T cd05694 2 LVEGMVLS-------GCVSS--------------VEDHGYILDIGIPGTTGFLPKKDAGN 40 (74)
T ss_pred CCCCCEEE-------EEEEE--------------EeCCEEEEEeCCCCcEEEEEHHHCCc
Confidence 35678888 89999 99999999995 69999999887644
No 165
>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=66.90 E-value=12 Score=31.07 Aligned_cols=51 Identities=20% Similarity=0.103 Sum_probs=37.1
Q ss_pred EEEEEEeeeccee-EEEc-CCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 279 EGKVTTVHLYQGA-FVDI-GGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 279 EGkVtnItdF~GA-FVDI-GGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
+|+|+-...-.|- ||.. +|+.|=+||+|.+.-.. ...|++||.|+..|..=
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~g-~~~l~~G~~V~f~~~~~ 55 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMDG-YRTLKAGQKVQFEVVQG 55 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhcC-CCCCCCCCEEEEEEEEC
Confidence 5999987764454 7755 34469999999995332 25789999999976654
No 166
>PRK14998 cold shock-like protein CspD; Provisional
Probab=66.04 E-value=18 Score=30.97 Aligned_cols=51 Identities=20% Similarity=0.166 Sum_probs=38.1
Q ss_pred EEEEEEeeeccee-EEEc-CCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 279 EGKVTTVHLYQGA-FVDI-GGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 279 EGkVtnItdF~GA-FVDI-GGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
+|+|+.-..-.|- ||.. +|+.|=+||||.|.-.. ...+.+||.|...|..=
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~g-~~~l~~G~~V~f~~~~~ 55 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMDG-YRTLKAGQSVRFDVHQG 55 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeecccC-CCCCCCCCEEEEEEEEC
Confidence 5899988774453 7755 44569999999996332 35789999999998765
No 167
>KOG1857 consensus Transcription accessory protein TEX, contains S1 domain [Transcription]
Probab=65.49 E-value=2.1 Score=48.48 Aligned_cols=77 Identities=27% Similarity=0.369 Sum_probs=46.9
Q ss_pred hhhhcccCCCCCCCCEEEEEEEEeeecceeEEEcC-CceeeeeEcccc---cccc----cccccccCCEEEEEEEEeeCC
Q 005716 262 YEEGMYELPFYYPGQICEGKVTTVHLYQGAFVDIG-GVYDGWVPIKGN---DWYW----IRHHIKVGMHVIVEILAKRDP 333 (681)
Q Consensus 262 f~egv~~L~~LkeGqIVEGkVtnItdF~GAFVDIG-Gv~DGLVHISEI---SW~r----I~dVLKVGDeVkVKVLsIdD~ 333 (681)
|...+.-+.+-..|-+|.|..+|.+.| |.|+++| +..-|||.+... .|.+ ..=-+-+||.+++.|+.+ +-
T Consensus 533 ~~KS~~~~~~T~~~AvV~~~L~N~tl~-~~~~~~gV~~~~~l~~~~~~Te~~~sKtD~~r~~~~g~ger~eA~I~H~-~~ 610 (623)
T KOG1857|consen 533 FKKSIVCLEDTQIGAVVTGKLENATLF-GIFVDIGVVGKSGLIPIRNVTEAKLSKTDKRRSLGLGPGERVEAQILHI-DI 610 (623)
T ss_pred hhhheeeeehhhhhHHHhccccccccc-cccccCCcccccccchhhhhccccccccccccccCcccchhhhhhhccc-cc
Confidence 566666666667777777777777777 7777776 334566666544 3432 112555677777777777 33
Q ss_pred CCCeeee
Q 005716 334 YRFRFPI 340 (681)
Q Consensus 334 eR~RISL 340 (681)
-+-||-|
T Consensus 611 ~~s~i~~ 617 (623)
T KOG1857|consen 611 PRSRITL 617 (623)
T ss_pred CcceeEe
Confidence 3444443
No 168
>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=62.82 E-value=1.9 Score=33.18 Aligned_cols=23 Identities=17% Similarity=0.131 Sum_probs=20.9
Q ss_pred CCCCCcccccCccccceeeehhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~a 413 (681)
...+|+|+.+.++++||+|++..
T Consensus 11 v~~~G~~v~l~~~~~g~l~~~~l 33 (68)
T cd04472 11 IKDFGAFVEILPGKDGLVHISEL 33 (68)
T ss_pred EEEeEEEEEeCCCCEEEEEhHHc
Confidence 67799999999999999999865
No 169
>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=62.00 E-value=3.4 Score=36.48 Aligned_cols=35 Identities=9% Similarity=0.014 Sum_probs=30.3
Q ss_pred CCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhh
Q 005716 358 DFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 358 ~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~a 413 (681)
+.|.|+. |.|.+ ..++|+|+++-.+++|++|++..
T Consensus 2 ~~G~vV~-------G~V~~--------------v~~~gl~v~L~~g~~G~v~~sei 36 (100)
T cd05693 2 SEGMLVL-------GQVKE--------------ITKLDLVISLPNGLTGYVPITNI 36 (100)
T ss_pred CCCCEEE-------EEEEE--------------EcCCCEEEECCCCcEEEEEHHHh
Confidence 3566777 89999 89999999999999999999865
No 170
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=61.42 E-value=1 Score=49.75 Aligned_cols=86 Identities=12% Similarity=0.113 Sum_probs=63.7
Q ss_pred eeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeee-eeccCCCccc-----cccccCC--CCCccccCCCCCc
Q 005716 300 DGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIE-MRFVQPNIDH-----LIFNRFD--FAPIFHRDEDKNP 371 (681)
Q Consensus 300 DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLS-LK~~~pnPW~-----~I~erf~--vgpI~~r~~d~n~ 371 (681)
.+-|.+++.. .+..-+++||.|++.|... + -+|++++ .|++.-.-|. .+.+.|+ .|.|++
T Consensus 72 ~~eI~L~eAk--~~~~~~~vGD~ie~~I~~~-~--fgRia~q~aKq~i~Qkire~ere~i~~eyk~~~GeIV~------- 139 (470)
T PRK09202 72 TKEISLEEAR--KIDPDAEVGDYIEEEIESV-D--FGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIIT------- 139 (470)
T ss_pred cceeeHHHHh--hhCccccCCCeEEEEEccc-c--CChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEE-------
Confidence 3555555542 3344689999999999988 4 3455443 4454444455 8999998 899999
Q ss_pred hhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehh
Q 005716 372 DELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHN 412 (681)
Q Consensus 372 geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~ 412 (681)
|+|.| ...+|.||.+ -+|+|++|.+.
T Consensus 140 G~V~r--------------i~~~giiVDL-ggvea~LP~sE 165 (470)
T PRK09202 140 GVVKR--------------VERGNIIVDL-GRAEAILPRKE 165 (470)
T ss_pred EEEEE--------------EecCCEEEEE-CCeEEEecHHH
Confidence 99999 7788999998 58999999653
No 171
>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=60.77 E-value=2.8 Score=33.13 Aligned_cols=23 Identities=9% Similarity=0.011 Sum_probs=20.2
Q ss_pred CCCCCcccccCc-cccceeeehhh
Q 005716 391 KPEEEGLLSTHP-YVDKLWQIHNA 413 (681)
Q Consensus 391 ~~efgafve~hP-~VegL~hIs~a 413 (681)
...+|.||++.. +++||+|++..
T Consensus 13 i~~~g~~v~l~~~~~~g~i~~~~l 36 (77)
T cd05708 13 VEDYGVFIDIDGTNVSGLCHKSEI 36 (77)
T ss_pred EEcceEEEEECCCCeEEEEEHHHC
Confidence 889999999985 79999999754
No 172
>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=59.88 E-value=2.9 Score=33.08 Aligned_cols=23 Identities=13% Similarity=0.092 Sum_probs=20.8
Q ss_pred CCCCCcccccCccccceeeehhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNA 413 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~a 413 (681)
..++|+||.+..+++|++|++..
T Consensus 11 i~~~~~~v~l~~~~~g~l~~~e~ 33 (70)
T cd05687 11 VDDDEVLVDIGYKSEGIIPISEF 33 (70)
T ss_pred EeCCEEEEEeCCCceEEEEHHHh
Confidence 88899999999999999998854
No 173
>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=58.96 E-value=52 Score=24.83 Aligned_cols=48 Identities=17% Similarity=0.100 Sum_probs=31.4
Q ss_pred EEEEEee-ecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 280 GKVTTVH-LYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 280 GkVtnIt-dF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
|+|.... .| |.++..++..+=+||.+.+.- . ...+..||.|.|+|..-
T Consensus 2 G~i~~~~~g~-gfv~~~~~~~~i~v~~~~~~~-~-~~~~~~Gd~V~~~i~~~ 50 (64)
T smart00357 2 GVVKWFNKGF-GFIRPDDGGKDVFVHPSQIQG-G-LKSLREGDEVEFKVVSP 50 (64)
T ss_pred eEEEEEcCCe-eEEecCCCCccEEEEhHHhhc-C-CCcCCCCCEEEEEEEEc
Confidence 6666555 35 655554443478888876542 2 33467799999999874
No 174
>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=58.65 E-value=16 Score=28.33 Aligned_cols=62 Identities=21% Similarity=0.239 Sum_probs=38.0
Q ss_pred EEEEEEEEe-eecce--eEEEcCCceeeeeEccccccc----ccccccccCCEEEEEEEEeeCCCCCe-eeeeeec
Q 005716 277 ICEGKVTTV-HLYQG--AFVDIGGVYDGWVPIKGNDWY----WIRHHIKVGMHVIVEILAKRDPYRFR-FPIEMRF 344 (681)
Q Consensus 277 IVEGkVtnI-tdF~G--AFVDIGGv~DGLVHISEISW~----rI~dVLKVGDeVkVKVLsIdD~eR~R-ISLSLK~ 344 (681)
.|.|+|+++ ..- | +|+.|... .|-|-+ +-|. +..+.|++|+.|.|. =.+ ...+.+ +.|.+..
T Consensus 2 ~v~G~V~~~~~~~-~~~~~~~l~D~-tg~i~~--~~~~~~~~~~~~~l~~g~~v~v~-G~v-~~~~~~~~~l~~~~ 71 (75)
T PF01336_consen 2 TVEGRVTSIRRSG-GKIVFFTLEDG-TGSIQV--VFFNEEYERFREKLKEGDIVRVR-GKV-KRYNGGELELIVPK 71 (75)
T ss_dssp EEEEEEEEEEEEE-TTEEEEEEEET-TEEEEE--EEETHHHHHHHHTS-TTSEEEEE-EEE-EEETTSSEEEEEEE
T ss_pred EEEEEEEEEEcCC-CCEEEEEEEEC-CccEEE--EEccHHhhHHhhcCCCCeEEEEE-EEE-EEECCccEEEEECE
Confidence 478999999 332 2 56666543 454443 3344 456799999999988 344 334555 7776644
No 175
>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=57.70 E-value=19 Score=28.33 Aligned_cols=51 Identities=20% Similarity=0.131 Sum_probs=31.2
Q ss_pred CEEEEEEEEeeecceeEEEc----CCceeeeeEccccccccccc-ccccCCEEEEEEEEe
Q 005716 276 QICEGKVTTVHLYQGAFVDI----GGVYDGWVPIKGNDWYWIRH-HIKVGMHVIVEILAK 330 (681)
Q Consensus 276 qIVEGkVtnItdF~GAFVDI----GGv~DGLVHISEISW~rI~d-VLKVGDeVkVKVLsI 330 (681)
..+.|+|++|... |.++.+ |++. =|. +.++-..+.+ -|++|+.|.+.|.+-
T Consensus 7 N~l~g~I~~i~~~-g~~~~v~l~~~~~~-~l~--a~i~~~~~~~l~l~~G~~v~~~ik~~ 62 (69)
T TIGR00638 7 NQLKGKVVAIEDG-DVNAEVDLLLGGGT-KLT--AVITLESVAELGLKPGKEVYAVIKAP 62 (69)
T ss_pred cEEEEEEEEEEEC-CCeEEEEEEECCCC-EEE--EEecHHHHhhCCCCCCCEEEEEEECc
Confidence 3689999999876 766544 4321 111 1222222222 689999999988654
No 176
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=57.01 E-value=34 Score=31.21 Aligned_cols=72 Identities=18% Similarity=0.010 Sum_probs=50.5
Q ss_pred hhcccCCCCCCCCEEEEEEEEeeecceeEE-EcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeee
Q 005716 264 EGMYELPFYYPGQICEGKVTTVHLYQGAFV-DIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPI 340 (681)
Q Consensus 264 egv~~L~~LkeGqIVEGkVtnItdF~GAFV-DIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISL 340 (681)
.....+....+|+ +.|+|+..-.- |.|- -+..+..=|+||+.=-=. +=-++.||.|.|.+... |..+.+|-.
T Consensus 10 ~~~~~~~~p~e~e-~~g~V~~~lG~-~~~~V~~~dG~~~la~i~GK~Rk--~IwI~~GD~VlVe~~~~-~~~kg~Iv~ 82 (100)
T PRK04012 10 VTRVRLPMPEEGE-VFGVVEQMLGA-NRVRVRCMDGVERMGRIPGKMKK--RMWIREGDVVIVAPWDF-QDEKADIIW 82 (100)
T ss_pred ceeEEccCCCCCE-EEEEEEEEcCC-CEEEEEeCCCCEEEEEEchhhcc--cEEecCCCEEEEEeccc-CCCEEEEEE
Confidence 4455667777777 57999999775 6663 565556889998853222 22688999999999888 566666643
No 177
>PF02598 Methyltrn_RNA_3: Putative RNA methyltransferase; InterPro: IPR003750 This entry describes proteins of unknown function.; PDB: 1K3R_B.
Probab=56.59 E-value=29 Score=36.26 Aligned_cols=47 Identities=32% Similarity=0.307 Sum_probs=30.8
Q ss_pred CCCCEEEEEEEEeeecce---eEEEcCCceeeeeEcccccccccccccccCCEEEEEEEE
Q 005716 273 YPGQICEGKVTTVHLYQG---AFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILA 329 (681)
Q Consensus 273 keGqIVEGkVtnItdF~G---AFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLs 329 (681)
..|...+|.|+.-..- + .|||||.. ..|-|.. ..|.+|..|+|++.+
T Consensus 113 ~~~~yREGvv~~~~~~-~~~~~~VdiGl~--~~v~i~~-------~~l~~g~RVTV~~~~ 162 (291)
T PF02598_consen 113 EWGPYREGVVVRKPSK-GGKGSYVDIGLD--KPVEIDK-------QELPPGTRVTVRIKS 162 (291)
T ss_dssp -TT-EEEEEEEEE-SS-S---EEEESSSS--EEEESSS-----------SS-EEEEEEEE
T ss_pred cccceeEEEEEeCCCC-CCceEEEEeCCC--cEEeecc-------cccCCCCEEEEEecC
Confidence 5788899999998887 5 99999964 3333332 378999999999998
No 178
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=55.09 E-value=69 Score=35.71 Aligned_cols=63 Identities=13% Similarity=0.128 Sum_probs=38.7
Q ss_pred EEEEEEEEeeecce--eEEEcCCc---eeeeeEccccc---ccccccccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 277 ICEGKVTTVHLYQG--AFVDIGGV---YDGWVPIKGND---WYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 277 IVEGkVtnItdF~G--AFVDIGGv---~DGLVHISEIS---W~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
.|.|.|.++... | +||||-.. ..-++..+.++ +..+.. |.+|+.|.|+=.=+. ..++-++|.+
T Consensus 58 ~v~G~v~~~R~~-g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~-l~~g~~v~v~G~v~~-t~~ge~el~~ 128 (491)
T PRK00484 58 SVAGRVMLKRVM-GKASFATLQDGSGRIQLYVSKDDVGEEALEAFKK-LDLGDIIGVEGTLFK-TKTGELSVKA 128 (491)
T ss_pred EEEEEEEEEecC-CceEEEEEEcCCccEEEEEECCcCCHHHHHHHhc-CCCCCEEEEEEEEEE-cCCCcEEEEE
Confidence 588999999997 8 99999432 23344333332 233344 899999988643332 2234555544
No 179
>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=53.78 E-value=27 Score=30.50 Aligned_cols=53 Identities=13% Similarity=0.130 Sum_probs=32.0
Q ss_pred EEEEEEEEeeecce--eEEEcCCc---eeeeeEccccc---ccccccccccCCEEEEEEEEe
Q 005716 277 ICEGKVTTVHLYQG--AFVDIGGV---YDGWVPIKGND---WYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 277 IVEGkVtnItdF~G--AFVDIGGv---~DGLVHISEIS---W~rI~dVLKVGDeVkVKVLsI 330 (681)
.+.|.|.+|... | +||||=.+ ...++.-+++. +..+.+.|+.|+.|.|.=.=.
T Consensus 3 ~v~GwV~~~R~~-g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~ 63 (108)
T cd04322 3 SVAGRIMSKRGS-GKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPF 63 (108)
T ss_pred EEEEEEEEEecC-CCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEE
Confidence 478999999986 7 89999322 22233222211 112223489999998865333
No 180
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=53.67 E-value=6.3 Score=39.49 Aligned_cols=74 Identities=16% Similarity=0.141 Sum_probs=48.6
Q ss_pred EEEEEEEeeCCCCCeeeeeeeccCCCcccc-----ccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcc
Q 005716 323 VIVEILAKRDPYRFRFPIEMRFVQPNIDHL-----IFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGL 397 (681)
Q Consensus 323 VkVKVLsIdD~eR~RISLSLK~~~pnPW~~-----I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgaf 397 (681)
+-|-|+++.+-+.++|-.. +..-.+. +.=+--.+-|+. |+|.+ ..+||+|
T Consensus 44 ~~v~V~~v~~igeG~I~~G----DG~~y~~V~f~al~fkP~~gEVV~-------GeVv~--------------~~~~G~f 98 (183)
T COG1095 44 LVVLVLDVKEIGEGIIVPG----DGSTYHEVKFRALVFKPFRGEVVE-------GEVVE--------------VVEFGAF 98 (183)
T ss_pred EEEEEEEeeEeeccEEecC----CCcEEEEEEEEEEEEEeccccEEE-------EEEEE--------------EeecceE
Confidence 5566666655566666421 1222221 111222388888 99999 9999999
Q ss_pred cccCccccceeeehhhhhhhccccccCccc
Q 005716 398 LSTHPYVDKLWQIHNAEQLILDDMEANPDK 427 (681)
Q Consensus 398 ve~hP~VegL~hIs~aEQmiLdd~e~npdk 427 (681)
|.+-| .+||+|+|+ |.|| -.++|.
T Consensus 99 V~igp-~dglvh~sq----i~dd-~~~~d~ 122 (183)
T COG1095 99 VRIGP-LDGLVHVSQ----IMDD-YIDYDE 122 (183)
T ss_pred EEecc-ccccccHhh----ccCc-ccccCc
Confidence 99995 899999994 7787 555554
No 181
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=53.64 E-value=20 Score=38.96 Aligned_cols=45 Identities=29% Similarity=0.369 Sum_probs=34.2
Q ss_pred CEEEEEEEEeeecce----eEEEcCCceeeeeEccccccccccc------ccccCCEEEEEEEEe
Q 005716 276 QICEGKVTTVHLYQG----AFVDIGGVYDGWVPIKGNDWYWIRH------HIKVGMHVIVEILAK 330 (681)
Q Consensus 276 qIVEGkVtnItdF~G----AFVDIGGv~DGLVHISEISW~rI~d------VLKVGDeVkVKVLsI 330 (681)
.++.|+|++|.+= + +++||||. .=|.+|.. .+++||.|-+.|+++
T Consensus 294 NiLp~~v~~i~~~-~~~V~v~ld~~g~---------~l~Arit~~srd~L~l~~G~~v~AqIKsV 348 (352)
T COG4148 294 NILPGKVVGIEDD-DGQVDVQLDCGGK---------TLWARITPWARDELALKPGQWVYAQIKSV 348 (352)
T ss_pred hccceeEEEEEcC-CCcEEEEEEcCCc---------EEEEEccHhhHHhhcCCCCCeEEEEEEEE
Confidence 3688999999885 4 46677765 34555532 899999999999987
No 182
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=53.16 E-value=42 Score=29.56 Aligned_cols=67 Identities=18% Similarity=0.185 Sum_probs=47.3
Q ss_pred EEEEEEEEeeecc--eeEEEcCCceeeeeEccccccc----ccc-cccccCCEEEEEEE-EeeCCCCCeeeeeeeccCC
Q 005716 277 ICEGKVTTVHLYQ--GAFVDIGGVYDGWVPIKGNDWY----WIR-HHIKVGMHVIVEIL-AKRDPYRFRFPIEMRFVQP 347 (681)
Q Consensus 277 IVEGkVtnItdF~--GAFVDIGGv~DGLVHISEISW~----rI~-dVLKVGDeVkVKVL-sIdD~eR~RISLSLK~~~p 347 (681)
-|+|.|++++... -+|.+|= ||=--|+=+-|. ++. ..++.|++|.|.+- ++ -..+++++|.+.++.|
T Consensus 25 wV~GEIs~~~~~~~gh~YftLk---D~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~g~~~~-y~~~G~~sl~v~~i~P 99 (99)
T PF13742_consen 25 WVEGEISNLKRHSSGHVYFTLK---DEEASISCVIFRSRARRIRGFDLKDGDKVLVRGRVSF-YEPRGSLSLIVEDIDP 99 (99)
T ss_pred EEEEEEeecEECCCceEEEEEE---cCCcEEEEEEEHHHHhhCCCCCCCCCCEEEEEEEEEE-ECCCcEEEEEEEEeEC
Confidence 5999999999821 2455552 333444445564 345 57899999999874 44 5678999999988876
No 183
>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=51.39 E-value=96 Score=24.84 Aligned_cols=67 Identities=12% Similarity=0.110 Sum_probs=40.8
Q ss_pred EEEEEEEEeee-cce-eEEEcC---CceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 277 ICEGKVTTVHL-YQG-AFVDIG---GVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 277 IVEGkVtnItd-F~G-AFVDIG---Gv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
.+.|.|++|.. -.| ||+.|- +..++.+--+ .+....+.++.|+.|.|...--.+..+.+++|.+..+
T Consensus 3 ~v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~~--~~~~~~~~l~~g~~v~v~g~v~~~~~~~~~~l~v~~i 74 (78)
T cd04489 3 WVEGEISNLKRPSSGHLYFTLKDEDASIRCVMWRS--NARRLGFPLEEGMEVLVRGKVSFYEPRGGYQLIVEEI 74 (78)
T ss_pred EEEEEEecCEECCCcEEEEEEEeCCeEEEEEEEcc--hhhhCCCCCCCCCEEEEEEEEEEECCCCEEEEEEEEE
Confidence 36788888753 125 777773 2223333221 2345667999999998887655344456777777654
No 184
>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=49.52 E-value=4.8 Score=45.78 Aligned_cols=45 Identities=7% Similarity=0.022 Sum_probs=35.1
Q ss_pred CccccccccCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCc-cccceeeehhh
Q 005716 348 NIDHLIFNRFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHP-YVDKLWQIHNA 413 (681)
Q Consensus 348 nPW~~I~erf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP-~VegL~hIs~a 413 (681)
+-|....-+..+|.+|. |.|.. ..+||.||++-+ +|+||+|++..
T Consensus 616 ~~~~~~yl~~~iG~~~~-------g~V~~--------------v~~fGifV~L~~~~~eGlvhis~l 661 (709)
T TIGR02063 616 DWKKAEYMSEKIGEEFE-------GVISG--------------VTSFGLFVELENNTIEGLVHISTL 661 (709)
T ss_pred HHHHHHhhhccCCcEEE-------EEEEE--------------EEeCCEEEEecCCceEEEEEeeec
Confidence 33444333445688888 99999 899999999998 89999999854
No 185
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=49.45 E-value=40 Score=38.67 Aligned_cols=51 Identities=18% Similarity=0.184 Sum_probs=34.1
Q ss_pred EEEEEEEEeeecce---eEEEc---CCceeeeeEcccc-----cccccccccccCCEEEEEEE
Q 005716 277 ICEGKVTTVHLYQG---AFVDI---GGVYDGWVPIKGN-----DWYWIRHHIKVGMHVIVEIL 328 (681)
Q Consensus 277 IVEGkVtnItdF~G---AFVDI---GGv~DGLVHISEI-----SW~rI~dVLKVGDeVkVKVL 328 (681)
.|.|.|.+|... | +|+|| ||...-++..+.+ .|..+...|.+|+.|.|.=.
T Consensus 136 ~v~Grv~~~R~~-G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~ 197 (585)
T PTZ00417 136 NVTGRIMRVSAS-GQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGF 197 (585)
T ss_pred EEEEEEEeeecC-CCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeE
Confidence 588999999998 8 79999 2333444543322 13333346889999888755
No 186
>PF08402 TOBE_2: TOBE domain; InterPro: IPR013611 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (e.g. P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT). Found in ABC transporters immediately after the ATPase domain. A strong RPE motif is found at the presumed N terminus of the 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: 1Q12_A 1Q1B_C 2AWN_D 3RLF_B 3PUX_B 2R6G_B 3PUV_B 1Q1E_A 3PV0_B 2AWO_A ....
Probab=48.46 E-value=92 Score=23.96 Aligned_cols=49 Identities=18% Similarity=0.181 Sum_probs=29.8
Q ss_pred CEEEEEEEEeeecceeE----EEcCCceeeeeEcccccccccccccccCCEEEEEEE
Q 005716 276 QICEGKVTTVHLYQGAF----VDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEIL 328 (681)
Q Consensus 276 qIVEGkVtnItdF~GAF----VDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVL 328 (681)
..+.|+|+.+.-. |.. |+++++..-+++...-. . ...+++|+.|.+.+-
T Consensus 16 ~~~~g~V~~~~~~-G~~~~~~v~~~~~~~~~~~~~~~~--~-~~~~~~G~~v~l~~~ 68 (75)
T PF08402_consen 16 NRLPGTVVSVEFL-GSETRYTVRLEGGEELVVRVPNSQ--R-DSPLEPGDEVRLSWD 68 (75)
T ss_dssp TEEEEEEEEEEEE-SSEEEEEEEETTSSEEEEEEESSG----TTT--TTSEEEEEEE
T ss_pred CeEEEEEEEEEEC-CCEEEEEEEECCCCEEEEEecCcc--c-cCCCCCCCEEEEEEC
Confidence 4899999999976 875 55565422233322222 1 257889999998763
No 187
>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=48.13 E-value=56 Score=27.04 Aligned_cols=50 Identities=18% Similarity=0.181 Sum_probs=31.1
Q ss_pred EEEEEEEEeeecce--eEEEcCCc-----eeeeeEcccccccccccccccCCEEEEEEE
Q 005716 277 ICEGKVTTVHLYQG--AFVDIGGV-----YDGWVPIKGNDWYWIRHHIKVGMHVIVEIL 328 (681)
Q Consensus 277 IVEGkVtnItdF~G--AFVDIGGv-----~DGLVHISEISW~rI~dVLKVGDeVkVKVL 328 (681)
.+.|-|.++... | +||+|-.+ ..-++.-+...+..+ .-+++|+.|.|.=.
T Consensus 3 ~v~Gwv~~~R~~-g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~-~~l~~gs~V~v~G~ 59 (82)
T cd04318 3 TVNGWVRSVRDS-KKISFIELNDGSCLKNLQVVVDKELTNFKEI-LKLSTGSSIRVEGV 59 (82)
T ss_pred EEEEeEEEEEcC-CcEEEEEEECCCCccCEEEEEeCcccCHHHH-hcCCCceEEEEEEE
Confidence 478999999985 5 79999222 233343333333223 35789999887643
No 188
>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=47.80 E-value=60 Score=27.95 Aligned_cols=53 Identities=15% Similarity=0.146 Sum_probs=38.1
Q ss_pred EEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc----cccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR----HHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~----dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
.++|+|++|... .+-|=|..+ -++.-+. +-|++|++|.|..-.+ ..+|+-=+|
T Consensus 4 ~veG~I~~id~~-~~titLdDG---------ksy~lp~ef~~~~L~~G~kV~V~yd~~---~gk~vitdi 60 (61)
T PF07076_consen 4 DVEGTIKSIDPE-TMTITLDDG---------KSYKLPEEFDFDGLKPGMKVVVFYDEV---DGKRVITDI 60 (61)
T ss_pred cceEEEEEEcCC-ceEEEecCC---------CEEECCCcccccccCCCCEEEEEEEcc---CCcEEeeec
Confidence 589999999998 888888644 3443333 4899999998877666 256665443
No 189
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.61 E-value=33 Score=33.92 Aligned_cols=47 Identities=19% Similarity=0.138 Sum_probs=38.8
Q ss_pred EEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEE
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILA 329 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLs 329 (681)
-+.|+|+.+..- .+-||+||+ -=.||+|.-.+.. +++|++|++.+.-
T Consensus 4 ~l~G~v~~~~~~-~~ii~~~Gv-GY~v~v~~~~~~~----l~~g~~v~l~t~~ 50 (186)
T PRK14600 4 SLSGIVEEVRSD-YIILNVGNV-GYIVYLSAKVLST----CKIGDNIKLYIET 50 (186)
T ss_pred eEEEEEEEEcCC-EEEEEECCE-EEEEEecHHHHHh----hCCCCeEEEEEEE
Confidence 478999999997 999999986 6678988766654 3789999999864
No 190
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=45.63 E-value=30 Score=30.20 Aligned_cols=42 Identities=24% Similarity=0.358 Sum_probs=29.2
Q ss_pred EEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEE
Q 005716 278 CEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEI 327 (681)
Q Consensus 278 VEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKV 327 (681)
+-|+|..|... .|.||.||+ ..+++-.-+ .-+++||-|.|-+
T Consensus 5 iP~~V~~i~~~-~A~v~~~G~------~~~v~l~lv-~~~~vGD~VLVH~ 46 (76)
T TIGR00074 5 IPGQVVEIDEN-IALVEFCGI------KRDVSLDLV-GEVKVGDYVLVHV 46 (76)
T ss_pred cceEEEEEcCC-EEEEEcCCe------EEEEEEEee-CCCCCCCEEEEec
Confidence 45899999998 899999986 122222222 2478999988764
No 191
>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=45.61 E-value=1.1e+02 Score=34.20 Aligned_cols=64 Identities=9% Similarity=0.118 Sum_probs=38.5
Q ss_pred EEEEEEEEeeecce--eEEEcCC---ceeeeeEccccc---ccccccccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 277 ICEGKVTTVHLYQG--AFVDIGG---VYDGWVPIKGND---WYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 277 IVEGkVtnItdF~G--AFVDIGG---v~DGLVHISEIS---W~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
.|.|.|.++... | +|++|-. ....++..+.++ +..+...|++|+.|.|.=.=... .++-++|.+
T Consensus 57 ~v~Grv~~~R~~-gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t-~~gelel~~ 128 (496)
T TIGR00499 57 SIAGRIMARRSM-GKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKT-KTGELSVHV 128 (496)
T ss_pred EEEEEEEEEecC-CCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEEC-CCCcEEEEe
Confidence 578999999986 7 8999943 334444444332 22333458999999886422322 234454443
No 192
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=45.30 E-value=7 Score=29.26 Aligned_cols=24 Identities=13% Similarity=0.012 Sum_probs=21.2
Q ss_pred CCCCCcccccCccccceeeehhhh
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNAE 414 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~aE 414 (681)
...+|.|+.+.+++.|++|++...
T Consensus 13 v~~~g~~v~i~~~~~g~l~~~~~~ 36 (72)
T smart00316 13 ITPFGAFVDLGNGVEGLIPISELS 36 (72)
T ss_pred EEccEEEEEeCCCCEEEEEHHHCC
Confidence 778999999999999999997654
No 193
>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=45.29 E-value=67 Score=25.13 Aligned_cols=49 Identities=22% Similarity=0.143 Sum_probs=28.8
Q ss_pred EEEEEEEEeeecce----eEEEcCCceeeeeEccccccccccc-ccccCCEEEEEEEE
Q 005716 277 ICEGKVTTVHLYQG----AFVDIGGVYDGWVPIKGNDWYWIRH-HIKVGMHVIVEILA 329 (681)
Q Consensus 277 IVEGkVtnItdF~G----AFVDIGGv~DGLVHISEISW~rI~d-VLKVGDeVkVKVLs 329 (681)
.+.|+|..|..- | +.+++|++.+=... ++...... -|++||+|.+.|..
T Consensus 6 ~l~g~V~~ie~~-g~~~~v~~~~~~~~~l~a~---it~~~~~~L~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 6 QLPGTVESIENL-GSEVEVTLDLGGGETLTAR---ITPESAEELGLKPGDEVYASIKA 59 (64)
T ss_dssp EEEEEEEEEEES-SSEEEEEEEETTSEEEEEE---EEHHHHHHCT-STT-EEEEEE-G
T ss_pred EEEEEEEEEEEC-CCeEEEEEEECCCCEEEEE---EcHHHHHHcCCCCCCEEEEEEeh
Confidence 589999999997 9 66677765201111 11111222 57899999998754
No 194
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=45.13 E-value=6.9 Score=40.26 Aligned_cols=34 Identities=3% Similarity=0.043 Sum_probs=29.6
Q ss_pred CCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCc--cccceeeehhh
Q 005716 359 FAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHP--YVDKLWQIHNA 413 (681)
Q Consensus 359 vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP--~VegL~hIs~a 413 (681)
.|.++. |+|.+ ..++|+||++.. +++||+|+|..
T Consensus 8 ~GdiV~-------G~V~~--------------I~~~G~fV~L~e~~gieGlI~iSEl 43 (262)
T PRK03987 8 EGELVV-------GTVKE--------------VKDFGAFVTLDEYPGKEGFIHISEV 43 (262)
T ss_pred CCCEEE-------EEEEE--------------EECCEEEEEECCCCCcEEEEEHHHc
Confidence 478888 99999 899999999974 79999999954
No 195
>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=45.10 E-value=36 Score=35.37 Aligned_cols=68 Identities=21% Similarity=0.093 Sum_probs=50.0
Q ss_pred hhhhcccCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccc---ccccccc-----ccccCCEEEEEEEEeeC
Q 005716 262 YEEGMYELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGN---DWYWIRH-----HIKVGMHVIVEILAKRD 332 (681)
Q Consensus 262 f~egv~~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEI---SW~rI~d-----VLKVGDeVkVKVLsIdD 332 (681)
|-+=.++++.++ |+++.|++.++.+- |.-||+| ++..-++.+++ .|..++. -+=....|+|.|+.+++
T Consensus 63 fGei~~~le~v~-Ge~y~G~l~s~~~~-G~~~~v~-G~~~~ip~d~L~~Lg~g~~~Qi~~rFG~V~hlPvev~~v~~~~ 138 (225)
T PF09883_consen 63 FGEIVYSLEPVK-GETYVGTLISWDED-GYGVDVD-GIFVPIPKDELKPLGPGSPRQIRRRFGLVQHLPVEVEFVKVED 138 (225)
T ss_pred hCCCCchhcccC-CceEEEEEEeeccc-ceEEEee-cccccCcHHHhcccCCCCHHHHHHHhCcccCCceEEEEEEccc
Confidence 333446677777 99999999999996 8888887 35888888887 4655543 23345678999999953
No 196
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=45.08 E-value=15 Score=41.23 Aligned_cols=11 Identities=18% Similarity=0.516 Sum_probs=6.8
Q ss_pred cchhHHHHHHH
Q 005716 602 MSYDDVIKQKM 612 (681)
Q Consensus 602 msy~d~~~~~~ 612 (681)
|+-.|++++-+
T Consensus 26 lTi~DtlkKE~ 36 (458)
T PF10446_consen 26 LTINDTLKKEN 36 (458)
T ss_pred ccHHHHHHHHH
Confidence 55667776544
No 197
>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=43.81 E-value=70 Score=27.96 Aligned_cols=55 Identities=18% Similarity=0.166 Sum_probs=35.6
Q ss_pred CCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEee
Q 005716 275 GQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKR 331 (681)
Q Consensus 275 GqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsId 331 (681)
||.++=+|.+++.- |--+-.||-..|+. ++---+..--.-|.+||++++.||.||
T Consensus 1 G~~L~LvV~~~~ed-gsv~fs~g~v~g~t-v~AtryH~~g~nl~pGqK~kaviLhvD 55 (65)
T cd05700 1 GDQLKLVVQDVTED-GSVMFSGGQVSGLT-VLASRYHKEGVNVTPGCKLKAVILHVD 55 (65)
T ss_pred CceEEEEEeeeccC-CcEEEecCCcCCcE-EEEEEEEecceecCCCceeEEEEEEEe
Confidence 67788888888776 65554565545552 111112222237889999999999993
No 198
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=42.64 E-value=10 Score=44.83 Aligned_cols=43 Identities=12% Similarity=0.105 Sum_probs=35.2
Q ss_pred cCCCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCccccceeeehhhhhhhcc
Q 005716 356 RFDFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPYVDKLWQIHNAEQLILD 419 (681)
Q Consensus 356 rf~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~VegL~hIs~aEQmiLd 419 (681)
..+.|.|+. |.|++ -+.|||||-+-=..+||+|||.-.---+.
T Consensus 655 dLk~Gm~le-------g~Vrn--------------v~~fgafVdIgv~qDglvHis~ls~~fv~ 697 (780)
T COG2183 655 DLKPGMILE-------GTVRN--------------VVDFGAFVDIGVHQDGLVHISQLSDKFVK 697 (780)
T ss_pred hccCCCEEE-------EEEEE--------------eeeccceEEeccccceeeeHHHhhhhhcC
Confidence 445577777 99999 99999999999999999999986654444
No 199
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=41.68 E-value=36 Score=30.79 Aligned_cols=44 Identities=27% Similarity=0.462 Sum_probs=30.9
Q ss_pred EEEEEEEeeecce-eEEEcCCceeeeeEcccccccccccccccCCEEEEEE
Q 005716 278 CEGKVTTVHLYQG-AFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEI 327 (681)
Q Consensus 278 VEGkVtnItdF~G-AFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKV 327 (681)
+.|+|..|.+-.| |-||.||+ ..+++-.-+-+-+++||-|-|-|
T Consensus 5 iPgqI~~I~~~~~~A~Vd~gGv------kreV~l~Lv~~~v~~GdyVLVHv 49 (82)
T COG0298 5 IPGQIVEIDDNNHLAIVDVGGV------KREVNLDLVGEEVKVGDYVLVHV 49 (82)
T ss_pred cccEEEEEeCCCceEEEEeccE------eEEEEeeeecCccccCCEEEEEe
Confidence 4588889998655 99999987 22333333444788999998865
No 200
>PRK11642 exoribonuclease R; Provisional
Probab=41.28 E-value=10 Score=44.52 Aligned_cols=34 Identities=9% Similarity=0.146 Sum_probs=29.9
Q ss_pred CCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccCcc-ccceeeehh
Q 005716 358 DFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTHPY-VDKLWQIHN 412 (681)
Q Consensus 358 ~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~hP~-VegL~hIs~ 412 (681)
.+|.+|. |.|.. .++||.||++.++ |+||+|++.
T Consensus 642 ~iGe~f~-------G~Is~--------------V~~fGifVeL~~~~vEGlV~vs~ 676 (813)
T PRK11642 642 QVGNVFK-------GVISS--------------VTGFGFFVRLDDLFIDGLVHVSS 676 (813)
T ss_pred cCCcEEE-------EEEEE--------------eecCceEEEECCCCeeeeEEEee
Confidence 4688888 88988 8999999999875 999999974
No 201
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=40.46 E-value=54 Score=27.89 Aligned_cols=41 Identities=34% Similarity=0.400 Sum_probs=27.4
Q ss_pred EEEEEEEee--ecceeEEEcCCceeeeeEcccccccccccccccCCEEEEE
Q 005716 278 CEGKVTTVH--LYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVE 326 (681)
Q Consensus 278 VEGkVtnIt--dF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVK 326 (681)
+-|+|+.|. .. -|-||.||. ..+++-.-+.+ +++||-|.|-
T Consensus 5 iP~~Vv~v~~~~~-~A~v~~~G~------~~~V~~~lv~~-v~~Gd~VLVH 47 (68)
T PF01455_consen 5 IPGRVVEVDEDGG-MAVVDFGGV------RREVSLALVPD-VKVGDYVLVH 47 (68)
T ss_dssp EEEEEEEEETTTT-EEEEEETTE------EEEEEGTTCTS-B-TT-EEEEE
T ss_pred ccEEEEEEeCCCC-EEEEEcCCc------EEEEEEEEeCC-CCCCCEEEEe
Confidence 568999997 65 899999975 23333333444 8999998874
No 202
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=40.44 E-value=87 Score=27.81 Aligned_cols=50 Identities=22% Similarity=0.202 Sum_probs=33.9
Q ss_pred CCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEee
Q 005716 270 PFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKR 331 (681)
Q Consensus 270 ~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsId 331 (681)
+-+++|++++=+|+.+.+- .||..-|- ..-=.-.-.++|++|+|+|.++.
T Consensus 11 ~PVeeGe~y~V~I~d~g~~----------GDGiarve--GfvVFVp~a~~Gd~V~vkI~~v~ 60 (73)
T COG3269 11 PPVEEGETYEVEIEDVGDQ----------GDGIARVE--GFVVFVPGAEVGDEVKVKITKVK 60 (73)
T ss_pred CCcccCCEEEEEEEEeccC----------CCceEEEE--EEEEEeCCCCCCCeeeEEEEEee
Confidence 4578899998777766654 26655544 11111245789999999999993
No 203
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=39.90 E-value=95 Score=32.53 Aligned_cols=55 Identities=22% Similarity=0.154 Sum_probs=42.4
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccccc----ccccccccCCEEEEEEEEe
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWY----WIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~----rI~dVLKVGDeVkVKVLsI 330 (681)
.+|+.|=|+|++=.-- +--|||||-+-+.+ |=++.. |-+--|++||.|-++|...
T Consensus 64 ~~~D~VIGiV~~~~gd-~ykVDigg~~~a~L--~~laFe~AtkrNrPnl~vGdliyakv~~a 122 (230)
T KOG1004|consen 64 VKGDHVIGIVTSKSGD-IYKVDIGGSEPASL--SYLAFEGATKRNRPNLQVGDLIYAKVVDA 122 (230)
T ss_pred CCCCEEEEEEEeccCc-eEEEecCCCCeeee--eeccccCccccCCCccccccEEEEEEEec
Confidence 5799999999987764 77899998544444 445553 4445999999999999988
No 204
>PLN00208 translation initiation factor (eIF); Provisional
Probab=39.69 E-value=93 Score=30.50 Aligned_cols=73 Identities=16% Similarity=0.080 Sum_probs=50.5
Q ss_pred hhhcccCCCCCCCCEEEEEEEEeeecceeE-EEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeee
Q 005716 263 EEGMYELPFYYPGQICEGKVTTVHLYQGAF-VDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPI 340 (681)
Q Consensus 263 ~egv~~L~~LkeGqIVEGkVtnItdF~GAF-VDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISL 340 (681)
.....+|..-.+||++ |+|+.+--- |-| |-|..++.=|.||+-=-=. +=-+.+||.|.|.+-.. +..+.+|..
T Consensus 20 ~~~~~el~~p~egq~~-g~V~~~lGn-~~~~V~c~dG~~rLa~IpGKmRK--rIWI~~GD~VlVel~~~-d~~KgdIv~ 93 (145)
T PLN00208 20 DDEKRELIFKEDGQEY-AQVLRMLGN-GRCEALCIDGTKRLCHIRGKMRK--KVWIAAGDIILVGLRDY-QDDKADVIL 93 (145)
T ss_pred ccceeecccCCCCcEE-EEEEEEcCC-CEEEEEECCCCEEEEEEecccee--eEEecCCCEEEEEccCC-CCCEEEEEE
Confidence 3446788888999976 799988765 555 3555556889998863222 22688999999996666 555555543
No 205
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=39.22 E-value=42 Score=30.38 Aligned_cols=43 Identities=26% Similarity=0.407 Sum_probs=29.8
Q ss_pred EEEEEEEeeecceeEEEcCCceeeeeEccccccccccc-----ccccCCEEEEEE
Q 005716 278 CEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRH-----HIKVGMHVIVEI 327 (681)
Q Consensus 278 VEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~d-----VLKVGDeVkVKV 327 (681)
+-|+|+.|... .|-||.||+ ..+++-.-+-+ -+++||-|.|-+
T Consensus 5 iP~kVv~i~~~-~A~vd~~Gv------~reV~l~Lv~~~~~~~~~~vGDyVLVHa 52 (90)
T PRK10409 5 VPGQIRTIDGN-QAKVDVCGI------QRDVDLTLVGSCDENGQPRVGQWVLVHV 52 (90)
T ss_pred cceEEEEEcCC-eEEEEcCCe------EEEEEEeeecccCCCCccCCCCEEEEec
Confidence 45899999987 899999986 12233222322 378999998865
No 206
>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=39.21 E-value=75 Score=26.56 Aligned_cols=48 Identities=17% Similarity=0.092 Sum_probs=30.2
Q ss_pred EEEEEEEEeeecce--eEEEcCCceeeeeEc----cccc-ccccccccccCCEEEEEE
Q 005716 277 ICEGKVTTVHLYQG--AFVDIGGVYDGWVPI----KGND-WYWIRHHIKVGMHVIVEI 327 (681)
Q Consensus 277 IVEGkVtnItdF~G--AFVDIGGv~DGLVHI----SEIS-W~rI~dVLKVGDeVkVKV 327 (681)
.+.|-|.++.+. | +|++|-.+ .|.|.+ +..+ +..+ .-|+.|+.|.|+=
T Consensus 3 ~v~Gwv~~~R~~-g~~~Fi~LrD~-~~~iQ~v~~~~~~~~~~~~-~~l~~es~V~V~G 57 (84)
T cd04323 3 KVFGWVHRLRSQ-KKLMFLVLRDG-TGFLQCVLSKKLVTEFYDA-KSLTQESSVEVTG 57 (84)
T ss_pred EEEEEEEEEecC-CCcEEEEEEcC-CeEEEEEEcCCcchhHHHH-hcCCCcCEEEEEE
Confidence 478999999986 7 99999322 344332 2211 2222 2488899988763
No 207
>PLN02502 lysyl-tRNA synthetase
Probab=38.93 E-value=1.5e+02 Score=33.87 Aligned_cols=63 Identities=19% Similarity=0.191 Sum_probs=37.6
Q ss_pred EEEEEEEEeeecce--eEEEcCCceeeeeE----ccccc-----ccccccccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 277 ICEGKVTTVHLYQG--AFVDIGGVYDGWVP----IKGND-----WYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 277 IVEGkVtnItdF~G--AFVDIGGv~DGLVH----ISEIS-----W~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
.|.|.|.++... | +|+||-.. .|-|- .+.+. +..+...|.+|+.|.|.=.=... .++-++|..
T Consensus 112 ~v~GrV~~~R~~-Gk~~F~~LrD~-~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t-~~gelel~~ 185 (553)
T PLN02502 112 SVAGRIMAKRAF-GKLAFYDLRDD-GGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKT-KKGELSIFP 185 (553)
T ss_pred EEEEEEEEEecC-CCeEEEEEecC-CccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEec-CCCCEEEEE
Confidence 468999999997 8 69999433 34333 22221 33344458999999886432312 234444444
No 208
>PF13437 HlyD_3: HlyD family secretion protein
Probab=37.64 E-value=99 Score=26.06 Aligned_cols=66 Identities=21% Similarity=0.318 Sum_probs=45.4
Q ss_pred EEEEEEEeeecceeEEEcCCceeeeeEccccccccc--------ccccc-cCCEEEEEEEEeeCCCCCeeeeeeeccCCC
Q 005716 278 CEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI--------RHHIK-VGMHVIVEILAKRDPYRFRFPIEMRFVQPN 348 (681)
Q Consensus 278 VEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI--------~dVLK-VGDeVkVKVLsIdD~eR~RISLSLK~~~pn 348 (681)
+.|+|.++.--.|.||.-| +-|+.|...+--++ ...|+ +|+.|++++..- ..+-+...+..+.+.
T Consensus 6 ~~G~V~~~~~~~G~~v~~g---~~l~~i~~~~~~~v~~~v~~~~~~~i~~~g~~v~v~~~~~---~~~~~~g~V~~I~~~ 79 (105)
T PF13437_consen 6 FDGVVVSINVQPGEVVSAG---QPLAEIVDTDDLWVEAYVPEKDIARIKDPGQKVTVRLDPG---PEKTIEGKVSSISPS 79 (105)
T ss_pred CCEEEEEEeCCCCCEECCC---CEEEEEEccceEEEEEEEChHhhcceEeCCCEEEEEECCC---CCcEEEEEEEEEeCc
Confidence 4688888777779998887 44666665532222 13787 999999998732 234777788877775
Q ss_pred c
Q 005716 349 I 349 (681)
Q Consensus 349 P 349 (681)
+
T Consensus 80 ~ 80 (105)
T PF13437_consen 80 P 80 (105)
T ss_pred c
Confidence 5
No 209
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=36.18 E-value=1.3e+02 Score=29.91 Aligned_cols=78 Identities=22% Similarity=0.184 Sum_probs=51.0
Q ss_pred CCCCcc-hhhhcccCCCCCCCCEEEEEEEEeeecceeE-EEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCC
Q 005716 256 RKRGKD-YEEGMYELPFYYPGQICEGKVTTVHLYQGAF-VDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDP 333 (681)
Q Consensus 256 DPR~~~-f~egv~~L~~LkeGqIVEGkVtnItdF~GAF-VDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~ 333 (681)
++|++- -.....+|..=.+||++ |+|+.+-.- |.| |-|-.++.=|.||+-=-=++ =-|.+||.|.|.+-.. +.
T Consensus 12 ~~rgk~~~~~~~rel~~~eegq~~-g~V~~~LGn-~~f~V~c~dG~~rLa~I~GKmRK~--IWI~~GD~VlVel~~y-d~ 86 (155)
T PTZ00329 12 RRRGKNDNEGEKRELVFKEEGQEY-AQVLRMLGN-GRLEAYCFDGVKRLCHIRGKMRKR--VWINIGDIILVSLRDF-QD 86 (155)
T ss_pred cccccccCccceeeeccCCCCcEE-EEEEEEcCC-CEEEEEECCCCEEEEEeeccceee--EEecCCCEEEEeccCC-CC
Confidence 345554 33456788888899976 799998665 555 34544458899998632221 2688899999976555 44
Q ss_pred CCCee
Q 005716 334 YRFRF 338 (681)
Q Consensus 334 eR~RI 338 (681)
.+.+|
T Consensus 87 ~KgdI 91 (155)
T PTZ00329 87 SKADV 91 (155)
T ss_pred CEEEE
Confidence 44454
No 210
>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=35.53 E-value=74 Score=27.42 Aligned_cols=49 Identities=20% Similarity=0.207 Sum_probs=30.6
Q ss_pred EEEEEEEEeeecce---eEEEcCC---ceeeeeEccc--c---cccccccccccCCEEEEEE
Q 005716 277 ICEGKVTTVHLYQG---AFVDIGG---VYDGWVPIKG--N---DWYWIRHHIKVGMHVIVEI 327 (681)
Q Consensus 277 IVEGkVtnItdF~G---AFVDIGG---v~DGLVHISE--I---SW~rI~dVLKVGDeVkVKV 327 (681)
.+.|-|.++... | +|++|-. ....+++-.+ + .+..+ ..|+.|+.|.|.=
T Consensus 3 ~i~Gwv~~~R~~-g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~-~~l~~es~V~V~G 62 (102)
T cd04320 3 LIRARVHTSRAQ-GAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWA-GSLSKESIVDVEG 62 (102)
T ss_pred EEEEEEEEeecC-CCceEEEEEecCCceEEEEEeCCcccCCHHHHHHH-hcCCCccEEEEEE
Confidence 478999999997 8 9999932 2233343222 1 12112 2478898887764
No 211
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=35.50 E-value=91 Score=28.76 Aligned_cols=74 Identities=20% Similarity=0.202 Sum_probs=44.7
Q ss_pred cccCCCCCCCC---EEEEEEEEeeec------ce--eE--EEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeC
Q 005716 266 MYELPFYYPGQ---ICEGKVTTVHLY------QG--AF--VDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRD 332 (681)
Q Consensus 266 v~~L~~LkeGq---IVEGkVtnItdF------~G--AF--VDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD 332 (681)
+..|.+|++|+ -+.|+|++|..- .| .| +-||.. +|=|+.+ .|..-.+.+++|+.|.|+=-.+ .
T Consensus 4 ~~kI~dL~~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~-TG~I~~t--lW~~~a~~l~~GdvV~I~na~v-~ 79 (129)
T PRK06461 4 ITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDE-TGRVKLT--LWGEQAGSLKEGEVVEIENAWT-T 79 (129)
T ss_pred ceEHHHcCCCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECC-CCEEEEE--EeCCccccCCCCCEEEEECcEE-e
Confidence 44567777774 356888866431 02 12 345654 6765543 4876566789999999881122 1
Q ss_pred CCCCeeeeeee
Q 005716 333 PYRFRFPIEMR 343 (681)
Q Consensus 333 ~eR~RISLSLK 343 (681)
..+.+++|++-
T Consensus 80 ~f~G~lqL~i~ 90 (129)
T PRK06461 80 LYRGKVQLNVG 90 (129)
T ss_pred eeCCEEEEEEC
Confidence 24677777764
No 212
>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=34.93 E-value=54 Score=29.34 Aligned_cols=50 Identities=16% Similarity=0.239 Sum_probs=23.4
Q ss_pred EEEEEEEEeee--cceeEEEcCCceeeeeEcc----cccccccc-cccccCCEEEEEE
Q 005716 277 ICEGKVTTVHL--YQGAFVDIGGVYDGWVPIK----GNDWYWIR-HHIKVGMHVIVEI 327 (681)
Q Consensus 277 IVEGkVtnItd--F~GAFVDIGGv~DGLVHIS----EISW~rI~-dVLKVGDeVkVKV 327 (681)
.|+|+|.+|.. ..-.++..+.. ++..++. .-+-.... .-|+.||+|+|+=
T Consensus 71 ~vtG~V~~I~~~~~~~~~~~~~~~-~~~~~v~~~~~~~~~~~~~~~~l~~G~~Vti~G 127 (144)
T PF12869_consen 71 EVTGTVSSIDKGFGDNYVVLLGTE-NGFAGVQCYFSNDQEKRASVAKLKKGQKVTIKG 127 (144)
T ss_dssp EEEEEEEEEEE-STT-EEEEEE-T-T-S-S--EEEEEEGGGHHHHHH--TTSEEEEEE
T ss_pred EEEEEEEEEEEcCCCcEEEEccCC-CCceeEEEEEccchhhhhhHhcCCCCCEEEEEE
Confidence 48999999965 21235555542 4443332 11100111 1399999998863
No 213
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=34.59 E-value=47 Score=36.38 Aligned_cols=48 Identities=23% Similarity=0.272 Sum_probs=32.5
Q ss_pred EEEEEEEEeeecce--eEEEcCCceeeeeEc----cc--ccccccccccccCCEEEEEE
Q 005716 277 ICEGKVTTVHLYQG--AFVDIGGVYDGWVPI----KG--NDWYWIRHHIKVGMHVIVEI 327 (681)
Q Consensus 277 IVEGkVtnItdF~G--AFVDIGGv~DGLVHI----SE--ISW~rI~dVLKVGDeVkVKV 327 (681)
.|.|.|.+|... | +||+|-.+ .|.+.+ +. -.|..++ -|++|+.|.|+=
T Consensus 20 ~i~G~v~~~R~~-g~~~Fi~lrD~-~g~iq~~~~~~~~~~~~~~~~-~l~~~s~v~v~G 75 (450)
T PRK03932 20 TVRGWVRTKRDS-GKIAFLQLRDG-SCFKQLQVVKDNGEEYFEEIK-KLTTGSSVIVTG 75 (450)
T ss_pred EEEEEEEEEEeC-CCeEEEEEECC-CCcEEEEEEcCCChHHHHHHh-cCCCCcEEEEEE
Confidence 468999999997 8 99999654 554432 22 1133333 488999998874
No 214
>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=33.86 E-value=1e+02 Score=26.70 Aligned_cols=59 Identities=19% Similarity=0.051 Sum_probs=41.5
Q ss_pred EEEEEEEeeecceeE-EEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeee
Q 005716 278 CEGKVTTVHLYQGAF-VDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPI 340 (681)
Q Consensus 278 VEGkVtnItdF~GAF-VDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISL 340 (681)
+.|+|+.+-.- |.| |.+..+..=|.||+.=-=+ +=-++.||.|.|..... |+.+.+|.-
T Consensus 2 ~~g~V~~~~g~-~~~~V~~~~g~~~la~i~gK~rk--~iwI~~GD~V~Ve~~~~-d~~kg~Iv~ 61 (77)
T cd05793 2 EYGQVEKMLGN-GRLEVRCFDGKKRLCRIRGKMRK--RVWINEGDIVLVAPWDF-QDDKADIIY 61 (77)
T ss_pred EEEEEEEEcCC-CEEEEEECCCCEEEEEEchhhcc--cEEEcCCCEEEEEeccc-cCCEEEEEE
Confidence 56899998775 555 4565556888888853211 22688999999998888 666677643
No 215
>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=33.66 E-value=70 Score=28.90 Aligned_cols=49 Identities=12% Similarity=0.028 Sum_probs=29.6
Q ss_pred EEEEEEEEeeecce--eEEEcCCc---eeeeeEccccc-ccccccccccCCEEEEEE
Q 005716 277 ICEGKVTTVHLYQG--AFVDIGGV---YDGWVPIKGND-WYWIRHHIKVGMHVIVEI 327 (681)
Q Consensus 277 IVEGkVtnItdF~G--AFVDIGGv---~DGLVHISEIS-W~rI~dVLKVGDeVkVKV 327 (681)
.+.|-|.++... | +||+|-.+ ...++--+... +..+ .-|++|+.|.|.=
T Consensus 18 ~i~Gwv~~~R~~-gk~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~-~~l~~gs~V~V~G 72 (135)
T cd04317 18 TLCGWVQRRRDH-GGLIFIDLRDRYGIVQVVFDPEEAPEFELA-EKLRNESVIQVTG 72 (135)
T ss_pred EEEEeEehhccc-CCEEEEEEecCCeeEEEEEeCCchhHHHHH-hCCCCccEEEEEE
Confidence 368999999997 8 89999322 12222212111 2222 2588899988764
No 216
>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=32.34 E-value=79 Score=31.21 Aligned_cols=48 Identities=17% Similarity=0.076 Sum_probs=37.6
Q ss_pred EEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
-+.|+|+.+..- .+-||+||+ -=.|++|......+ +.|+.|++.+.-+
T Consensus 4 ~l~G~v~~~~~~-~vvi~v~Gv-GY~v~v~~~~~~~l----~~g~~v~l~t~~~ 51 (191)
T TIGR00084 4 FLFGKVIEVSKP-KIIIEVNGV-GYELQVPMTCAYEL----NLEQKAQVFTHLV 51 (191)
T ss_pred eEEEEEEEEcCC-EEEEEECCE-EEEEEecHHHHHhc----CCCCeEEEEEEEE
Confidence 378999999997 999999985 55678876555443 4599999988665
No 217
>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=31.79 E-value=88 Score=34.14 Aligned_cols=68 Identities=24% Similarity=0.244 Sum_probs=40.3
Q ss_pred CCCE--EEEEEEEeeecce--eEEEcC---CceeeeeEccccc---ccccccccccCCEEEEEEEEeeC-CCCCeeeeee
Q 005716 274 PGQI--CEGKVTTVHLYQG--AFVDIG---GVYDGWVPIKGND---WYWIRHHIKVGMHVIVEILAKRD-PYRFRFPIEM 342 (681)
Q Consensus 274 eGqI--VEGkVtnItdF~G--AFVDIG---Gv~DGLVHISEIS---W~rI~dVLKVGDeVkVKVLsIdD-~eR~RISLSL 342 (681)
.|+. |.|.|.++... | +||+|- |.+..++.-+.++ |..+ ..|.+|+.|.|.=.=+.. ...+.+.|.+
T Consensus 11 ~g~~v~i~G~v~~~R~~-g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~-~~l~~~s~v~v~G~v~~~~~~~~~~el~~ 88 (428)
T TIGR00458 11 DGQEVTFMGWVHEIRDL-GGLIFVLLRDREGLIQITAPAKKVSKNLFKWA-KKLNLESVVAVRGIVKIKEKAPGGFEIIP 88 (428)
T ss_pred CCCEEEEEEEEEEEecC-CCcEEEEEEeCCeeEEEEEECCcCCHHHHHHH-hCCCCCcEEEEEEEEEecCCCCCcEEEEE
Confidence 4554 57999999997 8 899993 2334445444332 3333 358899999886322212 2224455554
Q ss_pred e
Q 005716 343 R 343 (681)
Q Consensus 343 K 343 (681)
+
T Consensus 89 ~ 89 (428)
T TIGR00458 89 T 89 (428)
T ss_pred e
Confidence 3
No 218
>PF14444 S1-like: S1-like
Probab=31.23 E-value=1.1e+02 Score=26.11 Aligned_cols=44 Identities=30% Similarity=0.242 Sum_probs=28.1
Q ss_pred EEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEE
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILA 329 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLs 329 (681)
++.|.||++.+-+| | +|+.|.-|--.-. -.+-++||+|.|..+-
T Consensus 3 ~~~GvVTkl~~~yG-~------IDe~vFF~~~vv~--G~~P~vGdrV~v~A~~ 46 (58)
T PF14444_consen 3 VFTGVVTKLCDDYG-F------IDEDVFFQTDVVK--GNVPKVGDRVLVEAIY 46 (58)
T ss_pred eEEEEEEEEeCCcc-e------EcccEEEEcccEe--cCCCccCCEEEEEEEe
Confidence 57899999987633 2 2555555432211 2366899999887653
No 219
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=31.00 E-value=1.7e+02 Score=32.05 Aligned_cols=66 Identities=18% Similarity=0.113 Sum_probs=38.4
Q ss_pred CCCE--EEEEEEEeeecce--eEEEcCCceeeee----Ecccc--cccccccccccCCEEEEE-EEEeeCCCCCeeeeee
Q 005716 274 PGQI--CEGKVTTVHLYQG--AFVDIGGVYDGWV----PIKGN--DWYWIRHHIKVGMHVIVE-ILAKRDPYRFRFPIEM 342 (681)
Q Consensus 274 eGqI--VEGkVtnItdF~G--AFVDIGGv~DGLV----HISEI--SW~rI~dVLKVGDeVkVK-VLsIdD~eR~RISLSL 342 (681)
.|+. |.|.|.++... | +||+|-.+ .|.| .-+.+ .+..+ ..|++|+.|.|. ++.........+.|.+
T Consensus 15 ~g~~V~i~GrV~~~R~~-gk~~Fl~LrD~-~g~iQ~v~~~~~~~~~~~~~-~~L~~gs~V~v~G~v~~~~~~~~~~el~~ 91 (437)
T PRK05159 15 DGEEVTLAGWVHEIRDL-GGIAFLILRDR-SGIIQVVVKKKVDEELFETI-KKLKRESVVSVTGTVKANPKAPGGVEVIP 91 (437)
T ss_pred CCCEEEEEEEeEeeecC-CCeEEEEEEcC-CcEEEEEEeCCccHHHHHHH-hCCCCCcEEEEEEEEEcCCCCCCCEEEEE
Confidence 4554 68999999996 8 99999533 3433 22211 11222 368999999988 3444221123355544
No 220
>KOG2830 consensus Protein phosphatase 2A-associated protein [Signal transduction mechanisms]
Probab=30.85 E-value=86 Score=34.17 Aligned_cols=35 Identities=20% Similarity=0.377 Sum_probs=27.1
Q ss_pred hhhhcccceeeccce-EEEcchhHHHHHHHHHHHhh
Q 005716 584 MRDAHNKSIVGKGMV-WYEMSYDDVIKQKMQREARS 618 (681)
Q Consensus 584 ~~~~hn~~ivg~~~~-w~emsy~d~~~~~~~~e~~~ 618 (681)
.+...+++|.|-|.- =--||-+++.-|.|.+.-+.
T Consensus 240 ~r~~~q~kVfG~Gyp~lPtMsvdE~~~~~~~~g~a~ 275 (324)
T KOG2830|consen 240 TRNETQKKVFGLGYPGLPTMTVDEFLDQEFEEGIAK 275 (324)
T ss_pred HHHHHhhhhhhcCCCCCccccHHHHHHHHHHhhhcc
Confidence 455678889998765 46799999999999887443
No 221
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=30.63 E-value=16 Score=42.54 Aligned_cols=31 Identities=10% Similarity=0.052 Sum_probs=26.7
Q ss_pred CCCCCcccccCccccceeeehhhhhhhcccc
Q 005716 391 KPEEEGLLSTHPYVDKLWQIHNAEQLILDDM 421 (681)
Q Consensus 391 ~~efgafve~hP~VegL~hIs~aEQmiLdd~ 421 (681)
+.++|+||++.|+..||.|+|+.-|--+-+-
T Consensus 679 ~rd~G~~V~l~p~~~~Llh~sqL~~e~iakp 709 (760)
T KOG1067|consen 679 IRDTGVMVELYPMQQGLLHNSQLDQEKIAKP 709 (760)
T ss_pred ecccceEEEecCCchhhccchhcccccccCh
Confidence 8899999999999999999999777655443
No 222
>TIGR00999 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters).
Probab=30.55 E-value=1e+02 Score=29.69 Aligned_cols=63 Identities=17% Similarity=0.330 Sum_probs=41.4
Q ss_pred EEEEEEEeeecceeEEEcCCceeeeeEcccccccccc--------cccccCCEEEEEEEEeeCCCCCeeeeeeeccCCC
Q 005716 278 CEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR--------HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQPN 348 (681)
Q Consensus 278 VEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~--------dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~pn 348 (681)
+.|+|+.+.-..|.+|.-| +-|+.|.+.+...+. ..|++|+.|.+.+-+ ...++..+..+.+.
T Consensus 95 ~dG~V~~~~~~~G~~v~~g---~~l~~i~~~~~~~i~~~v~~~~~~~i~~g~~v~i~~~~-----~~~~~g~v~~I~~~ 165 (265)
T TIGR00999 95 FDGYITQKSVTLGDYVAPQ---AELFRVADLGAVWVEAEVPAKDVSRIRKGSKATVLLEN-----GRPLPARVDYVGPE 165 (265)
T ss_pred CCeEEEEEEcCCCCEeCCC---CceEEEEcCCcEEEEEEECHHHHhhCCCCCEEEEEECC-----CCEEEEEEEEEccc
Confidence 5688888877789998776 456776666543331 378999998887644 13455555555443
No 223
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=30.47 E-value=1.8e+02 Score=26.52 Aligned_cols=65 Identities=20% Similarity=0.134 Sum_probs=41.5
Q ss_pred cCCCCCCCCEEEEEEEEeeecceeE-EEcCCceeeeeEccccccccccc--ccccCCEEEEEEEEeeCCCCCee
Q 005716 268 ELPFYYPGQICEGKVTTVHLYQGAF-VDIGGVYDGWVPIKGNDWYWIRH--HIKVGMHVIVEILAKRDPYRFRF 338 (681)
Q Consensus 268 ~L~~LkeGqIVEGkVtnItdF~GAF-VDIGGv~DGLVHISEISW~rI~d--VLKVGDeVkVKVLsIdD~eR~RI 338 (681)
.|++-.+|+ +.|+|+.+--- |.| |-+..+..=|.||+. +++. -++.||.|.|...+..++.+.+|
T Consensus 12 ~~p~~~e~e-~~g~V~~~lG~-~~~~V~~~dG~~~la~i~G----K~Rk~iwI~~GD~VlVsp~d~~~~~kg~I 79 (99)
T TIGR00523 12 RLPRKEEGE-ILGVIEQMLGA-GRVKVRCLDGKTRLGRIPG----KLKKRIWIREGDVVIVKPWEFQGDDKCDI 79 (99)
T ss_pred eCCCCCCCE-EEEEEEEEcCC-CEEEEEeCCCCEEEEEEch----hhcccEEecCCCEEEEEEccCCCCccEEE
Confidence 445445665 67999999775 555 355544577888875 3333 68899999995555522334444
No 224
>KOG0343 consensus RNA Helicase [RNA processing and modification]
Probab=30.29 E-value=43 Score=39.31 Aligned_cols=127 Identities=25% Similarity=0.225 Sum_probs=60.5
Q ss_pred CCCCcccccCccccceeeehhhhhh---hccccccCcccc--CCccccccCCCcccCccCCeeehhhhhhhhhhhHHHHh
Q 005716 392 PEEEGLLSTHPYVDKLWQIHNAEQL---ILDDMEANPDKY--KGKKLSELTDDEEFDDENSVEYTKVNYKKALLAKIILK 466 (681)
Q Consensus 392 ~efgafve~hP~VegL~hIs~aEQm---iLdd~e~npdky--~~~~~~~l~d~ed~de~n~v~~t~~~~k~~~lpk~~~~ 466 (681)
++-++.==.+|.|+=.+|.---|+. | |--+--.-| .|..|.=|+-.|.. +--...++..+|..-+|
T Consensus 372 TDv~aRGLDFpaVdwViQ~DCPedv~tYI--HRvGRtAR~~~~G~sll~L~psEeE-------~~l~~Lq~k~I~i~~i~ 442 (758)
T KOG0343|consen 372 TDVAARGLDFPAVDWVIQVDCPEDVDTYI--HRVGRTARYKERGESLLMLTPSEEE-------AMLKKLQKKKIPIKEIK 442 (758)
T ss_pred ehhhhccCCCcccceEEEecCchhHHHHH--HHhhhhhcccCCCceEEEEcchhHH-------HHHHHHHHcCCCHHhhc
Confidence 3334444467888888887544331 1 111111112 25555555544311 11112223345555566
Q ss_pred cCcccccHHHHHHHHHHHHHHH------HHHHHhcccccccccccccccchhhhhhhhhcHHHHHHHHhhhhhhhh-cCC
Q 005716 467 TSVKELDLEAALAEREHHNKLQ------REAKERGEQYKVYKLRRNFEMDEYNFIHWRRSLEEREALIRDISCRQA-LGL 539 (681)
Q Consensus 467 ~~~keLdleaa~~ERe~~~kL~------~eA~erGe~yki~~lrrn~emdEyd~~hwrRs~EErEAL~RDi~cR~a-lGL 539 (681)
++...|- +..++|. .+-++.|.++-|.-+| .++-+|+..=++--.+||.+=-. |||
T Consensus 443 i~~~k~~--------~i~~~l~~ll~~~~eLk~~aqka~isY~r---------si~~~rdK~~f~~~~l~~~afa~s~Gl 505 (758)
T KOG0343|consen 443 IDPEKLT--------SIRNKLEALLAKDPELKEYAQKAFISYLR---------SIYLMRDKRVFDVEKLDIEAFADSLGL 505 (758)
T ss_pred cCHHHhh--------hHHHHHHHHHhhCHHHHHHHHHHHHHHHH---------HHHhhccchhhcchhccHHHHHHhcCC
Confidence 6544332 1223332 2445555566666554 34555555555555566655544 787
Q ss_pred CCCCC
Q 005716 540 PLEEP 544 (681)
Q Consensus 540 P~eeP 544 (681)
|..--
T Consensus 506 ~~~p~ 510 (758)
T KOG0343|consen 506 PGTPR 510 (758)
T ss_pred CCCch
Confidence 76543
No 225
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.09 E-value=93 Score=31.00 Aligned_cols=48 Identities=17% Similarity=0.007 Sum_probs=38.0
Q ss_pred EEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
-+.|+|..+..- .+-||+||+ -=.||+|......+ ++|++|++.+--+
T Consensus 4 ~l~G~i~~~~~~-~vvi~~~Gv-GY~V~vs~~~~~~l----~~g~~v~l~t~~~ 51 (197)
T PRK14603 4 YLSGVVLEKREG-SAVLLAGGV-GLEVQCPAPTLARL----VEGQEAELHTRLV 51 (197)
T ss_pred eEEEEEEEecCC-EEEEEECCE-EEEEEcCHHHHHHc----CCCCeEEEEEEEE
Confidence 378999999996 899999986 55788885544443 5799999998766
No 226
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=29.59 E-value=1.7e+02 Score=22.65 Aligned_cols=64 Identities=20% Similarity=0.196 Sum_probs=35.8
Q ss_pred EEEEEEEee----ecce---eEEEcCCceeeeeEcccc--cccccccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 278 CEGKVTTVH----LYQG---AFVDIGGVYDGWVPIKGN--DWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 278 VEGkVtnIt----dF~G---AFVDIGGv~DGLVHISEI--SW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
+.|.|+++. .- | +|+-+... .|-+-+.=. .|.+..+.+++|+.|.|.- .+ +..+++++|.+..+
T Consensus 2 i~g~v~~~~~~~~k~-g~~~~~~~l~D~-tg~~~~~~f~~~~~~~~~~l~~g~~v~v~G-~v-~~~~~~~~l~~~~i 74 (84)
T cd04485 2 VAGLVTSVRRRRTKK-GKRMAFVTLEDL-TGSIEVVVFPETYEKYRDLLKEDALLLVEG-KV-ERRDGGLRLIAERI 74 (84)
T ss_pred EEEEEEEeEEEEcCC-CCEEEEEEEEeC-CCeEEEEECHHHHHHHHHHhcCCCEEEEEE-EE-EecCCceEEEeecc
Confidence 456665543 33 5 67766543 555432111 1233567899999887764 34 23345677776554
No 227
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.10 E-value=97 Score=30.69 Aligned_cols=49 Identities=16% Similarity=0.053 Sum_probs=38.6
Q ss_pred EEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
-+.|+|+.+.+- -+-||+||+ -=.|++|.-.+..+. +.|++|++.+.-+
T Consensus 4 ~l~G~v~~~~~~-~vvi~~~Gv-GY~v~~s~~~~~~l~---~~g~~~~l~t~~~ 52 (194)
T PRK14605 4 SLNGILEASGKD-WAVINVSGV-GFRCYMPATSPALIG---GLGQRVRVFTHLH 52 (194)
T ss_pred eEEEEEEEecCC-EEEEEECCE-EEEEEeCHHHHHhcc---cCCCeEEEEEEEE
Confidence 478999999997 899999985 556888866665443 4699999998765
No 228
>PHA02945 interferon resistance protein; Provisional
Probab=28.77 E-value=23 Score=32.18 Aligned_cols=39 Identities=13% Similarity=0.078 Sum_probs=25.6
Q ss_pred CCCCccccc--CccccceeeehhhhhhhccccccCccccCCcc
Q 005716 392 PEEEGLLST--HPYVDKLWQIHNAEQLILDDMEANPDKYKGKK 432 (681)
Q Consensus 392 ~efgafve~--hP~VegL~hIs~aEQmiLdd~e~npdky~~~~ 432 (681)
.+||||+.+ +|+.+||+|||.- ++-+-|.-|-|.-+|++
T Consensus 22 ~d~ga~v~L~EY~g~eg~i~~sev--eva~~wvK~rd~l~Gqk 62 (88)
T PHA02945 22 NGYALYIDLFDYPHSEAILAESVQ--MHMNRYFKYRDKLVGKT 62 (88)
T ss_pred cCceEEEEecccCCcEEEEEeehh--hhccceEeeeeEecCCE
Confidence 789999887 4669999999943 33444555533334444
No 229
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.49 E-value=1e+02 Score=30.66 Aligned_cols=48 Identities=19% Similarity=-0.058 Sum_probs=37.5
Q ss_pred EEEEEEEEeeecceeEEE-cCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 277 ICEGKVTTVHLYQGAFVD-IGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVD-IGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
-++|+|..+.+- .+.|| +||+ -=.|++|.-....+ ++|++|++.+.-+
T Consensus 4 ~l~G~v~~~~~~-~vvid~v~GV-GY~v~i~~~~~~~l----~~g~~v~l~t~~~ 52 (183)
T PRK14601 4 AIEGIITKKEPT-FIVLKTASGV-SYGIFISLFCSAKI----QKGEKHELFITQI 52 (183)
T ss_pred EEEEEEEEecCC-EEEEEcCCCE-EEEEEecHHHHHHc----CCCCeEEEEEEEE
Confidence 378999999996 99999 5875 55788876555444 5799999988655
No 230
>KOG1857 consensus Transcription accessory protein TEX, contains S1 domain [Transcription]
Probab=28.41 E-value=27 Score=40.10 Aligned_cols=45 Identities=11% Similarity=-0.141 Sum_probs=41.7
Q ss_pred hhcccCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEccccc
Q 005716 264 EGMYELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGND 309 (681)
Q Consensus 264 egv~~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEIS 309 (681)
-||-....+-+|+-++|++-+=||| |.|+|+|.+.+|+-||+-+.
T Consensus 565 ~gV~~~~~l~~~~~~Te~~~sKtD~-~r~~~~g~ger~eA~I~H~~ 609 (623)
T KOG1857|consen 565 IGVVGKSGLIPIRNVTEAKLSKTDK-RRSLGLGPGERVEAQILHID 609 (623)
T ss_pred CCcccccccchhhhhcccccccccc-ccccCcccchhhhhhhcccc
Confidence 4678889999999999999999999 99999999999999998776
No 231
>TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.
Probab=27.86 E-value=1.1e+02 Score=31.38 Aligned_cols=70 Identities=16% Similarity=0.158 Sum_probs=41.8
Q ss_pred EEEEEEEEeee-cceeEEEcCCceeeeeEcccc-c--cc--ccc----cccccCCEEEEEEEEeeCCCCCeeeeeeeccC
Q 005716 277 ICEGKVTTVHL-YQGAFVDIGGVYDGWVPIKGN-D--WY--WIR----HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQ 346 (681)
Q Consensus 277 IVEGkVtnItd-F~GAFVDIGGv~DGLVHISEI-S--W~--rI~----dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~ 346 (681)
-+.|+|.++.. -.|.+|.-|. -|+.|... + |- .|. ..|++||.|+|++-+.....-+.+.-.+..+.
T Consensus 277 P~dG~V~~~~~~~~G~~v~~g~---~l~~i~~~~~~~~v~~~v~~~~~~~i~~G~~v~v~~~~~~~~~~~~~~g~V~~i~ 353 (423)
T TIGR01843 277 PVDGTVQSLKVHTVGGVVQPGE---TLMEIVPEDDPLEIEAKLSPKDIGFVHVGQPAEIKFSAFPYRRYGILNGKVKSIS 353 (423)
T ss_pred CCCcEEEEEEEEccCceecCCC---eeEEEecCCCcEEEEEEEChhhhhhhCCCCceEEEEecCCCcccCCccEEEEEEC
Confidence 36799988753 2599998774 45555432 2 21 222 28999999999988773221123444455555
Q ss_pred CCc
Q 005716 347 PNI 349 (681)
Q Consensus 347 pnP 349 (681)
+.+
T Consensus 354 ~~~ 356 (423)
T TIGR01843 354 PDT 356 (423)
T ss_pred CCc
Confidence 544
No 232
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.60 E-value=1e+02 Score=31.08 Aligned_cols=48 Identities=6% Similarity=-0.130 Sum_probs=37.4
Q ss_pred EEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
-++|+|+.+..- .+-||+||+ -=.||+|.-....+ +.|++|++.+.-+
T Consensus 4 ~l~G~v~~~~~~-~vvidv~GV-GY~v~vs~~~~~~l----~~g~~v~l~t~~~ 51 (196)
T PRK13901 4 KIYGKIIEKKES-SIVIMATPF-EFELLVSSFCLAEL----RLLEDVEILTYLH 51 (196)
T ss_pred EEEEEEEEEeCC-EEEEEeCCE-EEEEEecHHHHHhc----CCCCcEEEEEEEE
Confidence 378999999996 899999986 66788887555444 4699999988433
No 233
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=27.60 E-value=1.6e+02 Score=29.44 Aligned_cols=48 Identities=21% Similarity=0.052 Sum_probs=34.0
Q ss_pred CCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 271 FYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 271 ~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
.++.|++++++|.++..- + +|+.++.. +.-.....-+||.|.|+|..+
T Consensus 144 ~~~~~e~~~v~Ie~l~~~---------G-~GVak~~g--~~vfV~galpGE~V~vri~k~ 191 (201)
T PRK12336 144 AIEEGKTYEVEITGTGRK---------G-DGVAKKGK--YTIFVPGAKKGEVVKVKIKKI 191 (201)
T ss_pred CCccCCEEEEEEEEccCC---------C-ceEEEECC--EEEEeCCCCCCCEEEEEEEEe
Confidence 366788888888887754 2 88888743 222223445899999999988
No 234
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=27.16 E-value=51 Score=35.36 Aligned_cols=67 Identities=16% Similarity=0.170 Sum_probs=54.0
Q ss_pred CCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccc----c---------ccccccccCCEEEEEEEEeeCCCCCeee
Q 005716 273 YPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDW----Y---------WIRHHIKVGMHVIVEILAKRDPYRFRFP 339 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW----~---------rI~dVLKVGDeVkVKVLsIdD~eR~RIS 339 (681)
++|++|-|+|..|+.- --=||++...|+.+..|-|.- . ..+++++.||-|-+.|-.+- ..+-++
T Consensus 84 EvGDvVVgRV~eVq~K-RWkvd~nsk~d~vL~LsSvNLPGg~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~--~dGs~s 160 (301)
T KOG3013|consen 84 EVGDVVVGRVIEVQQK-RWKVDLNSKQDAVLMLSSVNLPGGIQRRKSEEDELQMRSFLKEGDLIVAEVQNVF--HDGSLS 160 (301)
T ss_pred ccCCEEEEEeeeeecc-eeEEecccccceEEEeecccCCchhhhccchhhHHHHHHHhhccCeehHHHHHhc--cCCeEE
Confidence 6899999999999996 889999999999999998853 1 13469999999999998882 234555
Q ss_pred eee
Q 005716 340 IEM 342 (681)
Q Consensus 340 LSL 342 (681)
|--
T Consensus 161 LhT 163 (301)
T KOG3013|consen 161 LHT 163 (301)
T ss_pred EEe
Confidence 543
No 235
>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=27.12 E-value=79 Score=24.64 Aligned_cols=19 Identities=21% Similarity=0.181 Sum_probs=17.2
Q ss_pred CCCEEEEEEEEeeecceeEE
Q 005716 274 PGQICEGKVTTVHLYQGAFV 293 (681)
Q Consensus 274 eGqIVEGkVtnItdF~GAFV 293 (681)
.+++++|+++.|.+. |+.+
T Consensus 11 ~~~~~~G~~~gId~~-G~L~ 29 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDD-GALL 29 (48)
T ss_dssp TSCEEEEEEEEEETT-SEEE
T ss_pred CCeEEEEEEEEECCC-CEEE
Confidence 578999999999998 9987
No 236
>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=27.10 E-value=88 Score=25.79 Aligned_cols=44 Identities=11% Similarity=0.052 Sum_probs=28.7
Q ss_pred ccCCEEEEEEEEeeCCCCCeeeeee----------eccCCCccccccccCCCCCccc
Q 005716 318 KVGMHVIVEILAKRDPYRFRFPIEM----------RFVQPNIDHLIFNRFDFAPIFH 364 (681)
Q Consensus 318 KVGDeVkVKVLsIdD~eR~RISLSL----------K~~~pnPW~~I~erf~vgpI~~ 364 (681)
++||.|..+|+++.+ +.+.+.+ -.+..++=..+...+++|+++.
T Consensus 5 ~~GdiV~G~V~~v~~---~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~ 58 (82)
T cd04454 5 DVGDIVIGIVTEVNS---RFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLIL 58 (82)
T ss_pred CCCCEEEEEEEEEcC---CEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEE
Confidence 789999999999953 3333333 2233333344666688888887
No 237
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=26.76 E-value=1.4e+02 Score=29.15 Aligned_cols=49 Identities=18% Similarity=0.148 Sum_probs=39.2
Q ss_pred EEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
-+.|+|+.+..- .+-||+||+ -=.|++|.-++..+. ++|+.|.+.++-.
T Consensus 4 ~i~G~i~~~~~~-~~ii~~~gv-GY~v~~~~~~~~~l~---~~~~~~~l~~~~~ 52 (192)
T PRK00116 4 YLKGKLVEKGPD-YVVIEVNGV-GYEVQVPMRTLYELP---EVGEEVKLYTHLV 52 (192)
T ss_pred eEEEEEEEEcCC-EEEEEECCE-EEEEEeCHHHHHhcc---CCCCeEEEEEEEE
Confidence 378999999996 899999985 556888877776553 5799999988765
No 238
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=26.71 E-value=3.4e+02 Score=24.19 Aligned_cols=63 Identities=25% Similarity=0.251 Sum_probs=42.4
Q ss_pred EEEEEEEEeeecceeE-EEcCCceeeeeEccccccc-ccccccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 277 ICEGKVTTVHLYQGAF-VDIGGVYDGWVPIKGNDWY-WIRHHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 277 IVEGkVtnItdF~GAF-VDIGGv~DGLVHISEISW~-rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
.+.|+|+.+-.= |-| |-|-.++.=+-|||.=-=. +| -+.+||.|.|..-.. |..+.||---.+
T Consensus 8 e~~g~V~e~L~~-~~f~v~~edg~~~~ahI~GKmr~~~i--~I~~GD~V~Ve~~~~-d~~kg~I~~Ry~ 72 (75)
T COG0361 8 EMEGTVIEMLPN-GRFRVELENGHERLAHISGKMRKNRI--RILPGDVVLVELSPY-DLTKGRIVYRYK 72 (75)
T ss_pred EEEEEEEEecCC-CEEEEEecCCcEEEEEccCcchheeE--EeCCCCEEEEEeccc-ccccccEEEEec
Confidence 578999998763 333 4554445667787752211 11 577899999999999 677788754443
No 239
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.08 E-value=1.1e+02 Score=30.47 Aligned_cols=50 Identities=18% Similarity=0.120 Sum_probs=36.1
Q ss_pred EEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
-+.|+|+.+..=.-+.||+||+ -=.|++|...+..+. +.|+.|++.+.-+
T Consensus 4 ~l~G~v~~~~~~~~vviev~Gv-GY~v~i~~~~~~~l~---~~g~~v~l~t~~~ 53 (203)
T PRK14602 4 YLEGRVAERRENSCVVLTPGGV-GYEVFLPAHTLARLP---EKGGQVSFFVHTV 53 (203)
T ss_pred eEEEEEEEEcCCcEEEEEeCCE-EEEEEcCHHHHHHhc---cCCCeEEEEEEEE
Confidence 3789999996531457899986 445888866665442 5799999998665
No 240
>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=25.95 E-value=23 Score=40.42 Aligned_cols=35 Identities=14% Similarity=0.126 Sum_probs=29.7
Q ss_pred CCCCccccCCCCCchhhhhccCCCCCCCCCCCCCCCCCcccccC-ccccceeeehhh
Q 005716 358 DFAPIFHRDEDKNPDELRRDCGRPPVPRKYPGVKPEEEGLLSTH-PYVDKLWQIHNA 413 (681)
Q Consensus 358 ~vgpI~~r~~d~n~geV~Rd~GRp~~pr~~p~~~~efgafve~h-P~VegL~hIs~a 413 (681)
.+|.+|. |.|.. .++||.||++- ++|+||||++..
T Consensus 571 ~iG~~~~-------g~I~~--------------v~~~GifV~L~~~~veGlV~~s~l 606 (654)
T TIGR00358 571 KVGTEFS-------GEISS--------------VTRFGMFVRLDDNGIDGLIHISTL 606 (654)
T ss_pred CCCcEEE-------EEEEe--------------EEcCcEEEEecCCceEEEEEeEeC
Confidence 3577777 88888 89999999997 889999999744
No 241
>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=25.41 E-value=1.1e+02 Score=26.51 Aligned_cols=48 Identities=23% Similarity=0.230 Sum_probs=30.3
Q ss_pred EEEEEEEEeeecce--eEEEcCCceeeeeEc----c--cccccccccccccCCEEEEEE
Q 005716 277 ICEGKVTTVHLYQG--AFVDIGGVYDGWVPI----K--GNDWYWIRHHIKVGMHVIVEI 327 (681)
Q Consensus 277 IVEGkVtnItdF~G--AFVDIGGv~DGLVHI----S--EISW~rI~dVLKVGDeVkVKV 327 (681)
.+.|-|.++... | +|++|-.+ .|.|-+ + +-.+..+ .-|..|+.|.|.=
T Consensus 3 ~v~Gwv~~~R~~-gk~~Fi~lrD~-~g~iQ~v~~~~~~~~~~~~~-~~l~~~s~v~V~G 58 (103)
T cd04319 3 TLAGWVYRKREV-GKKAFIVLRDS-TGIVQAVFSKDLNEEAYREA-KKVGIESSVIVEG 58 (103)
T ss_pred EEEEEEEeEEcC-CCeEEEEEecC-CeeEEEEEeCCCCHHHHHHH-hCCCCCCEEEEEE
Confidence 578999999996 7 89999433 344432 1 1112222 2478899988764
No 242
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=25.32 E-value=3.4e+02 Score=22.86 Aligned_cols=58 Identities=24% Similarity=0.162 Sum_probs=31.4
Q ss_pred EEEEEEEEeeecceeEEEcCCceee---eeEcccccccccccccccCCEEEEEEEEeeCCCCCeee
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDG---WVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFP 339 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DG---LVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RIS 339 (681)
.++|+|+.+.. |+|..+-+ .+| +.|++---.. -.--+.+||.|.|.+-.. +..+.+|-
T Consensus 8 ~~~G~Vi~~~~--~~~y~V~~-~~g~~~~c~~~Gklr~-~~i~i~vGD~V~ve~~~~-~~~~g~Iv 68 (72)
T PRK00276 8 EMEGTVVEALP--NAMFRVEL-ENGHEVLAHISGKMRK-NYIRILPGDKVTVELSPY-DLTKGRIT 68 (72)
T ss_pred EEEEEEEEEcC--CCEEEEEe-CCCCEEEEEEccceee-CCcccCCCCEEEEEEccc-CCCeEEEE
Confidence 46799988763 32333311 133 2333322221 111378999999998666 55556653
No 243
>TIGR00998 8a0101 efflux pump membrane protein (multidrug resistance protein A).
Probab=25.20 E-value=1.5e+02 Score=29.77 Aligned_cols=67 Identities=12% Similarity=0.159 Sum_probs=44.6
Q ss_pred EEEEEEEEeeecceeEEEcCCceeeeeEcccccccc----cc----cccccCCEEEEEEEEeeCCCCCeeeeeeeccCCC
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYW----IR----HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQPN 348 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~r----I~----dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~pn 348 (681)
-+.|+|+++.--.|.+|.-|. -|+.|...+--. |. ..|++||.|.|++-+. +....+.-.+..+.+.
T Consensus 210 P~~G~V~~~~~~~G~~v~~g~---~l~~i~~~~~~~v~~~v~e~~~~~i~~G~~v~v~~~~~--~~~~~~~G~V~~Is~~ 284 (334)
T TIGR00998 210 PFDGYVARRFVQVGQVVSPGQ---PLMAVVPAEQMYVEANFKETQLKNVRIGQPVTIRSDLY--GSDVVFEGKVTGISMG 284 (334)
T ss_pred CCCcEEEEEecCCCCEeCCCC---eeEEEEcCCcEEEEEecCHHHHhhCCCCCEEEEEEecC--CCCCEEEEEEEEECCC
Confidence 367899888877899998774 455555543222 21 3889999999997655 2234566666666665
No 244
>PF07405 DUF1506: Protein of unknown function (DUF1506); InterPro: IPR010875 This entry represents proteins found primarily in Borrelia species. Their function is unknown.
Probab=24.83 E-value=64 Score=31.11 Aligned_cols=58 Identities=16% Similarity=0.060 Sum_probs=38.7
Q ss_pred eecceeEEEcCCceeeeeEccccccc--------------ccccccccCCEEEEEEEEeeCCCCCeeeeeeec
Q 005716 286 HLYQGAFVDIGGVYDGWVPIKGNDWY--------------WIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRF 344 (681)
Q Consensus 286 tdF~GAFVDIGGv~DGLVHISEISW~--------------rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~ 344 (681)
+.|.|+|+||--..--.|+=|+|+.. .+.+.++++|-|-..|++| |..-+=+.|.||.
T Consensus 51 ~eF~Gv~i~I~P~E~v~i~~sNi~D~~~y~klYT~~~l~fE~~DrIsi~D~~yfeI~si-d~si~Y~TLvLk~ 122 (127)
T PF07405_consen 51 TEFKGVIIDIKPQELVEIYDSNIFDIQGYSKLYTYQNLNFELKDRISISDDVYFEIFSI-DSSIGYFTLVLKE 122 (127)
T ss_pred eEEEEEEEEeChHHeeeeccCCchhhhhhhheeehhhccchhhceeehhheeeeEEEee-eccccchhhhHhh
Confidence 55889999985321223444555431 2357999999999999999 5555556666654
No 245
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=24.12 E-value=1.1e+02 Score=27.27 Aligned_cols=43 Identities=23% Similarity=0.224 Sum_probs=28.2
Q ss_pred EEEEEEEeeecce---eEEEcCCceeeeeEcccccccccc---cccccCCEEEEEE
Q 005716 278 CEGKVTTVHLYQG---AFVDIGGVYDGWVPIKGNDWYWIR---HHIKVGMHVIVEI 327 (681)
Q Consensus 278 VEGkVtnItdF~G---AFVDIGGv~DGLVHISEISW~rI~---dVLKVGDeVkVKV 327 (681)
+-|+|.+|... + |-||.||+ ..+++-.-+. .-+++||-|.|-+
T Consensus 5 iP~kVi~i~~~-~~~~A~vd~~Gv------~r~V~l~Lv~~~~~~~~vGDyVLVHa 53 (82)
T PRK10413 5 VPGQVLAVGED-IHQLAQVEVCGI------KRDVNIALICEGNPADLLGQWVLVHV 53 (82)
T ss_pred cceEEEEECCC-CCcEEEEEcCCe------EEEEEeeeeccCCcccccCCEEEEec
Confidence 45889999885 5 99999886 2222222221 2368899998864
No 246
>PRK08402 replication factor A; Reviewed
Probab=24.02 E-value=2e+02 Score=31.29 Aligned_cols=76 Identities=18% Similarity=0.148 Sum_probs=50.5
Q ss_pred hcccCCCCCCCC---EEEEEEEEeee---cc---e----eE-EEcCCceeeeeEccccccccc-c---cccccCCEEEEE
Q 005716 265 GMYELPFYYPGQ---ICEGKVTTVHL---YQ---G----AF-VDIGGVYDGWVPIKGNDWYWI-R---HHIKVGMHVIVE 326 (681)
Q Consensus 265 gv~~L~~LkeGq---IVEGkVtnItd---F~---G----AF-VDIGGv~DGLVHISEISW~rI-~---dVLKVGDeVkVK 326 (681)
++..|.+|.+|+ .+.|+|+++.. |. | ++ +-||.. +|-|++ ..|..- . .-|++|+.|.++
T Consensus 61 ~~~kI~dl~~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~De-TG~ir~--TlW~~~a~~~~~~l~~Gdvi~I~ 137 (355)
T PRK08402 61 PLMHISDLVPGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDD-TGRARV--VLWDAKVAKYYNKINVGDVIKVI 137 (355)
T ss_pred CccCHHHccCCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcC-CCeEEE--EEechhhhhhcccCCCCCEEEEE
Confidence 466778888887 57899998854 21 3 11 345543 666644 468643 2 358999999987
Q ss_pred EEEeeCCCCCeeeeeee
Q 005716 327 ILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 327 VLsIdD~eR~RISLSLK 343 (681)
=-.+++..+++++|++=
T Consensus 138 ~a~V~e~~~G~~eLsvg 154 (355)
T PRK08402 138 DAQVRESLSGLPELHIN 154 (355)
T ss_pred CCEEeecCCCcEEEEEC
Confidence 66666666788888883
No 247
>CHL00010 infA translation initiation factor 1
Probab=23.60 E-value=4.7e+02 Score=22.61 Aligned_cols=65 Identities=26% Similarity=0.137 Sum_probs=34.7
Q ss_pred EEEEEEEeeecceeE-EEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 278 CEGKVTTVHLYQGAF-VDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 278 VEGkVtnItdF~GAF-VDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
++|+|+.+..= |.| |-+-.+..=+.|++-.-..+ +-.+.+||.|.|.+-.. +..+.+|---.|..
T Consensus 9 ~~G~Vik~lg~-~~y~V~~~~g~~~~c~~rGklr~~-~i~~~vGD~V~ve~~~~-~~~~g~Ii~r~~~~ 74 (78)
T CHL00010 9 MEGLVTESLPN-GMFRVRLDNGCQVLGYISGKIRRN-SIRILPGDRVKVELSPY-DLTKGRIIYRLRNK 74 (78)
T ss_pred EEEEEEEEcCC-CEEEEEeCCCCEEEEEeccceecC-CcccCCCCEEEEEEccc-CCCeEEEEEEecCC
Confidence 67999887631 222 22211112233443332221 12467899999998666 55566765544433
No 248
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.44 E-value=1.7e+02 Score=29.13 Aligned_cols=49 Identities=16% Similarity=0.101 Sum_probs=38.1
Q ss_pred EEEEEEEEeeecceeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 277 ICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 277 IVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
-+.|+|+.+..- -+-||+||+ -=.|++|.-.+..+. ++|+.|++.+.-+
T Consensus 4 ~i~G~i~~~~~~-~viie~~Gv-GY~v~vs~~~~~~l~---~~g~~v~l~t~~~ 52 (195)
T PRK14604 4 SIRGIIQSIGND-HLIVETGGV-GLLIYAPRSVLAAIG---AIGDEVFLYTHLI 52 (195)
T ss_pred eEEEEEEEEcCC-EEEEEECCE-EEEEEeCHHHHHHhc---cCCCeEEEEEEEE
Confidence 378999999996 899999985 556777765554432 5799999998766
No 249
>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=23.17 E-value=9.7 Score=40.69 Aligned_cols=94 Identities=14% Similarity=0.222 Sum_probs=63.7
Q ss_pred ccccccccCCEEEEEEEEeeCCCCCeeeeeeec-----cCCCccccccccCC--CCCccccCCCCCchhhhhccCCCCCC
Q 005716 312 WIRHHIKVGMHVIVEILAKRDPYRFRFPIEMRF-----VQPNIDHLIFNRFD--FAPIFHRDEDKNPDELRRDCGRPPVP 384 (681)
Q Consensus 312 rI~dVLKVGDeVkVKVLsIdD~eR~RISLSLK~-----~~pnPW~~I~erf~--vgpI~~r~~d~n~geV~Rd~GRp~~p 384 (681)
.+..-+++||.|++.|... +..| ....+.|+ +..--++.+.+.|. .|.|++ |+|.+
T Consensus 79 ~~d~~~~vGD~I~~~I~~~-~fgR-~aaq~aKqvi~Qkire~ere~i~~ey~~k~GeiV~-------G~V~~-------- 141 (341)
T TIGR01953 79 EIDPDVQIGDEVKKEIPPE-NFGR-IAAQTAKQVILQKIREAERERVYDEFSSKEGEIIS-------GTVKR-------- 141 (341)
T ss_pred hhccccccCCEEEEEeccc-CCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCEEE-------EEEEE--------
Confidence 3456899999999998544 3332 33334555 34667888999996 899999 99999
Q ss_pred CCCCCCCCCCCc-ccccCccccceeeehhhhhhhccccccCccccC-CccccccCC
Q 005716 385 RKYPGVKPEEEG-LLSTHPYVDKLWQIHNAEQLILDDMEANPDKYK-GKKLSELTD 438 (681)
Q Consensus 385 r~~p~~~~efga-fve~hP~VegL~hIs~aEQmiLdd~e~npdky~-~~~~~~l~d 438 (681)
....|. +|.+. +++|+++.+ ||. . .+.|. |..+.-+.-
T Consensus 142 ------v~~~g~v~VdiG-~~ea~LP~~--E~i-p------~E~~~~Gd~ik~~V~ 181 (341)
T TIGR01953 142 ------VNRRGNLYVELG-KTEGILPKK--EQI-P------GEKFRIGDRIKAYVY 181 (341)
T ss_pred ------EecCCcEEEEEC-CeEEEecHH--HcC-C------CcCCCCCCEEEEEEE
Confidence 666674 88774 899998843 444 2 12343 666555553
No 250
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). 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. Included in this group are archeal and archeal-like A
Probab=22.89 E-value=1.7e+02 Score=24.38 Aligned_cols=49 Identities=16% Similarity=0.079 Sum_probs=29.2
Q ss_pred EEEEEEEEeeecce--eEEEcCC---ceeeeeEccccc--ccccccccccCCEEEEEE
Q 005716 277 ICEGKVTTVHLYQG--AFVDIGG---VYDGWVPIKGND--WYWIRHHIKVGMHVIVEI 327 (681)
Q Consensus 277 IVEGkVtnItdF~G--AFVDIGG---v~DGLVHISEIS--W~rI~dVLKVGDeVkVKV 327 (681)
.+.|-|.++... | +|++|-. ....++..+... +..+ ..|+.|+.|.|.=
T Consensus 3 ~i~Gwv~~~R~~-g~~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~-~~l~~~s~V~v~G 58 (85)
T cd04100 3 TLAGWVHSRRDH-GGLIFIDLRDGSGIVQVVVNKEELGEFFEEA-EKLRTESVVGVTG 58 (85)
T ss_pred EEEEEEehhccC-CCEEEEEEEeCCeeEEEEEECCcChHHHHHH-hCCCCCCEEEEEe
Confidence 478999999886 5 7898822 122223222211 2222 3588999988863
No 251
>PF07757 AdoMet_MTase: Predicted AdoMet-dependent methyltransferase; InterPro: IPR011671 tRNA (uracil-O(2)-)-methyltransferase catalyses the formation of O(2)-methyl-uracil at position 44 (m2U44) in tRNA(Ser) [].; GO: 0008168 methyltransferase activity
Probab=22.89 E-value=22 Score=33.54 Aligned_cols=22 Identities=27% Similarity=0.305 Sum_probs=15.9
Q ss_pred eecceeEEEcCCceeeeeEcccc
Q 005716 286 HLYQGAFVDIGGVYDGWVPIKGN 308 (681)
Q Consensus 286 tdF~GAFVDIGGv~DGLVHISEI 308 (681)
..+ +-|||||++.-=||||=..
T Consensus 57 ~~~-~~FVDlGCGNGLLV~IL~~ 78 (112)
T PF07757_consen 57 QKF-QGFVDLGCGNGLLVYILNS 78 (112)
T ss_pred CCC-CceEEccCCchHHHHHHHh
Confidence 667 8899999994446787433
No 252
>PLN02856 fumarylacetoacetase
Probab=22.67 E-value=1.1e+02 Score=34.25 Aligned_cols=69 Identities=14% Similarity=0.145 Sum_probs=46.2
Q ss_pred cCCCCCCCCEE-EEEEEEeeecc-eeEEEcCCceeeeeEcccccccccccccccCCEEEEEEEEeeCCCCCeeeee
Q 005716 268 ELPFYYPGQIC-EGKVTTVHLYQ-GAFVDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAKRDPYRFRFPIE 341 (681)
Q Consensus 268 ~L~~LkeGqIV-EGkVtnItdF~-GAFVDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsIdD~eR~RISLS 341 (681)
+.-.|++|+++ +|||.+...-+ |.++.+-- .|.-.|. +.-..-+.+|+.||+|++.-..-. +..||.+.
T Consensus 343 ~g~tL~pGDLi~TGTpsG~~~~~~G~llElt~--~G~~p~~-l~~g~~r~fL~dGD~V~l~g~~~~--~g~~igfG 413 (424)
T PLN02856 343 NGCNLRPGDLLGSGTISGPEPGSLGCLLELTW--AGSREVS-LEGGTRRKFLEDGDEVVLSGWCKG--DGYRVGFG 413 (424)
T ss_pred CCeecCCCCEEEeCCCCCCccCCCCCEEEEEe--CCccceE-eccCCccccCCCCCEEEEEEEECC--CCccEeee
Confidence 34579999976 89998875432 77776631 3333333 444445679999999999988753 34587663
No 253
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The Poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=22.61 E-value=1.7e+02 Score=29.27 Aligned_cols=59 Identities=17% Similarity=0.328 Sum_probs=41.2
Q ss_pred cCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccc----cc-----ccccc--ccccCCEEEEEEEEe
Q 005716 268 ELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGN----DW-----YWIRH--HIKVGMHVIVEILAK 330 (681)
Q Consensus 268 ~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEI----SW-----~rI~d--VLKVGDeVkVKVLsI 330 (681)
+..-+++|++|.|+. +|++-.-++|++|.- +.|++-= |. =-+++ ++.-|.+|.|....-
T Consensus 75 tykyYk~GDvV~GtL-nIedESni~V~CgDL---iCkl~rdsGtVSf~dsKYCfirNg~vY~ngs~Vsv~LkEa 144 (160)
T PF03293_consen 75 TYKYYKVGDVVRGTL-NIEDESNITVQCGDL---ICKLSRDSGTVSFNDSKYCFIRNGVVYDNGSEVSVVLKEA 144 (160)
T ss_pred EEEEEeeCCEEEEEE-EecccCceEEEcCcE---EEEeeccCCeEEecCceEEEEECCEEecCCCEEEEEehhh
Confidence 445678999999986 577766899999844 4444432 22 22443 889999999987665
No 254
>PRK11578 macrolide transporter subunit MacA; Provisional
Probab=22.46 E-value=1.9e+02 Score=30.14 Aligned_cols=69 Identities=17% Similarity=0.200 Sum_probs=44.5
Q ss_pred EEEEEEEeeecceeEEEcCCceeeeeEccccccccc----c----cccccCCEEEEEEEEeeCCCCCeeeeeeeccCCCc
Q 005716 278 CEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWI----R----HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQPNI 349 (681)
Q Consensus 278 VEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI----~----dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~pnP 349 (681)
+.|+|+.+.--.|.+|+-|...+-|+.|.+++-..+ . ..|+.|+.|.|.+.+.. ...+.-.+..+.|.+
T Consensus 190 ~dG~V~~~~~~~G~~V~~~~~~~~l~~i~~~~~~~v~~~V~e~~~~~i~~g~~v~i~~~~~~---~~~~~g~V~~I~~~~ 266 (370)
T PRK11578 190 MAGEVTQITTLQGQTVIAAQQAPNILTLADMSTMLVKAQVSEADVIHLKPGQKAWFTVLGDP---LTRYEGVLKDILPTP 266 (370)
T ss_pred CCcEEEeeecCCCcEeecccCCceEEEEecCCcEEEEEEECHHHHhhCCCCCEEEEEEccCC---CCeEEEEEEEEccCc
Confidence 568888887777888876632245778777763332 1 26889999998875542 234555555555544
No 255
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.35 E-value=3.2e+02 Score=23.28 Aligned_cols=61 Identities=13% Similarity=0.183 Sum_probs=44.4
Q ss_pred cCCCCCCCCCcccchhhHHHHHHHhhhhceecchHHHHHhhhcccCCCchhHHHHHHHHHH
Q 005716 170 VAPRDWPPRGWEVDRKELEYIREAHKLQNVRVEIGELERKAKFEREGFNFDMYRVFLKQYN 230 (681)
Q Consensus 170 vpPRDWPP~gWeVd~kEL~fIREah~~~~~rv~~~~l~~~~~~~~~~~~l~r~k~FlkQY~ 230 (681)
+||.-=++..|..+..++..++..+.|...-++++++.........+-+++-++.++++=-
T Consensus 26 l~~~~~~~g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~ 86 (100)
T cd00592 26 LPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSLAALLALLDEKL 86 (100)
T ss_pred cCCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccccchHHHHHHHHHHHH
Confidence 3443335577889999999999999999999999999988776554433555555555433
No 256
>TIGR02142 modC_ABC molybdenum ABC transporter, ATP-binding protein. This model represents the ATP-binding cassette (ABC) protein of the three subunit molybdate ABC transporter. The three proteins of this complex are homologous to proteins of the sulfate ABC transporter. Molybdenum may be used in nitrogenases of nitrogen-fixing bacteria and in molybdopterin cofactors. In some cases, molybdate may be transported by a sulfate transporter rather than by a specific molybdate transporter.
Probab=22.10 E-value=2e+02 Score=30.13 Aligned_cols=50 Identities=22% Similarity=0.229 Sum_probs=33.9
Q ss_pred EEEEEEEEeeecce-eE----EEcCCceeeeeEcccccccccccccccCCEEEEEEEEe
Q 005716 277 ICEGKVTTVHLYQG-AF----VDIGGVYDGWVPIKGNDWYWIRHHIKVGMHVIVEILAK 330 (681)
Q Consensus 277 IVEGkVtnItdF~G-AF----VDIGGv~DGLVHISEISW~rI~dVLKVGDeVkVKVLsI 330 (681)
.+.|+|+.|..- | .. ||+|+. .=.+|++.-++... -+++|+.|.+.|.+.
T Consensus 297 ~~~~~v~~~~~~-~~~~~~~~~~~~~~-~l~~~~~~~~~~~~--~l~~g~~v~~~~~~~ 351 (354)
T TIGR02142 297 ILPARVVEIEDS-DIGRVGVVLESGGK-TLWARITRWARDEL--GIAPGTPVFAQIKAV 351 (354)
T ss_pred EEEEEEEEEEec-CCCeEEEEEEcCCc-EEEEEecHHHHHhc--CCCCCCEEEEEEEee
Confidence 589999999875 7 33 455532 33446665555443 388999999988765
No 257
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=22.00 E-value=3.1e+02 Score=24.22 Aligned_cols=61 Identities=20% Similarity=0.134 Sum_probs=41.3
Q ss_pred CCCCEEEEEEEEeeecceeE-EEcCCceeeeeEccccccccccc--ccccCCEEEEEEEEeeCCCCCeeee
Q 005716 273 YPGQICEGKVTTVHLYQGAF-VDIGGVYDGWVPIKGNDWYWIRH--HIKVGMHVIVEILAKRDPYRFRFPI 340 (681)
Q Consensus 273 keGqIVEGkVtnItdF~GAF-VDIGGv~DGLVHISEISW~rI~d--VLKVGDeVkVKVLsIdD~eR~RISL 340 (681)
.+|| +-|+|+.+.-- |-| |-+..++.=|+||+. +++. -++.||.|.|..... ++.+.+|--
T Consensus 3 ~e~q-~~g~V~~~lG~-~~~~V~~~dG~~~la~ipg----K~Rk~iwI~~GD~VlVe~~~~-~~~kg~Iv~ 66 (83)
T smart00652 3 EDGQ-EIAQVVKMLGN-GRLEVMCADGKERLARIPG----KMRKKVWIRRGDIVLVDPWDF-QDVKADIIY 66 (83)
T ss_pred CCCc-EEEEEEEEcCC-CEEEEEECCCCEEEEEEch----hhcccEEEcCCCEEEEEecCC-CCCEEEEEE
Confidence 4565 56899999765 555 355544577888875 3333 688999999988777 455556543
No 258
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=21.78 E-value=3.2e+02 Score=30.92 Aligned_cols=64 Identities=14% Similarity=0.107 Sum_probs=37.6
Q ss_pred EEEEEEEEeeecce--eEEEcCCc---eeeeeEccccc---ccccccccccCCEEEEEEEEeeCCCCCeeeeee
Q 005716 277 ICEGKVTTVHLYQG--AFVDIGGV---YDGWVPIKGND---WYWIRHHIKVGMHVIVEILAKRDPYRFRFPIEM 342 (681)
Q Consensus 277 IVEGkVtnItdF~G--AFVDIGGv---~DGLVHISEIS---W~rI~dVLKVGDeVkVKVLsIdD~eR~RISLSL 342 (681)
.|.|.|.++... | +|++|-.+ ..-++..+++. +......+.+|+.|.|.=.=+.. .++-++|.+
T Consensus 69 ~v~Grv~~~R~~-Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t-~~gelel~~ 140 (505)
T PRK12445 69 SVAGRMMTRRIM-GKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKT-QTGELSIHC 140 (505)
T ss_pred EEEEEEEEEecC-CCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEec-CCCcEEEEE
Confidence 579999999997 8 89999322 22233333332 22122358899999886433322 234455444
No 259
>TIGR03794 NHPM_micro_HlyD NHPM bacteriocin system secretion protein. Members of this protein family are homologs of the HlyD membrane fusion protein of type I secretion systems. Their occurrence in prokaryotic genomes is associated with the occurrence of a novel class of microcin (small bacteriocins) with a propeptide region related to nitrile hydratase. We designate the class of bacteriocin as Nitrile Hydratase Propeptide Microcin, or NHPM. This family, therefore, is designated as NHPM bacteriocin system secretion protein. Some but not all NHPM-class putative microcins belong to the TOMM (thiazole/oxazole modified microcin) class as assessed by the presence of the scaffolding protein and/or cyclodehydratase in the same gene clusters.
Probab=21.65 E-value=1.7e+02 Score=31.04 Aligned_cols=70 Identities=16% Similarity=0.150 Sum_probs=45.0
Q ss_pred EEEEEEEeeecceeEEEcCCceeeeeEccccc------cc--ccc----cccccCCEEEEEEEEeeCCCCCeeeeeeecc
Q 005716 278 CEGKVTTVHLYQGAFVDIGGVYDGWVPIKGND------WY--WIR----HHIKVGMHVIVEILAKRDPYRFRFPIEMRFV 345 (681)
Q Consensus 278 VEGkVtnItdF~GAFVDIGGv~DGLVHISEIS------W~--rI~----dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~ 345 (681)
+.|+|+.+.--.|.+|.-|.. |+.|...+ |- .+. ..|++||.|.|++-+++...-+.|.-.++.+
T Consensus 260 ~dG~V~~~~~~~G~~v~~g~~---l~~i~~~~~~~~~l~v~~~v~e~~~~~v~~G~~v~v~~~~~~~~~~~~~~g~V~~I 336 (421)
T TIGR03794 260 HSGRVIELNYTPGQLVAAGAP---LASLEVEDQTDEGLEGVAYFPVAEGKKIRPGMSVQITPSTVKAERDGYIRGTVTSV 336 (421)
T ss_pred CCeEEEEeeCCCCCEecCCCc---EEEEEccCCCCCcEEEEEEECHHHHhhCCCCCEEEEEEcccccceeeeEEEEEEEe
Confidence 668888876556888877743 44442111 11 121 2789999999998887332224577788777
Q ss_pred CCCcc
Q 005716 346 QPNID 350 (681)
Q Consensus 346 ~pnPW 350 (681)
.+.|-
T Consensus 337 s~~~~ 341 (421)
T TIGR03794 337 SEYPA 341 (421)
T ss_pred cCCCC
Confidence 77654
No 260
>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein. This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.
Probab=21.06 E-value=1.8e+02 Score=31.47 Aligned_cols=72 Identities=17% Similarity=0.194 Sum_probs=42.1
Q ss_pred EEEEEEEeeecce-eEEEcCCceeeeeEc----ccccc-cccc----cccccCCEEEEEEEEeeCCCCCeeeeeeeccCC
Q 005716 278 CEGKVTTVHLYQG-AFVDIGGVYDGWVPI----KGNDW-YWIR----HHIKVGMHVIVEILAKRDPYRFRFPIEMRFVQP 347 (681)
Q Consensus 278 VEGkVtnItdF~G-AFVDIGGv~DGLVHI----SEISW-~rI~----dVLKVGDeVkVKVLsIdD~eR~RISLSLK~~~p 347 (681)
+.|+|.......| .+|.-|...--+|+. +.+-. -.|. ..|++||.|.|++-+. ......+.-.+..+.+
T Consensus 323 ~dG~V~~~~~~~G~~~V~~G~~l~~IvP~~~~~~~l~v~~~V~e~di~~v~~Gq~V~v~~~a~-~~~~~~~~G~V~~Is~ 401 (457)
T TIGR01000 323 EDGVLHLNPETKGIKYVPKGTLIAQIYPILEKERKLKVTAYLPSNDISGIKVGQKVRFKLTQN-VPKPIILDGTITSISS 401 (457)
T ss_pred CCeEEEecccCCCCcEeCCCCEEEEEecCCCCCCcEEEEEEeCHHHHhhcCCCCeEEEEEecC-CCCceEEEEEEEEEcC
Confidence 5688875544446 577666544444433 11211 1222 2789999999998862 2222357777777777
Q ss_pred Ccc
Q 005716 348 NID 350 (681)
Q Consensus 348 nPW 350 (681)
++-
T Consensus 402 ~~~ 404 (457)
T TIGR01000 402 APT 404 (457)
T ss_pred CCc
Confidence 763
No 261
>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=20.75 E-value=1.3e+02 Score=28.34 Aligned_cols=53 Identities=13% Similarity=0.186 Sum_probs=34.9
Q ss_pred EEEEEEEeeecceeE-EEcCCceeeeeEcccccccc----cccccccCCEEEE--EEEEe
Q 005716 278 CEGKVTTVHLYQGAF-VDIGGVYDGWVPIKGNDWYW----IRHHIKVGMHVIV--EILAK 330 (681)
Q Consensus 278 VEGkVtnItdF~GAF-VDIGGv~DGLVHISEISW~r----I~dVLKVGDeVkV--KVLsI 330 (681)
+.|+|+.|.+-.-|| +-...+.+-||||.=-++.- ..-+++.||+|+. .++.+
T Consensus 42 ~~G~v~~i~~T~HA~~i~~~~G~eiLiHiGidTv~l~g~gF~~~vk~Gd~V~~G~~l~~~ 101 (124)
T cd00210 42 VDGTIVQIFPTKHAIGIESDSGVEILIHIGIDTVKLNGEGFTSHVEEGQRVKQGDKLLEF 101 (124)
T ss_pred CCeEEEEEccCCCEEEEEeCCCcEEEEEeeeeeeecCCCceEEEecCCCEEcCCCEEEEE
Confidence 579999996632355 44443459999998666642 2337788888865 46666
No 262
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-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). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=20.65 E-value=2.8e+02 Score=20.35 Aligned_cols=62 Identities=15% Similarity=0.134 Sum_probs=36.3
Q ss_pred EEEEEEEeeecc----eeEEEcCCceeeeeEcccccccc----cccccccCCEEEEEEEEeeCCCCCeeeeeee
Q 005716 278 CEGKVTTVHLYQ----GAFVDIGGVYDGWVPIKGNDWYW----IRHHIKVGMHVIVEILAKRDPYRFRFPIEMR 343 (681)
Q Consensus 278 VEGkVtnItdF~----GAFVDIGGv~DGLVHISEISW~r----I~dVLKVGDeVkVKVLsIdD~eR~RISLSLK 343 (681)
+.|+|.++.... -+++-|-...+|-+.+ +-|.. ....+++|+.|.|. ..+ +..+.+..|.+.
T Consensus 2 v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~--~~~~~~~~~~~~~~~~g~~v~v~-g~v-~~~~~~~~l~~~ 71 (75)
T cd03524 2 IVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRV--TLFGELAEELENLLKEGQVVYIK-GKV-KKFRGRLQLIVE 71 (75)
T ss_pred eEEEEEeecccccCCeEEEEEEEcCCCCEEEE--EEEchHHHHHHhhccCCCEEEEE-EEE-EecCCeEEEEee
Confidence 568888887542 1555554321144443 34432 34589999999988 666 334455555554
No 263
>COG2421 Predicted acetamidase/formamidase [Energy production and conversion]
Probab=20.48 E-value=1.7e+02 Score=31.85 Aligned_cols=65 Identities=14% Similarity=0.044 Sum_probs=48.6
Q ss_pred chhhhcccCCCCCCCCEEEEEEEEeeecceeEEEcCCceeeeeEcccccccccc--------cccccCCEEEEEEEEee
Q 005716 261 DYEEGMYELPFYYPGQICEGKVTTVHLYQGAFVDIGGVYDGWVPIKGNDWYWIR--------HHIKVGMHVIVEILAKR 331 (681)
Q Consensus 261 ~f~egv~~L~~LkeGqIVEGkVtnItdF~GAFVDIGGv~DGLVHISEISW~rI~--------dVLKVGDeVkVKVLsId 331 (681)
.|...+.-...+++|++|.=.+......|+ -...++-|+..++|.+|+ +.-+.||.++|+|++|.
T Consensus 12 ~~~~~~~pv~~v~~Gd~V~iet~d~~~gq~------~~~~~~~~~~~iD~~rv~p~TGPi~v~gA~pGD~L~V~i~~i~ 84 (305)
T COG2421 12 RFDPSLPPVETVKPGDTVTIETLDALGGQI------KAEETLEDIFKIDFSRVHPLTGPIYVEGAEPGDALEVEIEDIK 84 (305)
T ss_pred ccCCCCCcceecCCCCEEEEEEEeccCccc------cccchhhhhcccCcccccCCCCCeEEeccCCCceEEEEEEeec
Confidence 466677778889999998755544433322 233578889999999876 37789999999999993
Done!