Query 013634
Match_columns 439
No_of_seqs 217 out of 1631
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 05:51:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013634.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013634hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00358 3_prime_RNase VacB a 100.0 6.1E-99 1E-103 804.9 50.3 422 3-439 222-654 (654)
2 PRK11642 exoribonuclease R; Pr 100.0 1E-97 2E-102 804.2 49.2 422 3-439 288-725 (813)
3 TIGR02063 RNase_R ribonuclease 100.0 3.5E-97 8E-102 800.9 51.7 422 3-439 274-709 (709)
4 PRK05054 exoribonuclease II; P 100.0 7.3E-95 1.6E-99 769.8 48.1 414 3-439 218-644 (644)
5 TIGR02062 RNase_B exoribonucle 100.0 1.3E-93 2.8E-98 758.7 50.4 412 3-437 214-638 (639)
6 COG0557 VacB Exoribonuclease R 100.0 9.2E-93 2E-97 764.0 48.4 422 3-439 276-704 (706)
7 KOG2102 Exosomal 3'-5' exoribo 100.0 1.3E-80 2.9E-85 675.5 35.0 423 3-438 501-925 (941)
8 PF00773 RNB: RNB domain CAUTI 100.0 1.4E-72 3E-77 559.9 26.1 290 2-305 28-324 (325)
9 COG4776 Rnb Exoribonuclease II 100.0 1.5E-70 3.3E-75 530.4 26.9 407 3-434 218-639 (645)
10 cd04471 S1_RNase_R S1_RNase_R: 99.3 6.1E-11 1.3E-15 93.5 11.3 81 354-439 3-83 (83)
11 cd05686 S1_pNO40 S1_pNO40: pNO 98.8 2.2E-08 4.8E-13 77.0 9.1 69 354-439 5-73 (73)
12 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.8 2.6E-08 5.7E-13 75.6 7.1 68 354-438 2-69 (69)
13 cd04460 S1_RpoE S1_RpoE: RpoE, 98.7 6.4E-08 1.4E-12 79.0 9.4 80 354-438 1-83 (99)
14 cd05690 S1_RPS1_repeat_ec5 S1_ 98.7 4.3E-08 9.2E-13 74.3 6.9 68 354-437 2-69 (69)
15 cd05689 S1_RPS1_repeat_ec4 S1_ 98.6 1.4E-07 3.1E-12 72.1 7.6 68 354-437 5-72 (72)
16 cd05706 S1_Rrp5_repeat_sc10 S1 98.6 2.5E-07 5.3E-12 71.0 8.7 68 354-438 5-72 (73)
17 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.6 1.6E-07 3.4E-12 71.9 7.3 67 355-438 3-71 (71)
18 cd05703 S1_Rrp5_repeat_hs12_sc 98.6 1.8E-07 4E-12 71.9 7.2 69 355-438 3-71 (73)
19 cd05707 S1_Rrp5_repeat_sc11 S1 98.6 1.5E-07 3.3E-12 71.2 6.5 67 354-437 2-68 (68)
20 cd05705 S1_Rrp5_repeat_hs14 S1 98.6 1.7E-07 3.8E-12 72.2 6.5 70 354-437 5-74 (74)
21 cd05698 S1_Rrp5_repeat_hs6_sc5 98.5 3.2E-07 6.8E-12 69.8 7.2 68 354-438 2-69 (70)
22 cd05708 S1_Rrp5_repeat_sc12 S1 98.5 5.1E-07 1.1E-11 69.7 8.5 69 354-438 4-72 (77)
23 PF00575 S1: S1 RNA binding do 98.5 5.4E-07 1.2E-11 69.2 8.3 68 354-438 6-73 (74)
24 cd05684 S1_DHX8_helicase S1_DH 98.5 6.9E-07 1.5E-11 69.7 8.8 68 354-438 2-71 (79)
25 cd04461 S1_Rrp5_repeat_hs8_sc7 98.5 3.4E-07 7.4E-12 72.2 7.0 68 354-438 16-83 (83)
26 COG1098 VacB Predicted RNA bin 98.5 1E-07 2.2E-12 78.5 4.1 67 354-438 7-73 (129)
27 PRK08582 hypothetical protein; 98.5 6.7E-07 1.5E-11 77.5 9.1 67 354-438 7-73 (139)
28 PRK07252 hypothetical protein; 98.5 6E-07 1.3E-11 75.7 8.4 68 354-438 5-72 (120)
29 PTZ00248 eukaryotic translatio 98.5 2.8E-07 6.1E-12 89.7 7.0 77 346-438 7-88 (319)
30 cd04452 S1_IF2_alpha S1_IF2_al 98.5 9.6E-07 2.1E-11 68.2 8.5 69 354-438 5-74 (76)
31 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.4 9E-07 1.9E-11 66.6 7.3 64 355-437 3-66 (66)
32 cd05685 S1_Tex S1_Tex: The C-t 98.4 6.3E-07 1.4E-11 67.3 6.0 67 354-437 2-68 (68)
33 PHA02945 interferon resistance 98.4 3.3E-06 7.1E-11 65.6 8.8 66 354-438 13-81 (88)
34 TIGR00448 rpoE DNA-directed RN 98.3 2.9E-06 6.3E-11 77.0 10.0 86 348-438 76-165 (179)
35 cd05704 S1_Rrp5_repeat_hs13 S1 98.3 1.4E-06 3E-11 66.8 6.3 66 354-438 5-71 (72)
36 cd05691 S1_RPS1_repeat_ec6 S1_ 98.3 3.3E-06 7.1E-11 64.5 7.7 68 354-438 2-69 (73)
37 cd04472 S1_PNPase S1_PNPase: P 98.2 5.3E-06 1.1E-10 62.3 7.6 67 354-438 2-68 (68)
38 cd05692 S1_RPS1_repeat_hs4 S1_ 98.2 5.2E-06 1.1E-10 62.3 7.4 67 354-438 2-68 (69)
39 cd05688 S1_RPS1_repeat_ec3 S1_ 98.2 5.7E-06 1.2E-10 62.1 7.3 66 354-437 3-68 (68)
40 PRK05807 hypothetical protein; 98.2 7.8E-06 1.7E-10 70.6 8.9 66 354-438 7-72 (136)
41 PRK08059 general stress protei 98.2 5.9E-06 1.3E-10 70.2 7.7 68 354-438 9-76 (123)
42 cd04473 S1_RecJ_like S1_RecJ_l 98.1 1.5E-05 3.3E-10 61.8 8.6 60 354-439 18-77 (77)
43 cd05694 S1_Rrp5_repeat_hs2_sc2 98.1 1.4E-05 3.1E-10 61.5 8.4 63 354-438 6-68 (74)
44 COG0539 RpsA Ribosomal protein 98.1 4.3E-06 9.4E-11 86.7 7.1 68 354-438 279-346 (541)
45 PRK03987 translation initiatio 98.1 7.5E-06 1.6E-10 78.4 8.1 69 354-438 10-79 (262)
46 PLN00207 polyribonucleotide nu 98.1 1.1E-05 2.4E-10 88.2 9.9 75 346-438 746-822 (891)
47 COG1095 RPB7 DNA-directed RNA 98.1 1.9E-05 4.2E-10 70.2 9.0 71 354-429 83-153 (183)
48 cd05687 S1_RPS1_repeat_ec1_hs1 98.1 1.8E-05 3.9E-10 60.0 7.4 68 354-438 2-69 (70)
49 COG0539 RpsA Ribosomal protein 98.1 1.8E-05 3.8E-10 82.2 9.5 67 354-438 194-260 (541)
50 smart00316 S1 Ribosomal protei 98.0 2.2E-05 4.8E-10 59.0 7.7 68 354-438 4-71 (72)
51 PRK08563 DNA-directed RNA poly 98.0 5.6E-05 1.2E-09 69.1 11.3 80 354-438 83-165 (187)
52 cd00164 S1_like S1_like: Ribos 98.0 2.4E-05 5.2E-10 57.6 6.6 64 357-437 2-65 (65)
53 PRK07899 rpsA 30S ribosomal pr 98.0 2.8E-05 6.1E-10 80.8 9.3 68 354-438 295-362 (486)
54 cd04465 S1_RPS1_repeat_ec2_hs2 97.9 6.2E-05 1.3E-09 56.6 7.5 65 354-438 2-66 (67)
55 cd05693 S1_Rrp5_repeat_hs1_sc1 97.8 2.7E-05 5.8E-10 63.6 4.9 84 354-438 5-94 (100)
56 COG1093 SUI2 Translation initi 97.8 1.5E-05 3.2E-10 74.4 3.2 69 354-438 13-82 (269)
57 PRK12269 bifunctional cytidyla 97.7 8.4E-05 1.8E-09 82.2 8.9 71 354-438 754-824 (863)
58 PRK07899 rpsA 30S ribosomal pr 97.7 0.00016 3.5E-09 75.3 10.2 67 354-438 210-276 (486)
59 PRK07400 30S ribosomal protein 97.7 9.8E-05 2.1E-09 73.0 8.2 67 354-438 198-264 (318)
60 PRK13806 rpsA 30S ribosomal pr 97.7 7.9E-05 1.7E-09 78.2 7.4 69 354-438 294-362 (491)
61 PRK13806 rpsA 30S ribosomal pr 97.7 8.7E-05 1.9E-09 77.9 7.5 68 354-438 381-448 (491)
62 cd05702 S1_Rrp5_repeat_hs11_sc 97.7 0.00014 3.1E-09 55.1 6.6 61 355-428 3-63 (70)
63 PRK11824 polynucleotide phosph 97.7 0.00032 7E-09 76.5 11.7 67 354-438 623-689 (693)
64 TIGR02696 pppGpp_PNP guanosine 97.7 9.5E-05 2.1E-09 79.4 7.3 70 354-437 649-718 (719)
65 PRK12269 bifunctional cytidyla 97.6 0.00011 2.3E-09 81.4 7.5 69 354-438 667-735 (863)
66 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 97.6 0.00014 3.1E-09 57.4 6.2 71 354-438 8-78 (86)
67 cd04453 S1_RNase_E S1_RNase_E: 97.5 0.00038 8.2E-09 55.4 7.5 63 354-428 9-73 (88)
68 PRK06299 rpsA 30S ribosomal pr 97.5 0.00019 4.1E-09 76.9 7.3 69 354-438 375-443 (565)
69 PRK06676 rpsA 30S ribosomal pr 97.4 0.0004 8.8E-09 70.9 8.1 68 354-438 279-346 (390)
70 TIGR00717 rpsA ribosomal prote 97.4 0.00041 8.8E-09 73.5 8.3 68 354-438 448-515 (516)
71 cd04455 S1_NusA S1_NusA: N-uti 97.4 0.00073 1.6E-08 50.8 7.3 62 354-437 5-66 (67)
72 PRK00087 4-hydroxy-3-methylbut 97.3 0.00054 1.2E-08 74.4 8.1 68 354-438 564-631 (647)
73 PTZ00162 DNA-directed RNA poly 97.3 0.0014 3.1E-08 59.1 9.4 72 354-429 83-154 (176)
74 TIGR00717 rpsA ribosomal prote 97.3 0.00045 9.8E-09 73.2 7.2 69 354-438 361-429 (516)
75 TIGR03591 polynuc_phos polyrib 97.3 0.00088 1.9E-08 73.0 9.5 65 354-436 620-684 (684)
76 PRK07400 30S ribosomal protein 97.3 0.0016 3.4E-08 64.6 9.8 64 353-438 119-182 (318)
77 PRK06676 rpsA 30S ribosomal pr 97.2 0.0017 3.6E-08 66.4 9.4 67 354-438 194-260 (390)
78 PRK06299 rpsA 30S ribosomal pr 97.2 0.00075 1.6E-08 72.3 6.9 69 354-438 288-356 (565)
79 cd04462 S1_RNAPII_Rpb7 S1_RNAP 97.1 0.0037 8E-08 49.7 8.9 68 354-428 3-72 (88)
80 cd04454 S1_Rrp4_like S1_Rrp4_l 97.1 0.0016 3.5E-08 50.9 6.5 67 354-438 8-74 (82)
81 COG1185 Pnp Polyribonucleotide 96.9 0.0022 4.9E-08 67.7 7.0 67 354-438 621-687 (692)
82 COG2183 Tex Transcriptional ac 96.8 0.0019 4E-08 69.4 5.6 68 354-438 660-727 (780)
83 PRK09202 nusA transcription el 96.7 0.016 3.6E-07 60.1 12.0 71 345-437 126-197 (470)
84 PRK00087 4-hydroxy-3-methylbut 96.5 0.0055 1.2E-07 66.6 7.3 67 354-438 479-545 (647)
85 PRK12327 nusA transcription el 96.4 0.035 7.7E-07 55.7 11.5 68 348-437 130-197 (362)
86 PHA02858 EIF2a-like PKR inhibi 96.2 0.0079 1.7E-07 46.5 4.3 64 359-439 22-86 (86)
87 TIGR01953 NusA transcription t 96.0 0.072 1.6E-06 53.2 11.5 69 347-437 126-195 (341)
88 PRK09521 exosome complex RNA-b 96.0 0.016 3.6E-07 52.9 6.4 66 354-438 66-140 (189)
89 PRK04163 exosome complex RNA-b 95.7 0.035 7.5E-07 52.6 7.3 71 354-438 65-135 (235)
90 cd05699 S1_Rrp5_repeat_hs7 S1_ 95.3 0.039 8.4E-07 41.9 5.0 67 355-437 3-70 (72)
91 KOG1067 Predicted RNA-binding 94.8 0.074 1.6E-06 55.1 6.9 60 354-428 670-729 (760)
92 TIGR00008 infA translation ini 93.5 0.53 1.2E-05 35.3 7.4 62 354-436 5-67 (68)
93 KOG3298 DNA-directed RNA polym 93.4 0.43 9.3E-06 41.7 7.8 70 354-428 83-152 (170)
94 KOG1070 rRNA processing protei 93.1 0.081 1.8E-06 60.1 3.7 68 354-438 601-668 (1710)
95 PRK12329 nusA transcription el 92.4 1.5 3.2E-05 45.0 11.3 70 348-437 148-222 (449)
96 PRK12442 translation initiatio 92.2 1.2 2.6E-05 34.9 8.1 63 354-437 7-70 (87)
97 cd05791 S1_CSL4 S1_CSL4: CSL4, 91.2 1 2.2E-05 36.0 7.1 69 354-438 8-84 (92)
98 PF08292 RNA_pol_Rbc25: RNA po 91.1 2.8 6E-05 35.4 9.9 71 354-427 5-76 (122)
99 PRK12328 nusA transcription el 91.0 2.7 5.9E-05 42.3 11.3 70 346-437 132-203 (374)
100 COG2996 Predicted RNA-bindinin 90.8 0.8 1.7E-05 43.6 6.9 59 354-438 157-215 (287)
101 KOG1070 rRNA processing protei 90.6 0.77 1.7E-05 52.6 7.7 68 354-438 1164-1231(1710)
102 COG1107 Archaea-specific RecJ- 88.3 0.36 7.9E-06 50.4 2.9 62 354-438 124-185 (715)
103 COG0361 InfA Translation initi 87.6 4.6 0.0001 30.9 7.8 62 354-436 7-69 (75)
104 TIGR00757 RNaseEG ribonuclease 84.5 2.7 5.8E-05 43.3 6.9 68 354-424 27-96 (414)
105 cd05790 S1_Rrp40 S1_Rrp40: Rrp 81.1 6.7 0.00015 30.9 6.4 59 354-428 8-66 (86)
106 PF13509 S1_2: S1 domain; PDB: 80.5 11 0.00023 27.5 7.0 48 356-426 5-52 (61)
107 COG1097 RRP4 RNA-binding prote 72.7 11 0.00024 35.4 6.4 64 354-428 66-129 (239)
108 PF10447 EXOSC1: Exosome compo 69.5 8.8 0.00019 30.0 4.3 59 354-424 6-81 (82)
109 PRK15464 cold shock-like prote 69.4 13 0.00029 28.0 5.2 53 356-426 5-59 (70)
110 KOG2916 Translation initiation 68.4 1.8 4E-05 40.9 0.3 76 346-437 6-86 (304)
111 PRK15463 cold shock-like prote 62.1 23 0.00049 26.7 5.2 53 356-426 5-59 (70)
112 PRK00276 infA translation init 60.1 64 0.0014 24.3 7.4 61 354-435 7-68 (72)
113 PRK10811 rne ribonuclease E; R 55.5 23 0.00049 40.1 5.8 67 354-426 40-108 (1068)
114 KOG1856 Transcription elongati 54.2 16 0.00035 41.6 4.5 59 355-428 988-1049(1299)
115 PRK09937 stationary phase/star 53.3 56 0.0012 24.9 6.1 52 357-426 3-56 (74)
116 PRK04012 translation initiatio 53.2 90 0.0019 25.4 7.6 62 354-437 21-83 (100)
117 cd05793 S1_IF1A S1_IF1A: Trans 52.6 83 0.0018 24.2 7.0 59 356-436 2-61 (77)
118 PF00313 CSD: 'Cold-shock' DNA 52.3 59 0.0013 23.7 6.0 51 356-424 1-53 (66)
119 PF02599 CsrA: Global regulato 51.8 39 0.00085 24.1 4.7 29 405-437 5-33 (54)
120 cd04456 S1_IF1A_like S1_IF1A_l 51.0 87 0.0019 24.1 6.8 49 357-425 3-52 (78)
121 PF03544 TonB_C: Gram-negative 50.1 28 0.00061 26.1 4.1 22 67-88 17-38 (79)
122 PRK09507 cspE cold shock prote 49.9 72 0.0016 23.9 6.1 54 355-426 3-58 (69)
123 cd04508 TUDOR Tudor domains ar 49.9 33 0.00071 23.1 4.0 33 354-386 13-46 (48)
124 COG4871 Uncharacterized protei 49.8 43 0.00094 29.5 5.4 51 134-185 63-113 (193)
125 PF13103 TonB_2: TonB C termin 48.8 27 0.00057 26.8 3.8 25 63-87 23-47 (85)
126 CHL00010 infA translation init 47.4 1.2E+02 0.0027 23.2 7.3 61 354-435 7-68 (78)
127 PRK01712 carbon storage regula 47.3 51 0.0011 24.5 4.7 28 406-437 6-33 (64)
128 COG1096 Predicted RNA-binding 45.4 65 0.0014 29.2 6.1 56 354-425 66-132 (188)
129 TIGR01352 tonB_Cterm TonB fami 44.6 40 0.00087 24.8 4.2 21 67-87 11-31 (74)
130 PRK00568 carbon storage regula 43.7 58 0.0013 25.0 4.7 28 406-437 6-33 (76)
131 cd05701 S1_Rrp5_repeat_hs10 S1 43.1 61 0.0013 24.0 4.5 59 355-427 3-61 (69)
132 PRK14998 cold shock-like prote 42.4 75 0.0016 24.1 5.3 52 357-426 3-56 (73)
133 COG1551 CsrA RNA-binding globa 41.9 61 0.0013 24.5 4.5 22 406-427 6-27 (73)
134 PRK10943 cold shock-like prote 41.8 90 0.002 23.3 5.6 53 355-425 3-57 (69)
135 PRK11712 ribonuclease G; Provi 41.2 67 0.0015 33.9 6.5 69 354-425 40-110 (489)
136 smart00333 TUDOR Tudor domain. 40.3 57 0.0012 22.8 4.2 34 354-387 17-51 (57)
137 TIGR02381 cspD cold shock doma 37.1 93 0.002 23.1 5.0 52 357-426 3-56 (68)
138 TIGR00202 csrA carbon storage 34.8 1E+02 0.0022 23.2 4.7 22 406-427 6-27 (69)
139 PTZ00329 eukaryotic translatio 34.2 1.5E+02 0.0033 26.1 6.5 62 354-437 32-94 (155)
140 smart00652 eIF1a eukaryotic tr 34.1 2.3E+02 0.0049 22.1 7.4 61 354-436 5-66 (83)
141 PRK10354 RNA chaperone/anti-te 33.4 2E+02 0.0043 21.5 6.3 53 356-426 5-59 (70)
142 PRK06763 F0F1 ATP synthase sub 33.3 1.3E+02 0.0029 27.5 6.1 33 351-383 37-69 (213)
143 PRK09890 cold shock protein Cs 32.2 2.2E+02 0.0047 21.3 6.5 53 356-426 5-59 (70)
144 cd04458 CSP_CDS Cold-Shock Pro 31.4 1.5E+02 0.0033 21.3 5.4 51 357-425 2-54 (65)
145 PF08605 Rad9_Rad53_bind: Fung 27.1 1.3E+02 0.0027 25.8 4.7 21 354-374 23-45 (131)
146 PF01176 eIF-1a: Translation i 26.0 1.1E+02 0.0025 22.4 3.8 52 355-426 4-56 (65)
147 PLN00208 translation initiatio 26.0 2.6E+02 0.0056 24.4 6.4 61 354-436 32-93 (145)
148 PF04225 OapA: Opacity-associa 22.5 57 0.0012 25.5 1.7 64 18-89 4-68 (85)
149 COG5428 Uncharacterized conser 22.2 1.1E+02 0.0024 22.9 3.0 21 69-89 31-51 (69)
150 KOG3297 DNA-directed RNA polym 22.1 5.4E+02 0.012 23.4 7.8 71 354-427 83-158 (202)
151 smart00743 Agenet Tudor-like d 22.0 1.9E+02 0.0041 20.5 4.4 33 354-386 18-53 (61)
152 PF03459 TOBE: TOBE domain; I 21.9 1.7E+02 0.0036 20.9 4.1 14 354-367 5-18 (64)
153 PF02575 YbaB_DNA_bd: YbaB/Ebf 20.4 74 0.0016 25.0 2.0 33 70-105 32-64 (93)
154 PF07076 DUF1344: Protein of u 20.1 3.6E+02 0.0077 19.8 5.2 49 355-426 4-52 (61)
No 1
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=100.00 E-value=6.1e-99 Score=804.92 Aligned_cols=422 Identities=27% Similarity=0.434 Sum_probs=387.4
Q ss_pred ccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCceeE
Q 013634 3 LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS 82 (439)
Q Consensus 3 ~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~~ 82 (439)
+++|+|+|||||||||+||++||+||+||++||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|.+
T Consensus 222 ~~~g~~~l~VHIADVs~~V~~~s~LD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~R~a~s~~~~id~~G~i~~ 301 (654)
T TIGR00358 222 LPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLNPNEDRLVLVCEMTISAQGRITD 301 (654)
T ss_pred eCCCcEEEEEEEechhheeCCCCHHHHHHHHhCcCccCCCCeecCCCHHHhcCccccCCCCcceEEEEEEEECCCCCEeE
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeEEecCceecHHHHHHHhcCCCC----CCchHHHHHHHHHHHHHHHHHHHhCCceeecCcceEEEecCCCCCeee
Q 013634 83 TRYTKSVIKSCAALSYVEAQARMDDSRL----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLD 158 (439)
Q Consensus 83 ~~~~~s~I~s~~~ltY~~v~~~l~~~~~----~~~~~~~l~~L~~~a~~l~~~R~~~Gal~~~~~~~~~~~d~~~~~~~~ 158 (439)
++|++|+|+|+++|||++|+++|++++. ..++.++|..|+++|++|+++|.++|++.|+.|+.+|.+|++ |.+..
T Consensus 302 ~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~lr~~R~~~Gai~~~~~e~~~~~d~~-g~~~~ 380 (654)
T TIGR00358 302 NEFYPATIESKARLTYDKVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRGLIDFEHPETKFIVDEE-GRVID 380 (654)
T ss_pred EEEEEEEEEECcEEcHHHHHHHHcCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHCCCcccCCCceeEEECCC-CCeeE
Confidence 9999999999999999999999987632 245778999999999999999999999999999999999865 78888
Q ss_pred eEeeccchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHcCCcccCC-----CHHHHHHHH
Q 013634 159 IGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS-----SSKALADSL 233 (439)
Q Consensus 159 v~~~~~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~g~~~~~~-----~~~~l~~~l 233 (439)
+.....++||.|||||||+||++||+|+.++ ++|++||+|++|++++++++.+++..+|+.++.. ++.+++..|
T Consensus 381 i~~~~~~~a~~lIeE~MilAN~~vA~~~~~~-~~p~iyR~h~~p~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l 459 (654)
T TIGR00358 381 IVAEVRRIAEKIIEEAMIVANICAARFLHNH-KVPGIYRVHPGPSKKKLQSLLEFLAELGLTLPGGNAENVTTLDGACWL 459 (654)
T ss_pred EEeccCcHHHHHHHHHHHHHHHHHHHHHHHc-CCCeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCcCCCChHHHHHHH
Confidence 8888899999999999999999999999997 8999999999999999999999999999986432 356788888
Q ss_pred HHHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHHHhCCCCCC-CC
Q 013634 234 DRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLP-SV 312 (439)
Q Consensus 234 ~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~~l~~~~~~-~~ 312 (439)
.++.+ .+ ...+++.+++|+|++|+| +..|.+|||||++.|||||||||||+||+|||||+++|.+++.. ..
T Consensus 460 ~~~~~-~~-~~~~l~~~llr~m~~A~y------~~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~a~l~~~~~~~~~ 531 (654)
T TIGR00358 460 REVKD-RP-EYEILVTRLLRSLSQAEY------SPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTER 531 (654)
T ss_pred HHhhC-CC-HHHHHHHHHHHhhccccc------CCCCCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCcccc
Confidence 87754 23 234778889999999999 67899999999999999999999999999999999999876432 22
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCC
Q 013634 313 FQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGS 391 (439)
Q Consensus 313 ~~~~~~l~~~~~~~n~~~~~a~~~~r~~~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~ 391 (439)
.++.++|..+|++||.+++.+++|||++.++|.|.||+++. ++|+|+|+++.++|+||+|+++|+||+||++++.++
T Consensus 532 ~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d-- 609 (654)
T TIGR00358 532 YQPQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHND-- 609 (654)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCc--
Confidence 24567899999999999999999999999999999999987 889999999999999999999999999999999987
Q ss_pred CceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCceeEEeC
Q 013634 392 GDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 439 (439)
Q Consensus 392 ~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~l~ 439 (439)
+|.+|+.+.++++++.++.|++||+|+|+|.+||.. +++|+|+|+
T Consensus 610 -~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~--~~~I~f~l~ 654 (654)
T TIGR00358 610 -YYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNME--TRSIIFELV 654 (654)
T ss_pred -ceEEeccccEEEeccCCcEECCCCEEEEEEEEEecc--cCeEEEEEC
Confidence 699999999999888889999999999999999976 899999974
No 2
>PRK11642 exoribonuclease R; Provisional
Probab=100.00 E-value=1e-97 Score=804.19 Aligned_cols=422 Identities=27% Similarity=0.439 Sum_probs=386.0
Q ss_pred ccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCceeE
Q 013634 3 LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS 82 (439)
Q Consensus 3 ~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~~ 82 (439)
+++|+|+|||||||||+||++||+||.||++||||+|||++++||||+.||+++|||+||++|+||||.++||.+|+|.+
T Consensus 288 ~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYlpd~viPMLP~~Lsn~lcSL~p~~dRla~s~~~~id~~G~v~~ 367 (813)
T PRK11642 288 KRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTISSKGRLTG 367 (813)
T ss_pred eCCCcEEEEEEecchhheeCCCCHHHHHHHHhCCeEeCCCceeeCCCHHHhcCccccCCCCceeEEEEEEEECCCCCCcC
Confidence 46788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeEEecCceecHHHHHHHhcCCCC----CCchHHHHHHHHHHHHHHHHHHHhCCceeecCcceEEEecCCCCCeee
Q 013634 83 TRYTKSVIKSCAALSYVEAQARMDDSRL----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLD 158 (439)
Q Consensus 83 ~~~~~s~I~s~~~ltY~~v~~~l~~~~~----~~~~~~~l~~L~~~a~~l~~~R~~~Gal~~~~~~~~~~~d~~~~~~~~ 158 (439)
++|++|+|+|+++|||++|+++|+++.. ..++.+.|..|+++|+.|+++|.++|+|+|+.||.+|.+|++ |.+..
T Consensus 368 ~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~Lr~~R~~~Gai~~d~~E~~i~ld~~-g~~~~ 446 (813)
T PRK11642 368 YKFYEAVMSSHARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKAREERGGISFESEEAKFIFNAE-RRIER 446 (813)
T ss_pred CEEEEEEEEECceECHHHHHHHHcCCcccchhhhHHHHHHHHHHHHHHHHHHHHHHCCCcccCCCceEEEECCC-CCEee
Confidence 9999999999999999999999987532 235678999999999999999999999999999999999976 67888
Q ss_pred eEeeccchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHcCCcccCC---CHHHHHHHHHH
Q 013634 159 IGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVS---SSKALADSLDR 235 (439)
Q Consensus 159 v~~~~~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~g~~~~~~---~~~~l~~~l~~ 235 (439)
+......+||.|||||||+||++||+|+.++ ++|++||+|+.|+++++++|.+++..+|+.++.. ++..++.+++.
T Consensus 447 i~~~~~~~a~~lIEE~MllAN~~vA~~l~~~-~~p~lyR~H~~P~~ekl~~l~~~l~~lG~~l~~~~~~~~~~~~~ll~~ 525 (813)
T PRK11642 447 IEQTQRNDAHKLIEECMILANISAARFVEKA-KEPALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLES 525 (813)
T ss_pred EEecccccHHHHHHHHHHHHHHHHHHHHHHC-CCCEEEEeCCCCCHHHHHHHHHHHHHcCCcccCCCCCCHHHHHHHHHH
Confidence 8888899999999999999999999999986 8999999999999999999999999999988542 45678888887
Q ss_pred HhCCChhHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHHHhCCCCCC-----
Q 013634 236 AVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLP----- 310 (439)
Q Consensus 236 ~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~~l~~~~~~----- 310 (439)
+.+ .|. ..+++.+++|+|++|.| +++|.+|||||++.|||||||||||+||+|||+|+++|.++.-.
T Consensus 526 ~~~-~~~-~~~l~~~llRsm~~A~Y------~~~~~gHfGLa~~~YtHFTSPIRRY~DLivHR~Lk~~L~~~~~~~~~~~ 597 (813)
T PRK11642 526 VAD-RPD-AEMLQTMLLRSMKQAIY------DPENRGHFGLALQSYAHFTSPIRRYPDLSLHRAIKYLLAKEQGHKGNTT 597 (813)
T ss_pred HhC-CcH-HHHHHHHHHHhcccccc------CCCCCCccccccccccccCchhhhhHHHHHHHHHHHHHhCCCCcccccc
Confidence 754 343 35788899999999999 67899999999999999999999999999999999999764321
Q ss_pred ---CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccC
Q 013634 311 ---SVFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPR 386 (439)
Q Consensus 311 ---~~~~~~~~l~~~~~~~n~~~~~a~~~~r~~~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l 386 (439)
.+....+.+..+|++||.+++.|.+|+|++.+++.|+||+++. +.|+|+|++|.++|+||+|++.++||+||++++
T Consensus 598 ~~~~~~~~~~~l~~~~~~~s~~er~A~~aeR~~~~~~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L 677 (813)
T PRK11642 598 ETGGYHYSMEEMLQLGQHCSMTERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSL 677 (813)
T ss_pred cccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeec
Confidence 1112235689999999999999999999999999999999877 889999999999999999999899999999999
Q ss_pred CCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCceeEEeC
Q 013634 387 GQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 439 (439)
Q Consensus 387 ~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~l~ 439 (439)
.++ ||.+++.+.+++|++.++.|++||+|+|+|..+|.. +++|.|+++
T Consensus 678 ~~d---~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~--~rkI~f~l~ 725 (813)
T PRK11642 678 DND---YYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMD--ERKIDFSLI 725 (813)
T ss_pred CCc---ceEecchheEEecccCCcEECCCCEEEEEEEEeecC--CCeEEEEEe
Confidence 987 799999999999988899999999999999999976 899999974
No 3
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=100.00 E-value=3.5e-97 Score=800.91 Aligned_cols=422 Identities=32% Similarity=0.479 Sum_probs=387.5
Q ss_pred ccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCceeE
Q 013634 3 LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS 82 (439)
Q Consensus 3 ~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~~ 82 (439)
.++|+|+|||||||||+||++||+||+||++||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|++
T Consensus 274 ~~~g~~~l~VhIADVs~~V~~~s~lD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~p~~~r~a~s~~~~id~~G~i~~ 353 (709)
T TIGR02063 274 LKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPERLSNGICSLNPNEDRLTLSCEMEIDKKGRVKK 353 (709)
T ss_pred cCCCCEEEEEEEechhhEeCCCChHHHHHHHhCeeEeCCCCcccCCChHHccCccccCCCCceEEEEEEEEECCCCCEEE
Confidence 45788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeEEecCceecHHHHHHHhcCCCC----CCchHHHHHHHHHHHHHHHHHHHhCCceeecCcceEEEecCCCCCeee
Q 013634 83 TRYTKSVIKSCAALSYVEAQARMDDSRL----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLD 158 (439)
Q Consensus 83 ~~~~~s~I~s~~~ltY~~v~~~l~~~~~----~~~~~~~l~~L~~~a~~l~~~R~~~Gal~~~~~~~~~~~d~~~~~~~~ 158 (439)
++|++|+|+|+++|||++|+++|++++. ..++.++|..|+++|++|+++|.++|+++|+.|+.+|.+|++ |.+..
T Consensus 354 ~~~~~svI~s~~~ltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~l~~~R~~~G~i~~~~~e~~~~~d~~-g~~~~ 432 (709)
T TIGR02063 354 YEFYEAVINSHARLTYNQVNDIIEGKDALDKKEPPLKEMLKNLFELYKILRKKRKKRGAIDFDSKEAKIILDEN-GKPID 432 (709)
T ss_pred eEEEEEEEEeCeEEcHHHHHHHHcCCccccchhhHHHHHHHHHHHHHHHHHHHHHhCCCcccCCccceeEECCC-CCeEE
Confidence 9999999999999999999999987642 245778999999999999999999999999999999999976 78888
Q ss_pred eEeeccchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHcCCcccC-----CCHHHHHHHH
Q 013634 159 IGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDV-----SSSKALADSL 233 (439)
Q Consensus 159 v~~~~~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~g~~~~~-----~~~~~l~~~l 233 (439)
+...++++||.|||||||+||++||+|+.++ ++|++||+|++|+++++++|.+++..+|++++. .++.+++.+|
T Consensus 433 i~~~~~~~a~~lIeE~MllAN~~vA~~l~~~-~~p~iyR~h~~P~~~~~~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~l 511 (709)
T TIGR02063 433 IVPRERGDAHKLIEEFMIAANETVAEHLEKA-KLPFIYRVHERPSEEKLQNLREFLKTLGITLKGGTSDKPQPKDFQKLL 511 (709)
T ss_pred EEeccchHHHHHHHHHHHHHHHHHHHHHHhC-CCCeEEecCCCCCHHHHHHHHHHHHHcCCCccCCCCCCCCHHHHHHHH
Confidence 8888899999999999999999999999876 899999999999999999999999999998753 2567888888
Q ss_pred HHHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHHHhCCCCC-C-C
Q 013634 234 DRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKL-P-S 311 (439)
Q Consensus 234 ~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~~l~~~~~-~-~ 311 (439)
..+.+ .|. ..+++.+++|+|++|.| +..|.+|||||++.|||||||||||+||+|||||+++|.+++. + .
T Consensus 512 ~~~~~-~~~-~~~l~~~llr~m~~A~y------~~~~~~HfgL~~~~YthfTSPIRRY~DLivHr~L~~~l~~~~~~~~~ 583 (709)
T TIGR02063 512 EKVKG-RPE-EELINTVLLRSMQQAKY------SPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTE 583 (709)
T ss_pred HHhhC-CcH-HHHHHHHHHHHhcCccc------CCCCCCccccccccccccCCccccchHHHHHHHHHHHHcCCCCCCcc
Confidence 88754 333 35788899999999999 6789999999999999999999999999999999999987642 2 1
Q ss_pred C--CCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCC
Q 013634 312 V--FQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQ 388 (439)
Q Consensus 312 ~--~~~~~~l~~~~~~~n~~~~~a~~~~r~~~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~ 388 (439)
. .++.++|+.+|.+||.+++.|++|||++.++|.|+||++.. +.|+|+|++|.++|+||.++++|+||+||++++.+
T Consensus 584 ~~~~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~ 663 (709)
T TIGR02063 584 KEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKD 663 (709)
T ss_pred ccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCC
Confidence 1 23456799999999999999999999999999999999887 88999999999999999999989999999999987
Q ss_pred CCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCceeEEeC
Q 013634 389 KGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 439 (439)
Q Consensus 389 ~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~l~ 439 (439)
+ +|.+++....+.+++.++.|++||+|+|+|.+||.. +++|.|+|.
T Consensus 664 d---~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~--~~~I~~~l~ 709 (709)
T TIGR02063 664 D---YYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLD--TGKIDFELV 709 (709)
T ss_pred C---cEEEcccceEEEeccCCcEECCCCEEEEEEEEEecc--cCeEEEEEC
Confidence 7 688999999999888889999999999999999976 899999974
No 4
>PRK05054 exoribonuclease II; Provisional
Probab=100.00 E-value=7.3e-95 Score=769.83 Aligned_cols=414 Identities=22% Similarity=0.309 Sum_probs=366.5
Q ss_pred ccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCceeE
Q 013634 3 LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS 82 (439)
Q Consensus 3 ~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~~ 82 (439)
+++|+|+|||||||||+||++||+||+||++||||+|||++++||||+.||+++|||+||++|+||||.|+||++|+|++
T Consensus 218 ~~~g~~~l~VHIADVs~yV~~gS~LD~eA~~RgtSvYlp~~vipMLP~~Ls~~~cSL~p~~~R~als~~~~id~~G~i~~ 297 (644)
T PRK05054 218 LPDGGLQLTVAIADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPNERRPALACRVTIDADGTIED 297 (644)
T ss_pred eCCCCEEEEEEEcchhhEeCCCCHHHHHHHHhCceEeCCCCcccCCChHHhcCccccCCCCCceEEEEEEEEeCCCCccc
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred -EEEEEeEEecCceecHHHHHHHhcCCCC----CCchHHHHHHHHHHHHHHHHHHHhCCceeecCcceEEEecCCCCCee
Q 013634 83 -TRYTKSVIKSCAALSYVEAQARMDDSRL----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPL 157 (439)
Q Consensus 83 -~~~~~s~I~s~~~ltY~~v~~~l~~~~~----~~~~~~~l~~L~~~a~~l~~~R~~~Gal~~~~~~~~~~~d~~~~~~~ 157 (439)
++|++|+|+|+++|||++|+++|+++.. ..++.+.|..|.+++++|+++|.++|++.++.||+++.+|++ |.+.
T Consensus 298 ~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~i~~~l~~L~~l~~~l~~~R~~~G~i~~d~~e~~i~ld~~-g~~~ 376 (644)
T PRK05054 298 DIRFFAAWIESKAKLAYDNVSDWLENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHALVFKDRPDYRFELGEK-GEVL 376 (644)
T ss_pred ccEEEEEEEEcCCeecHHHHHHHHhCCCccccchhHHHHHHHHHHHHHHHHHHHHHhCCCccccCCceEEEECCC-CCEE
Confidence 8999999999999999999999987642 345778899999999999999999999999999999999976 7888
Q ss_pred eeEeeccchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHcCCcccCCCH---HHHHHHHH
Q 013634 158 DIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSS---KALADSLD 234 (439)
Q Consensus 158 ~v~~~~~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~g~~~~~~~~---~~l~~~l~ 234 (439)
.+...+.++||.|||||||+||++||+|+.++ +.|++||+|+.|++++++++.+++..+|++++..+. ..++..+.
T Consensus 377 ~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~~-~~p~iyRvH~~P~~~~l~~l~~~~~~~g~~~~~~~~~~l~~~~~~~~ 455 (644)
T PRK05054 377 DIVAEPRRIANRIVEESMIAANICAARVLRDK-LGFGIYNVHSGFDPANAEQAVALLKEHGLHFDAEELLTLEGFCKLRR 455 (644)
T ss_pred EEEEecCcHHHHHHHHHHHHHHHHHHHHHHHc-CCCEEEECCCCCCHHHHHHHHHHHHHCCCCcCCCcccChHHHHHHHH
Confidence 89888999999999999999999999999997 789999999999999999999999999998865432 33444444
Q ss_pred HHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHHHhCCCCCCCCCC
Q 013634 235 RAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQ 314 (439)
Q Consensus 235 ~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~~l~~~~~~~~~~ 314 (439)
.+.+ .+. ..+..+++|+|++|.| ++.|.+|||||++.|||||||||||+||+|||||+++|.+++.+
T Consensus 456 ~l~~-~~~--~~l~~~llr~~~~a~y------s~~~~gHfgL~~~~YthfTSPIRRY~DLivHR~L~a~l~~~~~~---- 522 (644)
T PRK05054 456 ELDA-QPT--GYLDSRIRRFQSFAEI------STEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAE---- 522 (644)
T ss_pred HHhc-chH--HHHHHHHHHHHhceec------CCCCcCccccccccccccCChhhhhHHHHHHHHHHHHHcCCCCC----
Confidence 3322 222 1333346899999999 77899999999999999999999999999999999999886543
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCC
Q 013634 315 DRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP---TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGS 391 (439)
Q Consensus 315 ~~~~l~~~~~~~n~~~~~a~~~~r~~~~~~~~~~l~~~~---~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~ 391 (439)
..++.+|.+||.+++.+++|+|++.++|.++||++++ ++|+|+|++|.++|+||+|+++|+||+||++.+.++.
T Consensus 523 --~~~~~~~~~~s~~er~a~~aer~~~~~~~~~y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~- 599 (644)
T PRK05054 523 --RPQDEITVQLAERRRLNRMAERDVGDWLYARYLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVR- 599 (644)
T ss_pred --ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCc-
Confidence 1367899999999999999999999999999999987 3899999999999999999999999999999998761
Q ss_pred Cceee--cCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCceeEEeC
Q 013634 392 GDWYV--DEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 439 (439)
Q Consensus 392 ~~~~~--d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~l~ 439 (439)
..|.+ ++..+.+ ++++.|++||+|+|+|.+||.. +++|.|+++
T Consensus 600 ~~y~~~~~~~~~~~---~~~~~~~lGd~V~V~v~~vd~~--~~~i~~~~~ 644 (644)
T PRK05054 600 DELVCNQENGTVQI---KGETVYKLGDVIDVTLAEVRME--TRSIIARPV 644 (644)
T ss_pred cceEEccccceEEE---eCCEEEcCCCEEEEEEEEEccc--cCeEEEEEC
Confidence 12333 3444544 3458999999999999999976 999999874
No 5
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=100.00 E-value=1.3e-93 Score=758.71 Aligned_cols=412 Identities=22% Similarity=0.287 Sum_probs=365.0
Q ss_pred ccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCceeE
Q 013634 3 LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS 82 (439)
Q Consensus 3 ~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~~ 82 (439)
+++|+|+|||||||||+||++||+||+||++||||+|||++++||||+.||+++|||+||++|+|+||.|++|++|+|++
T Consensus 214 ~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYLp~~vipMLP~~Ls~~~cSL~p~e~R~als~~~~ld~~G~i~~ 293 (639)
T TIGR02062 214 LPNGKLQLIVAIADPTAYIAEGSKLDKAAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRITISKDGNIED 293 (639)
T ss_pred eCCCcEEEEEEEcCccccCCCCCHHHHHHHHhCCcEeCCCceecCCCHHHhcCccccCCCCCeeEEEEEEEEcCCCcEee
Confidence 56789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred -EEEEEeEEecCceecHHHHHHHhcCCCC----CCchHHHHHHHHHHHHHHHHHHHhCCceeecCcceEEEecCCCCCee
Q 013634 83 -TRYTKSVIKSCAALSYVEAQARMDDSRL----MDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPL 157 (439)
Q Consensus 83 -~~~~~s~I~s~~~ltY~~v~~~l~~~~~----~~~~~~~l~~L~~~a~~l~~~R~~~Gal~~~~~~~~~~~d~~~~~~~ 157 (439)
++|++|+|+|+++|||++|+++|+++.. .+++.++|..|.++|++|+++|.++|++.++.||+++.+|++ |.+.
T Consensus 294 ~~~~~~svIrs~~rltY~~v~~~l~~~~~~~~~~~~i~~~L~~L~~la~~l~~~R~~~G~i~ld~pE~~~~ld~~-g~~~ 372 (639)
T TIGR02062 294 KIEFFAATIKSKAKLVYDQVSDWLENTSDWQPESEEIAQQVRLLHQFCQARIEWRHTHALVFKDRPDYRFILSEK-GEVL 372 (639)
T ss_pred cCEEEEEEEEeCcEEeHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHhCCcccccCCceEEEECCC-CCEE
Confidence 7999999999999999999999987642 234677899999999999999999999999999999999976 7888
Q ss_pred eeEeeccchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHcCCcccCCC---HHHHHHHHH
Q 013634 158 DIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSS---SKALADSLD 234 (439)
Q Consensus 158 ~v~~~~~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~g~~~~~~~---~~~l~~~l~ 234 (439)
.+...+..+||.|||||||+||++||+|+.++ ..|++||+|+.|++++++++.+++..+|++++..+ ...++..+.
T Consensus 373 ~i~~~~~~~a~~lIeE~MllAN~~vA~~l~~~-~~p~iyR~H~~P~~~~l~~l~~~~~~~g~~~~~~~~~~~~~~~~~~~ 451 (639)
T TIGR02062 373 DIVAEPRRIANRIVEEAMIIANICAARFLRDK-LGFGIYNTHAGFDPANAENVVALLKTNGLHVDAEELATLDGFCKLRR 451 (639)
T ss_pred EEEEecCCHHHHHHHHHHHHHHHHHHHHHHHh-CCCeEEecCCCCCHHHHHHHHHHHHHcCCCCCcccccCHHHHHHHHH
Confidence 88888899999999999999999999999997 67999999999999999999999999999875432 333444444
Q ss_pred HHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHHHhCCCCCCCCCC
Q 013634 235 RAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQ 314 (439)
Q Consensus 235 ~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~~l~~~~~~~~~~ 314 (439)
.+.+ .+. ..+..+++|+|.+|.| +++|.+|||||++.|||||||||||+||+|||||+++|.+++.+.
T Consensus 452 ~~~~-~~~--~~l~~~~~r~~~~a~y------s~~~~~HfgL~~~~YthfTSPIRRY~DLivHR~L~~~l~~~~~~~--- 519 (639)
T TIGR02062 452 ELDA-QET--GYLDSRIRRYQSFAEI------STEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATR--- 519 (639)
T ss_pred Hhhc-chH--HHHHHHHHHHhhhccc------CCCCcCcchhccccccccCChhhhhHHHHHHHHHHHHHcCCCCCC---
Confidence 3322 221 3466677899999999 778999999999999999999999999999999999998765322
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCC
Q 013634 315 DRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP---TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGS 391 (439)
Q Consensus 315 ~~~~l~~~~~~~n~~~~~a~~~~r~~~~~~~~~~l~~~~---~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~ 391 (439)
.++.++.+|+.+++.|++|+|++.++|.+.||++++ ++|+|+|+++.++|++|.|++.|++|+|+++.+.++.
T Consensus 520 ---~~~~~~~~~s~~er~a~~aeR~~~~~~~~~yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~- 595 (639)
T TIGR02062 520 ---PQEDITVQLAERRRLNRIAERDVADWLYARFLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANR- 595 (639)
T ss_pred ---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCC-
Confidence 367889999999999999999999999999999986 4799999999999999999999999999999998731
Q ss_pred Cceeec--CCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCceeEE
Q 013634 392 GDWYVD--EQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLT 437 (439)
Q Consensus 392 ~~~~~d--~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~ 437 (439)
..|.++ +..+.++|+ +.|++||+|+|+|.+||.. +++|.|+
T Consensus 596 ~~~~~~~~~~~~~l~g~---~~~~lgd~v~V~v~~vd~~--~~~i~~~ 638 (639)
T TIGR02062 596 EELVCNQENGTVQIKGE---TVYKIGDVIDVVLTEVRME--TRSIIAR 638 (639)
T ss_pred cceEEcccccEEEEecc---EEEecCCEEEEEEEEeccc--cCcEeee
Confidence 134444 455677654 5999999999999999976 8999875
No 6
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=100.00 E-value=9.2e-93 Score=763.98 Aligned_cols=422 Identities=35% Similarity=0.560 Sum_probs=390.2
Q ss_pred ccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCceeE
Q 013634 3 LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS 82 (439)
Q Consensus 3 ~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~~ 82 (439)
+.+|+|+|||||||||+||+|||+||+||++||||||||++++||||+.||+++|||+||++|+|+||.|++|.+|+|.+
T Consensus 276 l~~g~~~LgVhIADVs~yV~p~s~LD~EA~~RgtSVYlp~~vipMLPe~Ls~~lcSL~p~~dRla~s~~m~ld~~g~v~~ 355 (706)
T COG0557 276 LRNGGYRLGVHIADVSHYVQPGSALDKEARKRGTSVYLPDRVIPMLPEALSNGLCSLNPGVDRLALSCEMTLDSEGRVKK 355 (706)
T ss_pred eCCCcEEEEEEEecceeecCCCChhhHHHHHcCCeEEcCCcccCCCchhhcCCccccCCCCceEEEEEEEEECCCCCEEE
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeEEecCceecHHHHHHHhcCC--CCCCchHHHHHHHHHHHHHHHHHHHhCCceeecCcceEEEecCCCCCeeeeE
Q 013634 83 TRYTKSVIKSCAALSYVEAQARMDDS--RLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIG 160 (439)
Q Consensus 83 ~~~~~s~I~s~~~ltY~~v~~~l~~~--~~~~~~~~~l~~L~~~a~~l~~~R~~~Gal~~~~~~~~~~~d~~~~~~~~v~ 160 (439)
++|++|+|+|.++|||++|+++|+++ ....++.+.|..+..+++.++++|.++|+++|+.+|.++.+|++ |.|..+.
T Consensus 356 ~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~l~~~l~~~~~l~~~l~~~R~~rg~i~~~~~E~ki~~d~~-~~~~~i~ 434 (706)
T COG0557 356 YEIYPSVIKSAARLTYEEVQAILDGKEDDKYAPLLDSLLELLELAKILKKKRLSRGAIDFDTPEAKIVLDEE-GRPVEIE 434 (706)
T ss_pred EEEEEEEEeccccCCHHHHHHHHhcCcchhcccchHHHHHHHHHHHHHHHHHHhCCCcccCCcceeEEECCC-CCeeeEE
Confidence 99999999999999999999999986 34457788999999999999999999999999999999999976 6889999
Q ss_pred eeccchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHcCCcccCCC----HHHHHHHHHHH
Q 013634 161 MYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSS----SKALADSLDRA 236 (439)
Q Consensus 161 ~~~~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~g~~~~~~~----~~~l~~~l~~~ 236 (439)
..+.++++.||||||++||++||+++.++ ..|.+||+|+.|+.++++.|.+++..+|+.+.... +..++..+++.
T Consensus 435 ~~~r~~a~~lIee~Ml~AN~~vA~~l~~~-~~~~~~R~h~~P~~ek~~~l~~~l~~lg~~~~~~~~~~~~~~~~~~l~~~ 513 (706)
T COG0557 435 IRERLDAEKLIEEFMLLANETVAEHLEKH-KIPLLYRTHERPSTEKLQSLREFLQNLGLVLPLGGSKPQPQDYQILLETV 513 (706)
T ss_pred EecccHHHHHHHHHHHHHHHHHHHHHHHc-CCCcceeCCCCCCHHHHHHHHHHHHHcCceecCCCCcCCHHHHHHHHhhc
Confidence 99999999999999999999999999998 67889999999999999999999999999887442 45667777765
Q ss_pred hCCChhHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHHHhCCCCCCCCCCCh
Q 013634 237 VGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPSVFQDR 316 (439)
Q Consensus 237 ~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~~l~~~~~~~~~~~~ 316 (439)
.+ .| ...++..+++|+|++|.| +..+.+|||||++.|||||||||||+||+|||||+++|.+++.+....+.
T Consensus 514 ~~-~~-~~~v~~~~~lRsm~~a~Y------s~~~~~HfgL~~~~YtHFTSPIRRY~DLivHR~L~~~l~~~~~~~~~~~~ 585 (706)
T COG0557 514 KG-RP-LEAVLQTLLLRSMKQAEY------SPDNVGHFGLALDYYTHFTSPIRRYPDLIVHRQLKALLSGEPIPEKKTSE 585 (706)
T ss_pred cC-Ch-HHHHHHHHHHHhhhcCee------cCCCCCceeccccchhccCCchhhchHHHHHHHHHHHhcCCCCCccchhH
Confidence 32 23 346788889999999999 67799999999999999999999999999999999999988765543335
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCcee
Q 013634 317 PQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWY 395 (439)
Q Consensus 317 ~~l~~~~~~~n~~~~~a~~~~r~~~~~~~~~~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~ 395 (439)
++|..+|.+||.+++.|.+|+|++..+|.|.||++++ +.|+|+|++|.++|++|+++++|+||+||++.++++ +|.
T Consensus 586 ~~l~~i~~~~s~~er~a~~aer~~~~~~~~~~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d---~y~ 662 (706)
T COG0557 586 EELDELAAHISSAERRAQEAERDVIDLLKAEYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDD---YYH 662 (706)
T ss_pred HHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCc---eee
Confidence 7899999999999999999999999999999999998 699999999999999999999999999999999987 699
Q ss_pred ecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCceeEEeC
Q 013634 396 VDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTLI 439 (439)
Q Consensus 396 ~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~l~ 439 (439)
+++....+.+++.++.|++||.|+|++.+++.. .++|+|+++
T Consensus 663 ~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~--~~~i~~~~v 704 (706)
T COG0557 663 FDERGQALVGEKSGKVYRLGDEVKVKVTSVDLD--ERKIDFELV 704 (706)
T ss_pred eccccceeeccccccccccCCEEEEEEEEEccc--ccceEEEec
Confidence 999888899999999999999999999999976 899999874
No 7
>KOG2102 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-80 Score=675.49 Aligned_cols=423 Identities=50% Similarity=0.793 Sum_probs=379.6
Q ss_pred ccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCceeE
Q 013634 3 LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEIIS 82 (439)
Q Consensus 3 ~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~~ 82 (439)
++||+|+|||||||||+||+|||+||.||++||||||||++.+||||+.|++++|||.||++|+||||.|++|.+|.|.+
T Consensus 501 l~nG~~evGVHIADVt~fV~pgs~lD~eA~~R~ttvyL~q~~i~MLP~~L~~~lcSL~~g~dr~aFSvvwel~~~~~i~~ 580 (941)
T KOG2102|consen 501 LPNGNLEVGVHIADVTHFVKPGSALDREAARRGTTVYLVQKRIPMLPKLLSEELCSLRPGVDRLAFSVVWELDSDGSILK 580 (941)
T ss_pred cCCCcEEEEEEeccchhhcCCCCccCHHHHhhcceEEeccccccCCchhhhhhheeccCCCceeeEEEEEEEcCCCceee
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEeEEecCceecHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHhCCceeecCcceEEEecCCCCCeeeeEee
Q 013634 83 TRYTKSVIKSCAALSYVEAQARMDDSRLMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPLDIGMY 162 (439)
Q Consensus 83 ~~~~~s~I~s~~~ltY~~v~~~l~~~~~~~~~~~~l~~L~~~a~~l~~~R~~~Gal~~~~~~~~~~~d~~~~~~~~v~~~ 162 (439)
.||++|+|+|+.+++|+++|++|+++...+++...|..|.++|+.|+++|+++|++.+..+++.+.+|++++.|.+++.+
T Consensus 581 ~~f~ksvI~s~~~lsye~Aq~~id~~~~~~~v~~~l~~l~~ia~~lr~~R~~~gal~l~~~e~~~~~d~~~~~p~~~e~~ 660 (941)
T KOG2102|consen 581 TWFGKSVIRSKAALSYEEAQDILDTPNSSDPLTSSLRLLHEIAKILRQKRLDNGALLLRSPELRFLLDEEKPNPQDVEVK 660 (941)
T ss_pred ceecchhcccchhhhHHHHHHHhcCCcccchhhhhHHHHHHHHHHHHHHHhccCCcccccHhHHhhhccCCCCcccccee
Confidence 99999999999999999999999999888899999999999999999999999999999999999999987788888888
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHcCCcccCCCHHHHHHHHHHHhC-CCh
Q 013634 163 QIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLDRAVG-DDP 241 (439)
Q Consensus 163 ~~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~g~~~~~~~~~~l~~~l~~~~~-~~~ 241 (439)
+..+++.+|||||++||..||+++.++|+..+++|.|+.|.+..++.+.+.+...|.+++..+++.|++++..+.+ ..|
T Consensus 661 ~~~~~n~lveEfmllaN~~vA~~I~~~f~~~alLR~hp~P~~~~~~~~~~~~~~~g~~ld~sS~~~L~~Sl~r~~~~~~p 740 (941)
T KOG2102|consen 661 ELTETNFLVEEFMLLANISVAEKILASFPSLALLRRHPSPPPENFKPLVSLCLELGFNLDTSSSKSLADSLDRIRDDDKP 740 (941)
T ss_pred eeehhhhHHHHHHHHHhHHHHHHHHHhCCchhhhccCCCCccccccHHHHHHHHcCCCccccchHHHhhhHhhhcCCchH
Confidence 8899999999999999999999999999999999999999999999999999999999999999999999999987 446
Q ss_pred hHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHH-HhCCCCCCCCCCChhHHH
Q 013634 242 YFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSA-SLGIYKLPSVFQDRPQLT 320 (439)
Q Consensus 242 ~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~-~l~~~~~~~~~~~~~~l~ 320 (439)
++..+++.|.+|+|..|.|+|+|+...+.++|||||++.|||||||||||+|++|||||++ +....+ ...+...+.
T Consensus 741 ~~~~~l~~l~~r~m~~A~yf~sg~~~~~~~~HygLa~p~YTHFTsPiRRY~DIivHrqL~~~~~~~~~---~~~~~~~l~ 817 (941)
T KOG2102|consen 741 YLNTLLRILATRSMTRAVYFCSGSSDTPQFHHYGLASPLYTHFTSPIRRYADIIVHRQLAAAFLERSP---TAPDRPNLS 817 (941)
T ss_pred HHHHHHHHHHhhhhhceeEEeecccCcchhhchhhcccchhhccCcccccchHHHHHHHHHHhhccCc---cccccccHH
Confidence 8888899999999999999999998888999999999999999999999999999999995 333322 223345899
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCeEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCe
Q 013634 321 SIADNLNYRHRNAQMASRGSVELHTLIYFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQ 400 (439)
Q Consensus 321 ~~~~~~n~~~~~a~~~~r~~~~~~~~~~l~~~~~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~ 400 (439)
.+|..||.+.+.++.|++++.++|.+.|+++.....+|+|..|.++|+.|++|++|+||.|+++.+... ...+..++
T Consensus 818 ~i~~~~N~r~~~a~~a~~~S~~l~~~~~~k~~~~~~~a~v~~V~~~~~~v~ipe~G~e~~v~l~~~~~~-~~~~~~~~-- 894 (941)
T KOG2102|consen 818 SLAANCNERKKAAKKAQEASTELYLCEYLKDKQVLEEAVVLFVRPNGIDVVIPEYGLEGRVYLDLLKPS-QTFFLDDE-- 894 (941)
T ss_pred HHHhhhhhhHHHHHHHHHhhHHHHHHHHHHhcccccceEEEEEecCceEEEEcccCceEEEEecccCCc-cceeeccc--
Confidence 999999999999999999999999999999997788999999999999999999999999999733221 11121111
Q ss_pred EEEEeeCCceEEeeCceEEEEEEEecCCCCCCceeEEe
Q 013634 401 QKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLTL 438 (439)
Q Consensus 401 ~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~l 438 (439)
....+...|.|.+.+......+...+|.+.+
T Consensus 895 -------~~~~~~~~~~v~~~~~~~~~~~~~~~l~~~~ 925 (941)
T KOG2102|consen 895 -------VSLRFEESDPVVVRIKLDKLVPQPDRLRIEL 925 (941)
T ss_pred -------ccccccccCCceeeecccccccCcceEEEEe
Confidence 1112667777777765445555566776654
No 8
>PF00773 RNB: RNB domain CAUTION: The Prosite pattern does not correspond to this Pfam.; InterPro: IPR001900 This entry represents the catalytic domain of ribonuclease II []. It includes characterised and related sequences to exoribonuclease II (RNase II) and ribonuclease R, a bacterial 3' --> 5' exoribonuclease homologous to RNase II [,,].; GO: 0003723 RNA binding, 0004540 ribonuclease activity; PDB: 2R7D_A 2R7F_A 2ID0_D 2IX1_A 2IX0_A 2VNU_D 2WP8_J.
Probab=100.00 E-value=1.4e-72 Score=559.87 Aligned_cols=290 Identities=41% Similarity=0.649 Sum_probs=232.6
Q ss_pred cccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCcee
Q 013634 2 KLQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEII 81 (439)
Q Consensus 2 ~~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~ 81 (439)
++++|+|+|||||||||+||++||+||++|++||+|+|||++++||||+.|++++|||.||++|+|||+.+++|++|+|.
T Consensus 28 ~~~~~~~~v~VHIaDvt~~i~~~s~ld~~A~~r~~s~Ylp~~~~pMlP~~l~~~~~SL~~~~~r~a~S~~~~l~~~G~i~ 107 (325)
T PF00773_consen 28 KLPDGKYEVGVHIADVTSFIPPDSPLDREARKRGTSVYLPEKVVPMLPPELSEDLCSLNPGKDRLAFSVIFTLDEDGEIL 107 (325)
T ss_dssp EETTTEEEEEEEEE-GGGTS-TTSHHHHHHHHH-B-EEETTEEE-SS-HHHHCTTSSTTBTSEEEEEEEEEEE-TTS-EE
T ss_pred ECCCCcEEEEEEcCCHHHhhccChHHHHHHHhcCccEECCCCccccCChhHhcccccCCCCCCceEEEEEEEEeeCCeEe
Confidence 35678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEeEEecCceecHHHHHHHhcCCCCCCc---hHHHHHHHHHHHHHHHHHHHhCCceee-cCcceEEEecCCCCCee
Q 013634 82 STRYTKSVIKSCAALSYVEAQARMDDSRLMDP---LTTDLRNMNSLAKKMRQRRIERGALTL-ASAEVKFQIDTETHDPL 157 (439)
Q Consensus 82 ~~~~~~s~I~s~~~ltY~~v~~~l~~~~~~~~---~~~~l~~L~~~a~~l~~~R~~~Gal~~-~~~~~~~~~d~~~~~~~ 157 (439)
+++|++|+|+|.++|||++|+++|++...... ..++|..|+++|+.|+++|.++|++.+ ..|+..+.++++ +.+.
T Consensus 108 ~~~i~~s~I~~~~~lty~~v~~~l~~~~~~~~~~~~~~~L~~l~~la~~l~~~R~~~Ga~~~~~~~~~~~~~~~~-~~~~ 186 (325)
T PF00773_consen 108 DYEIYPSIIRSVARLTYEEVDEILEGKSQEEPESPIEEDLKLLYELAKALRKKRLSRGAIELFNSPELKFSLDED-GPPK 186 (325)
T ss_dssp EEEEEEEEEEBSEEEEHHHHHHHHHTTTS--HCSHCHHHHHHHHHHHHHHHHHHHHTTS-----SHCEEEEEETT-TTEE
T ss_pred eeEEEEEEEecccccCHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHHhhhhccCccccCCCceEEEEecC-CCcc
Confidence 99999999999999999999999998765433 378999999999999999999999999 789999999875 5566
Q ss_pred eeEeec---cchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHcCCcccCCCHHHHHHHHH
Q 013634 158 DIGMYQ---IREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADSLD 234 (439)
Q Consensus 158 ~v~~~~---~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~g~~~~~~~~~~l~~~l~ 234 (439)
.+.... ..+|+.||+||||+||++||+|+.++ ++|++||+|+.|+..+++++.+.+ +++++.....++++.+.
T Consensus 187 ~~~~~~~~~~~~a~~lV~E~MilAN~~vA~~~~~~-~ip~iyR~~~~p~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~ 262 (325)
T PF00773_consen 187 EINRESSDESSPAHSLVEELMILANRAVAQFLSEN-GIPAIYRVQPEPDPERLEELLKLL---KLDLDETKSLTLQNLLQ 262 (325)
T ss_dssp EEEEE------HHHHHHHHHHHHHHHHHHHHHHHC-TTTSEEEEB-SSSCCCHHHHHHHH---T---STCHHHCHHCHHC
T ss_pred eEEEEeccCCchHHHHHHHHHHHHHHHHHHHHHHc-CCCceeeeCCCCCHHHHHHHHHHh---cCCCCCcchhhHHHHHH
Confidence 666554 88999999999999999999999986 999999999999999988887777 44444433334555555
Q ss_pred HHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHHHhC
Q 013634 235 RAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLG 305 (439)
Q Consensus 235 ~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~~l~ 305 (439)
. . ++.....+..++.++|++|+| +..|.+|||||++.|||||||||||+||+|||||+++|.
T Consensus 263 ~-~--~~~~~~~~~~~l~~~l~~a~y------~~~p~~H~~L~l~~Yt~~TSPlRRY~Dl~~hrql~~~L~ 324 (325)
T PF00773_consen 263 A-E--NPPNSLALRYLLLKTLPPAEY------STEPSGHFGLGLPAYTHFTSPLRRYADLVVHRQLKAALR 324 (325)
T ss_dssp C-C--CTTSSHHHHHHHHCCC--EEE------ESSGC-BTTTTBSS-B--S-TTTBHHHHHHHHHHHHHHH
T ss_pred h-c--CChHHHHHHHHHHHhhccccc------ccCCCcceeeeccccccccChhhhhHHHHHHHHHHHHhh
Confidence 4 1 222334567788999999999 678899999999999999999999999999999999985
No 9
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=100.00 E-value=1.5e-70 Score=530.45 Aligned_cols=407 Identities=24% Similarity=0.325 Sum_probs=352.3
Q ss_pred ccCCeEEEEEEEecCCcccCCCCHhhHHHHhcCceEEcCCCcccCCCccccccccCCCCCCceeEEEEEEEECCCCcee-
Q 013634 3 LQYSSLMFQLDIADVTNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKPLTEDICSLRADVERLAFSVIWELTPEAEII- 81 (439)
Q Consensus 3 ~~~g~~~v~VHIADvs~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~- 81 (439)
+++|.|.+-|+|||||+||.+||.||++|++|+.|.|||+..+||||++||+++|||.||+.|||+.|.++++++|.|.
T Consensus 218 ~~~~~~~L~vAIADPTAyI~~~s~ld~~A~~R~FTnYLPGfNIPMLPreLsd~lCSL~~ne~RPaL~C~it~~~~G~I~~ 297 (645)
T COG4776 218 LPDGDWQLIVAIADPTAYIAEGSKLDKEAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPALACRITIDKDGNITD 297 (645)
T ss_pred cCCCcEEEEEEecCCccccCCcchhhHHHHHHHHhhcCCCCCCCCCChhhhhhhhhccccccCceEEEEEEEecCCcccc
Confidence 5789999999999999999999999999999999999999999999999999999999999999999999999999996
Q ss_pred EEEEEEeEEecCceecHHHHHHHhcCCC----CCCchHHHHHHHHHHHHHHHHHHHhCCceeecCcceEEEecCCCCCee
Q 013634 82 STRYTKSVIKSCAALSYVEAQARMDDSR----LMDPLTTDLRNMNSLAKKMRQRRIERGALTLASAEVKFQIDTETHDPL 157 (439)
Q Consensus 82 ~~~~~~s~I~s~~~ltY~~v~~~l~~~~----~~~~~~~~l~~L~~~a~~l~~~R~~~Gal~~~~~~~~~~~d~~~~~~~ 157 (439)
+.+|+.+.|+|+++|.|++|.++|++.. .++++.+++..|+.+++++-++|..+.-+.-+.|+++|.+.+. |.+.
T Consensus 298 ~i~F~aA~i~SkakL~YdhVSDwlE~~~~WqPe~~~iAqqi~~L~~~~~aR~~WRk~hal~FkdrpdYrF~l~e~-g~V~ 376 (645)
T COG4776 298 KIRFFAATIESKAKLVYDHVSDWLENTGDWQPESEAIAQQIRLLHQFCQARIEWRKTHALVFKDRPDYRFILGEK-GEVL 376 (645)
T ss_pred chhhHHHhhhhhhhhhhhhHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhhceeeccCCCceEEEecCC-CceE
Confidence 6999999999999999999999998753 4567899999999999999999999988888999999999865 8888
Q ss_pred eeEeeccchHHHHHHHHHHHHHHHHHHHHHhhCCCceeeecCCCCChhhHHHHHHHHHHcCCcccCCCHHHHHHH-----
Q 013634 158 DIGMYQIREANQMVEEFMLAANVSVAEQILRQFPLCSLLRRHPSPTKEMLEPLLRTAAAVGLNLDVSSSKALADS----- 232 (439)
Q Consensus 158 ~v~~~~~~~a~~lVeE~MilAN~~vA~~~~~~~~~~~~~R~h~~p~~~~~~~l~~~~~~~g~~~~~~~~~~l~~~----- 232 (439)
+|....+..||+||||+||+||.|+|++|.++++ .++|.+|...++...+....++...|...+..+..++...
T Consensus 377 ~I~ae~RRiAnriVEE~MI~ANIcAa~~L~~~~g-fGI~N~HsGFd~~~~e~a~~~l~~~~~~~~~e~l~Tl~Gfc~lRr 455 (645)
T COG4776 377 DIVAEPRRIANRIVEESMIAANICAARVLREKLG-FGIYNVHSGFDPANAEAAAALLKTNGLNVDAEELLTLEGFCKLRR 455 (645)
T ss_pred eeehhHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-cceeeccccCCHHHHHHHHHHHHhcCcCCCHHHHhhhHHHHHHHH
Confidence 8888888999999999999999999999999854 6899999999999999999999999987765544444332
Q ss_pred -HHHHhCCChhHHHHHHHHHHhhccCceecccCCCCCCCcCcccccccccccccccccchhhHHHHHHHHHHhCCCCCCC
Q 013634 233 -LDRAVGDDPYFNKLIRILATRCMTQAVYFCSGDLTPPEFHHYGLAAPLYTHFTSPIRRYADVVVHRLLSASLGIYKLPS 311 (439)
Q Consensus 233 -l~~~~~~~~~~~~~l~~~~~r~m~~a~Y~~~~~~~~~~~~H~~Lg~~~YthfTSPiRRY~DlvvHrqL~~~l~~~~~~~ 311 (439)
|+.. ...|...-+| +|.+.+++++.|.||||||++.|+.||||||+|+|+||||.|++++.+++...
T Consensus 456 ~l~~~--~t~yld~RiR----------rfqsfae~~t~p~PHFglGl~~YATWTSPIRKY~DMiNHRLlKavi~~~~~~k 523 (645)
T COG4776 456 ELDAQ--PTGYLDSRIR----------RFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAEK 523 (645)
T ss_pred Hhhcc--ccchHHHHHH----------HHHhHHhhccCcCccccccchheeeccchhhhhhhHHHHHHHHHHHcCCCcCC
Confidence 2222 3344443333 23445667899999999999999999999999999999999999999875422
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCC
Q 013634 312 VFQDRPQLTSIADNLNYRHRNAQMASRGSVELHTLIYFRKRP---TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQ 388 (439)
Q Consensus 312 ~~~~~~~l~~~~~~~n~~~~~a~~~~r~~~~~~~~~~l~~~~---~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~ 388 (439)
. =+.+..++.++.|..+.+||+.-+|..|+||.... .+|.|.|.+|...|+.|.|-+.|...+|+-.-+.+
T Consensus 524 -P-----qedi~v~lae~Rr~nrmaERdv~DWLY~r~L~~k~~~~~~F~AEI~Di~R~G~RvrLleNGA~~FIPa~lih~ 597 (645)
T COG4776 524 -P-----QEDITVQLAERRRLNRMAERDVADWLYARFLADKAGTNTRFAAEIQDISRGGMRVRLLENGAIAFIPAPLIHA 597 (645)
T ss_pred -C-----chHHHHHHHHHHHhhhhhhhhhHHHHHHHHhccccccCchhhhhhhhhccCceEEEeccCCcceecchhhhcc
Confidence 1 13455678899999999999999999999999876 67999999999999999999999999998776665
Q ss_pred CC-CCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCce
Q 013634 389 KG-SGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKL 434 (439)
Q Consensus 389 ~~-~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i 434 (439)
.. +..++.+++++.+ ++..+|++||.|+|++.+|..+ .|.|
T Consensus 598 ~reei~~n~e~gtv~I---~ge~~Yk~~D~i~V~l~eVr~e--tRsi 639 (645)
T COG4776 598 NREELVCNQENGTVQI---KGETVYKVGDVIDVTLAEVRME--TRSI 639 (645)
T ss_pred chhheEecCCCceEEE---ccEEEEeeccEEEEEeHHHHHh--hhhh
Confidence 42 2346667777777 4578999999999999999865 5554
No 10
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=99.27 E-value=6.1e-11 Score=93.47 Aligned_cols=81 Identities=20% Similarity=0.336 Sum_probs=73.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.++|.|+++.++|++|.++.+|++|++|+++++++ +|.+|+...++.+++..+.|++||.|+|+|.++|.+ +++
T Consensus 3 ~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~---~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~--~~~ 77 (83)
T cd04471 3 EEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDD---YYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLD--RRK 77 (83)
T ss_pred CEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCC---cEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccc--cCE
Confidence 478999999999999999999999999999999866 588898888888767789999999999999999975 899
Q ss_pred eeEEeC
Q 013634 434 LQLTLI 439 (439)
Q Consensus 434 i~l~l~ 439 (439)
|.|+|+
T Consensus 78 i~~~l~ 83 (83)
T cd04471 78 IDFELV 83 (83)
T ss_pred EEEEEC
Confidence 999874
No 11
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=98.84 E-value=2.2e-08 Score=77.01 Aligned_cols=69 Identities=17% Similarity=0.113 Sum_probs=58.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.++|.|+++.++|+||.++.++.+|++|++++.+. ++ .+....|++||+|+|+|.++|.. + +
T Consensus 5 ~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~---~~-----------~~~~~~~~~Gd~v~vkv~~vd~~--~-k 67 (73)
T cd05686 5 QIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSC---RV-----------DDPSEVVDVGEKVWVKVIGREMK--D-K 67 (73)
T ss_pred CEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCC---cc-----------cCHhhEECCCCEEEEEEEEECCC--C-c
Confidence 678999999999999999987668999999998754 11 14467799999999999999975 4 9
Q ss_pred eeEEeC
Q 013634 434 LQLTLI 439 (439)
Q Consensus 434 i~l~l~ 439 (439)
|.||+.
T Consensus 68 i~ls~~ 73 (73)
T cd05686 68 MKLSLS 73 (73)
T ss_pred EEEEeC
Confidence 999874
No 12
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.76 E-value=2.6e-08 Score=75.61 Aligned_cols=68 Identities=25% Similarity=0.278 Sum_probs=58.2
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.++|.|+++.++|++|.+++ |++|+||.+++.++ ++ .+....|++||.++|+|.++|.+ +++
T Consensus 2 ~~v~g~V~~v~~~Gv~V~l~~-~v~g~i~~~~l~~~---~~-----------~~~~~~~~~Gd~i~~~V~~id~~--~~~ 64 (69)
T cd05697 2 QVVKGTIRKLRPSGIFVKLSD-HIKGLVPPMHLADV---RL-----------KHPEKKFKPGLKVKCRVLSVEPE--RKR 64 (69)
T ss_pred CEEEEEEEEEeccEEEEEecC-CcEEEEEHHHCCCc---cc-----------cCHHHcCCCCCEEEEEEEEEECC--CCE
Confidence 468999999999999999986 89999999998765 11 12356899999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.|+|
T Consensus 65 i~ls~ 69 (69)
T cd05697 65 LVLTL 69 (69)
T ss_pred EEEEC
Confidence 99986
No 13
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=98.74 E-value=6.4e-08 Score=79.05 Aligned_cols=80 Identities=15% Similarity=0.207 Sum_probs=68.1
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCC---
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPN--- 430 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~--- 430 (439)
+.+.|.|+++.++|++|.+. +++|+++++++.++ .+.+++...++.+.+.+..|++||.|+|+|.++|....
T Consensus 1 ~vv~g~V~~i~~~GifV~l~--~v~G~v~~~~l~~~---~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~ 75 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIG--PVDGLLHISQIMDD---YISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPR 75 (99)
T ss_pred CEEEEEEEEEEeccEEEEEc--CeEEEEEEEEccCC---ceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCC
Confidence 36899999999999999996 59999999999876 57788888888887778999999999999999996532
Q ss_pred CCceeEEe
Q 013634 431 RPKLQLTL 438 (439)
Q Consensus 431 ~~~i~l~l 438 (439)
..+|.||+
T Consensus 76 ~~~i~ls~ 83 (99)
T cd04460 76 ESKIGLTM 83 (99)
T ss_pred CceEEEEE
Confidence 25788775
No 14
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.71 E-value=4.3e-08 Score=74.30 Aligned_cols=68 Identities=21% Similarity=0.199 Sum_probs=55.9
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.+.|.|+++.++|+||.++. |++|++|.+++.+. .. ..+..+.|++||.|+|+|.++|.+ +++
T Consensus 2 ~~~~g~V~~i~~~G~fv~l~~-~~~Glv~~~~l~~~-----~~--------~~~~~~~~~~G~~v~v~v~~id~~--~~~ 65 (69)
T cd05690 2 TVVSGKIKSITDFGIFVGLDG-GIDGLVHISDISWT-----QR--------VRHPSEIYKKGQEVEAVVLNIDVE--RER 65 (69)
T ss_pred CEEEEEEEEEEeeeEEEEeCC-CCEEEEEHHHCCCc-----cc--------cCChhhEECCCCEEEEEEEEEECC--cCE
Confidence 468999999999999999986 89999999988632 00 123467899999999999999976 888
Q ss_pred eeEE
Q 013634 434 LQLT 437 (439)
Q Consensus 434 i~l~ 437 (439)
|.|+
T Consensus 66 i~l~ 69 (69)
T cd05690 66 ISLG 69 (69)
T ss_pred EeCC
Confidence 8764
No 15
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.62 E-value=1.4e-07 Score=72.10 Aligned_cols=68 Identities=16% Similarity=0.251 Sum_probs=55.8
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..++|.|+++.++|+||+++. |++|++|.+++++. ... .+....|++||.|+|+|.++|.+ +++
T Consensus 5 ~~~~g~V~~i~~~G~fv~l~~-~~~Gl~~~~~l~~~-----~~~--------~~~~~~~~~Gd~v~v~v~~id~~--~~~ 68 (72)
T cd05689 5 TRLFGKVTNLTDYGCFVELEE-GVEGLVHVSEMDWT-----NKN--------IHPSKVVSLGDEVEVMVLDIDEE--RRR 68 (72)
T ss_pred CEEEEEEEEEEeeEEEEEcCC-CCEEEEEEEeccCc-----ccc--------cCcccEeCCCCEEEEEEEEeeCC--cCE
Confidence 579999999999999999987 89999999988632 000 13457899999999999999976 788
Q ss_pred eeEE
Q 013634 434 LQLT 437 (439)
Q Consensus 434 i~l~ 437 (439)
|.|+
T Consensus 69 i~~~ 72 (72)
T cd05689 69 ISLG 72 (72)
T ss_pred EeCC
Confidence 8763
No 16
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.61 E-value=2.5e-07 Score=71.00 Aligned_cols=68 Identities=16% Similarity=0.228 Sum_probs=58.3
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|.++.++|++|.++. +++|++|.+++.++ |.. +....|++||.|+++|.++|.. +++
T Consensus 5 ~iv~g~V~~v~~~gi~v~l~~-~~~g~v~~s~l~~~----~~~----------~~~~~~~~Gd~v~~~V~~~d~~--~~~ 67 (73)
T cd05706 5 DILPGRVTKVNDRYVLVQLGN-KVTGPSFITDALDD----YSE----------ALPYKFKKNDIVRACVLSVDVP--NKK 67 (73)
T ss_pred CEEEEEEEEEeCCeEEEEeCC-CcEEEEEhhhccCc----ccc----------ccccccCCCCEEEEEEEEEeCC--CCE
Confidence 678999999999999999987 89999999999865 211 2356799999999999999976 789
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.||+
T Consensus 68 i~ls~ 72 (73)
T cd05706 68 IALSL 72 (73)
T ss_pred EEEEE
Confidence 99987
No 17
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.60 E-value=1.6e-07 Score=71.86 Aligned_cols=67 Identities=16% Similarity=0.173 Sum_probs=56.0
Q ss_pred EEE-EEEEEE-EcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 355 DTE-ARIVKI-RSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 355 ~~~-g~V~~v-~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
.++ |.|+++ .++|++|.+++ |++|++|.+++.+.. . .+....|++||.|+|+|.++|.. ++
T Consensus 3 v~~~g~V~~v~~~~G~~V~l~~-gv~G~i~~s~l~~~~------~--------~~~~~~~~vG~~v~~kV~~id~~--~~ 65 (71)
T cd05696 3 VVDSVKVTKVEPDLGAVFELKD-GLLGFVHISHLSDDK------V--------PSDTGPFKAGTTHKARIIGYSPM--DG 65 (71)
T ss_pred EeeeeEEEEEccCceEEEEeCC-CCEEEEEHHHCCcch------h--------cCcccccCCCCEEEEEEEEEeCC--CC
Confidence 567 899998 69999999987 899999999987541 0 12356799999999999999976 89
Q ss_pred ceeEEe
Q 013634 433 KLQLTL 438 (439)
Q Consensus 433 ~i~l~l 438 (439)
+|.|||
T Consensus 66 ~i~lS~ 71 (71)
T cd05696 66 LLQLSL 71 (71)
T ss_pred EEEEeC
Confidence 999986
No 18
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.58 E-value=1.8e-07 Score=71.86 Aligned_cols=69 Identities=10% Similarity=0.121 Sum_probs=57.4
Q ss_pred EEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCce
Q 013634 355 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKL 434 (439)
Q Consensus 355 ~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i 434 (439)
..+|.|..+.++|++|.|.+ +++|+|+.++++++ .... .+....|++||.|+++|..+|.+ +++|
T Consensus 3 ~V~g~V~~i~~~g~~V~l~~-~i~G~i~~~~ls~~----~~~~--------~~~~~~~~vG~~v~~kV~~id~~--~~~i 67 (73)
T cd05703 3 EVTGFVNNVSKEFVWLTISP-DVKGRIPLLDLSDD----VSVL--------EHPEKKFPIGQALKAKVVGVDKE--HKLL 67 (73)
T ss_pred EEEEEEEEEeCCEEEEEeCC-CcEEEEEHHHcCCc----cccc--------cCHHHhCCCCCEEEEEEEEEeCC--CCEE
Confidence 57899999999999999977 89999999998753 0000 12357799999999999999976 8999
Q ss_pred eEEe
Q 013634 435 QLTL 438 (439)
Q Consensus 435 ~l~l 438 (439)
.||+
T Consensus 68 ~Ls~ 71 (73)
T cd05703 68 RLSA 71 (73)
T ss_pred EEEe
Confidence 9987
No 19
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.57 E-value=1.5e-07 Score=71.16 Aligned_cols=67 Identities=18% Similarity=0.289 Sum_probs=56.6
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|+++.++|++|.++. +++|++|.++++++ ++ .+....|++||.|+|+|.++|.. +++
T Consensus 2 ~~v~g~V~~v~~~Gv~V~l~~-~~~G~v~~s~l~~~---~~-----------~~~~~~~~~Gd~v~~~v~~~d~~--~~~ 64 (68)
T cd05707 2 DVVRGFVKNIANNGVFVTLGR-GVDARVRVSELSDS---YL-----------KDWKKRFKVGQLVKGKIVSIDPD--NGR 64 (68)
T ss_pred CEEEEEEEEEECccEEEEeCC-CCEEEEEHHHCCch---hh-----------cCHhhccCCCCEEEEEEEEEeCC--CCE
Confidence 368999999999999999987 79999999999765 11 13467799999999999999976 788
Q ss_pred eeEE
Q 013634 434 LQLT 437 (439)
Q Consensus 434 i~l~ 437 (439)
|.||
T Consensus 65 i~ls 68 (68)
T cd05707 65 IEMT 68 (68)
T ss_pred EecC
Confidence 8775
No 20
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.56 E-value=1.7e-07 Score=72.19 Aligned_cols=70 Identities=11% Similarity=0.052 Sum_probs=56.8
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+...|.|.++.++|+||.+.+ |++|+||++++.+. ++. +. .+..+.|++||.|+++|.++|.+ +++
T Consensus 5 ~~V~g~V~~i~~~G~fV~l~~-~v~G~v~~~~ls~~---~~~-~~-------~~~~~~~~~G~~v~~kVl~id~~--~~~ 70 (74)
T cd05705 5 QLLRGYVSSVTKQGVFFRLSS-SIVGRVLFQNVTKY---FVS-DP-------SLYNKYLPEGKLLTAKVLSVNSE--KNL 70 (74)
T ss_pred CEEEEEEEEEeCCcEEEEeCC-CCEEEEEHHHccCc---ccc-Ch-------hhHhcccCCCCEEEEEEEEEECC--CCE
Confidence 578999999999999999976 99999999999875 111 10 01247899999999999999976 788
Q ss_pred eeEE
Q 013634 434 LQLT 437 (439)
Q Consensus 434 i~l~ 437 (439)
|.||
T Consensus 71 i~LS 74 (74)
T cd05705 71 VELS 74 (74)
T ss_pred EecC
Confidence 8775
No 21
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.53 E-value=3.2e-07 Score=69.75 Aligned_cols=68 Identities=24% Similarity=0.358 Sum_probs=57.3
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|.++.++|++|.++. +++|++|.++++++ +.. +....+++||.|+|+|.++|.. +++
T Consensus 2 ~~~~g~V~~v~~~G~~V~l~~-~~~gli~~s~l~~~----~~~----------~~~~~~~~G~~i~v~v~~~d~~--~~~ 64 (70)
T cd05698 2 LKTHGTIVKVKPNGCIVSFYN-NVKGFLPKSELSEA----FIK----------DPEEHFRVGQVVKVKVLSCDPE--QQR 64 (70)
T ss_pred CEEEEEEEEEecCcEEEEECC-CCEEEEEHHHcChh----hcC----------CHHHcccCCCEEEEEEEEEcCC--CCE
Confidence 368999999999999999976 79999999999764 211 2346799999999999999976 789
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.||+
T Consensus 65 i~ls~ 69 (70)
T cd05698 65 LLLSC 69 (70)
T ss_pred EEEEe
Confidence 99986
No 22
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.53 E-value=5.1e-07 Score=69.75 Aligned_cols=69 Identities=10% Similarity=0.226 Sum_probs=59.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.+.|.|+++.++|++|.+.+.+++|++|.+++.++ +.. +....|++||.|+|+|.++|.+ +++
T Consensus 4 ~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~----~~~----------~~~~~~~~Gd~v~v~i~~vd~~--~~~ 67 (77)
T cd05708 4 QKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDN----RVA----------DASKLFRVGDKVRAKVLKIDAE--KKR 67 (77)
T ss_pred CEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCC----ccC----------CHhHeecCCCEEEEEEEEEeCC--CCE
Confidence 578999999999999999987789999999998764 111 2457899999999999999976 889
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.|++
T Consensus 68 i~ls~ 72 (77)
T cd05708 68 ISLGL 72 (77)
T ss_pred EEEEE
Confidence 99886
No 23
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=98.52 E-value=5.4e-07 Score=69.23 Aligned_cols=68 Identities=22% Similarity=0.331 Sum_probs=59.6
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.++|.|.++.++|++|.+. .|++|+|+.+++.+. +. ......|++||.|+|+|.++|.+ +++
T Consensus 6 ~iv~g~V~~v~~~g~~V~l~-~~~~g~ip~~~l~~~----~~----------~~~~~~~~~G~~v~v~v~~vd~~--~~~ 68 (74)
T PF00575_consen 6 DIVEGKVTSVEDFGVFVDLG-NGIEGFIPISELSDD----RI----------DDPSEVYKIGQTVRVKVIKVDKE--KGR 68 (74)
T ss_dssp SEEEEEEEEEETTEEEEEES-TSSEEEEEGGGSSSS----EE----------SSSHGTCETTCEEEEEEEEEETT--TTE
T ss_pred CEEEEEEEEEECCEEEEEEC-CcEEEEEEeehhcCc----cc----------cccccccCCCCEEEEEEEEEECC--CCe
Confidence 68899999999999999998 699999999999864 11 24567899999999999999986 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.||+
T Consensus 69 i~lS~ 73 (74)
T PF00575_consen 69 IRLSL 73 (74)
T ss_dssp EEEES
T ss_pred EEEEE
Confidence 99985
No 24
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=98.51 E-value=6.9e-07 Score=69.68 Aligned_cols=68 Identities=15% Similarity=0.174 Sum_probs=56.4
Q ss_pred eEEEEEEEEEEcCeEEEEEeCC--ceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKF--GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR 431 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~--gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~ 431 (439)
+.++|.|+++.++|+||.+.+. |.+|++|.+++.+. ++ + .+....|++||.|+|+|.++| +
T Consensus 2 ~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~---~~--------~--~~~~~~~~~Gd~v~v~v~~vd----~ 64 (79)
T cd05684 2 KIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFE---GR--------V--ANPSDVVKRGQKVKVKVISIQ----N 64 (79)
T ss_pred CEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCC---CC--------c--CChhheeCCCCEEEEEEEEEe----C
Confidence 4689999999999999999864 89999999998765 22 1 134578999999999999998 5
Q ss_pred CceeEEe
Q 013634 432 PKLQLTL 438 (439)
Q Consensus 432 ~~i~l~l 438 (439)
+++.||+
T Consensus 65 ~~i~~s~ 71 (79)
T cd05684 65 GKISLSM 71 (79)
T ss_pred CEEEEEE
Confidence 7888876
No 25
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.50 E-value=3.4e-07 Score=72.18 Aligned_cols=68 Identities=16% Similarity=0.244 Sum_probs=59.1
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..++|.|.++.++|++|.+.. |++|++|.++++++ +. .+....|++||.|+|+|..+|.. +.+
T Consensus 16 ~i~~g~V~~v~~~G~fv~l~~-~~~g~v~~~el~~~----~~----------~~~~~~~~~Gd~v~vkV~~id~~--~~~ 78 (83)
T cd04461 16 MVVHGYVRNITPYGVFVEFLG-GLTGLAPKSYISDE----FV----------TDPSFGFKKGQSVTAKVTSVDEE--KQR 78 (83)
T ss_pred CEEEEEEEEEeeceEEEEcCC-CCEEEEEHHHCCcc----cc----------cCHHHhcCCCCEEEEEEEEEcCC--CCE
Confidence 789999999999999999976 89999999999765 11 13467899999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.|||
T Consensus 79 i~lsl 83 (83)
T cd04461 79 FLLSL 83 (83)
T ss_pred EEEeC
Confidence 99986
No 26
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=98.50 E-value=1e-07 Score=78.50 Aligned_cols=67 Identities=19% Similarity=0.247 Sum_probs=57.9
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
...+|.|++|.++|+||.|+. |-.|+||+++..+. |.. +.+..+++||.|.|+|.++|. +.+
T Consensus 7 ~~l~GkItgI~~yGAFV~l~~-g~tGLVHISEIa~~----fVk----------dI~d~L~vG~eV~vKVl~ide---~GK 68 (129)
T COG1098 7 SKLKGKITGITPYGAFVELEG-GKTGLVHISEIADG----FVK----------DIHDHLKVGQEVKVKVLDIDE---NGK 68 (129)
T ss_pred ceEEEEEEeeEecceEEEecC-CCcceEEehHhhhh----hHH----------hHHHHhcCCCEEEEEEEeecc---CCC
Confidence 568999999999999999987 89999999998875 322 357889999999999999995 688
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.|||
T Consensus 69 isLSI 73 (129)
T COG1098 69 ISLSI 73 (129)
T ss_pred cceeh
Confidence 88886
No 27
>PRK08582 hypothetical protein; Provisional
Probab=98.49 E-value=6.7e-07 Score=77.48 Aligned_cols=67 Identities=22% Similarity=0.309 Sum_probs=57.2
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..++|+|++|.++|+||.|++ +++|+||++++.+. |.. +....|++||.|+|+|.++|. .++
T Consensus 7 ~iv~G~V~~I~~fG~fV~L~~-~~~GlVhiSels~~----~v~----------~~~~~l~vGD~VkvkV~~id~---~gk 68 (139)
T PRK08582 7 SKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADN----YVK----------DINDHLKVGDEVEVKVLNVED---DGK 68 (139)
T ss_pred CEEEEEEEEEECCeEEEEECC-CCEEEEEeeccCcc----ccc----------ccccccCCCCEEEEEEEEECC---CCc
Confidence 689999999999999999986 89999999999765 211 234779999999999999985 478
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.|++
T Consensus 69 I~LSl 73 (139)
T PRK08582 69 IGLSI 73 (139)
T ss_pred EEEEE
Confidence 99886
No 28
>PRK07252 hypothetical protein; Provisional
Probab=98.49 E-value=6e-07 Score=75.74 Aligned_cols=68 Identities=16% Similarity=0.133 Sum_probs=58.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.+.|.|++|.++|++|.++. +++|++|++++.++ ++ .+....|++||.|+|+|.++|.+ +++
T Consensus 5 ~iv~G~V~~V~~~G~fVei~~-~~~GllhiseLs~~---~~-----------~~~~~~~~vGD~V~VkI~~iD~~--~~r 67 (120)
T PRK07252 5 DKLKGTITGIKPYGAFVALEN-GTTGLIHISEIKTG---FI-----------DNIHQLLKVGEEVLVQVVDFDEY--TGK 67 (120)
T ss_pred CEEEEEEEEEeCcEEEEEECC-CCEEEEEHHHcCCc---cc-----------cChhhccCCCCEEEEEEEEEeCC--CCE
Confidence 678999999999999999976 79999999999765 12 12356799999999999999976 789
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 68 i~lSl 72 (120)
T PRK07252 68 ASLSL 72 (120)
T ss_pred EEEEE
Confidence 98886
No 29
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.48 E-value=2.8e-07 Score=89.75 Aligned_cols=77 Identities=16% Similarity=0.217 Sum_probs=64.3
Q ss_pred HHHHhc-CC---eEEEEEEEEEEcCeEEEEEeCC-ceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEE
Q 013634 346 LIYFRK-RP---TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI 420 (439)
Q Consensus 346 ~~~l~~-~~---~~~~g~V~~v~~~g~~V~l~~~-gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V 420 (439)
|+|..+ .| ....|.|+.|.++|+||.|.+| |++|+||++++++. |. ++..+.+++||.|.|
T Consensus 7 cr~~~~~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~---ri-----------~~i~d~vkvGd~v~v 72 (319)
T PTZ00248 7 CRFYEQKFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKR---RI-----------RSINKLIRVGRHEVV 72 (319)
T ss_pred ccchhhhCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhccc---cc-----------CCHHHhcCCCCEEEE
Confidence 555544 34 6789999999999999999877 99999999999764 11 245678999999999
Q ss_pred EEEEecCCCCCCceeEEe
Q 013634 421 HMEVVEPQPNRPKLQLTL 438 (439)
Q Consensus 421 ~v~~vd~~~~~~~i~l~l 438 (439)
+|.+||.+ +++|.||+
T Consensus 73 kVl~VD~e--kg~IdLS~ 88 (319)
T PTZ00248 73 VVLRVDKE--KGYIDLSK 88 (319)
T ss_pred EEEEEeCC--CCEEEEEe
Confidence 99999976 89999986
No 30
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=98.46 E-value=9.6e-07 Score=68.16 Aligned_cols=69 Identities=14% Similarity=0.132 Sum_probs=58.2
Q ss_pred eEEEEEEEEEEcCeEEEEEeCC-ceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~-gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
..+.|.|+++.++|++|.+.++ |++|++|.+++.+++ + .+....|++||.|+|+|.++|.. ++
T Consensus 5 ~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~---~-----------~~~~~~~~~Gd~v~vkv~~~d~~--~~ 68 (76)
T cd04452 5 ELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRR---I-----------RSIRKLVKVGRKEVVKVIRVDKE--KG 68 (76)
T ss_pred CEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcc---c-----------CCHHHeeCCCCEEEEEEEEEECC--CC
Confidence 5789999999999999999765 699999999987651 1 12367799999999999999976 78
Q ss_pred ceeEEe
Q 013634 433 KLQLTL 438 (439)
Q Consensus 433 ~i~l~l 438 (439)
++.||+
T Consensus 69 ~i~ls~ 74 (76)
T cd04452 69 YIDLSK 74 (76)
T ss_pred EEEEEE
Confidence 899886
No 31
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.43 E-value=9e-07 Score=66.60 Aligned_cols=64 Identities=23% Similarity=0.286 Sum_probs=53.9
Q ss_pred EEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCce
Q 013634 355 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKL 434 (439)
Q Consensus 355 ~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i 434 (439)
..+|.|+.+.++|++|.+.+ |++|+++.+++.... .....|++||.|+++|..+|++ +++|
T Consensus 3 ~V~g~V~~i~~~G~~v~l~~-~v~g~v~~~~l~~~~----------------~~~~~~~~G~~i~~kVi~id~~--~~~i 63 (66)
T cd05695 3 LVNARVKKVLSNGLILDFLS-SFTGTVDFLHLDPEK----------------SSKSTYKEGQKVRARILYVDPS--TKVV 63 (66)
T ss_pred EEEEEEEEEeCCcEEEEEcC-CceEEEEHHHcCCcc----------------CcccCcCCCCEEEEEEEEEeCC--CCEE
Confidence 56899999999999999987 899999999886431 1146799999999999999986 7888
Q ss_pred eEE
Q 013634 435 QLT 437 (439)
Q Consensus 435 ~l~ 437 (439)
.||
T Consensus 64 ~LS 66 (66)
T cd05695 64 GLS 66 (66)
T ss_pred ecC
Confidence 775
No 32
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=98.41 E-value=6.3e-07 Score=67.27 Aligned_cols=67 Identities=13% Similarity=0.150 Sum_probs=55.6
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|+++.++|++|.+.. +.+|++|.+++.++ ++. +....|++||.|+|+|.++|.+ +++
T Consensus 2 ~~~~g~V~~i~~~G~fv~l~~-~~~g~~~~~~l~~~---~~~-----------~~~~~~~~Gd~v~v~i~~vd~~--~~~ 64 (68)
T cd05685 2 MVLEGVVTNVTDFGAFVDIGV-KQDGLIHISKMADR---FVS-----------HPSDVVSVGDIVEVKVISIDEE--RGR 64 (68)
T ss_pred CEEEEEEEEEecccEEEEcCC-CCEEEEEHHHCCCc---ccc-----------CHHHhcCCCCEEEEEEEEEECC--CCE
Confidence 368999999999999999976 79999999988764 121 2356799999999999999975 788
Q ss_pred eeEE
Q 013634 434 LQLT 437 (439)
Q Consensus 434 i~l~ 437 (439)
+.||
T Consensus 65 i~ls 68 (68)
T cd05685 65 ISLS 68 (68)
T ss_pred EecC
Confidence 8775
No 33
>PHA02945 interferon resistance protein; Provisional
Probab=98.35 E-value=3.3e-06 Score=65.64 Aligned_cols=66 Identities=8% Similarity=0.047 Sum_probs=55.6
Q ss_pred eEEEEEEEEEEcCeEEEEEeCC-ceEEEEEcccC--CCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPR--GQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPN 430 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~-gveg~v~~~~l--~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~ 430 (439)
+..-|+|.. .++|++|.|++| |+||++|.+.. ... | + +.+..+ .|++|.++|..||+.
T Consensus 13 elvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~---w----------v--K~rd~l-~GqkvV~KVirVd~~-- 73 (88)
T PHA02945 13 DVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNR---Y----------F--KYRDKL-VGKTVKVKVIRVDYT-- 73 (88)
T ss_pred cEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccc---e----------E--eeeeEe-cCCEEEEEEEEECCC--
Confidence 567899999 999999999999 99999999855 432 2 2 235666 999999999999976
Q ss_pred CCceeEEe
Q 013634 431 RPKLQLTL 438 (439)
Q Consensus 431 ~~~i~l~l 438 (439)
|..|+|||
T Consensus 74 kg~IDlSl 81 (88)
T PHA02945 74 KGYIDVNY 81 (88)
T ss_pred CCEEEeEe
Confidence 99999997
No 34
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=98.35 E-value=2.9e-06 Score=76.97 Aligned_cols=86 Identities=14% Similarity=0.205 Sum_probs=69.3
Q ss_pred HHhcCC-eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 348 YFRKRP-TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 348 ~l~~~~-~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
+++... +.++|+|+++.++|++|.+. .++|.++.+++.++ .+.+|+....+.+++.+..|++||.|+|+|.+++
T Consensus 76 ~f~p~~gEvv~G~V~~v~~~GifV~lg--~~~gi~~~~~l~~~---~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~ 150 (179)
T TIGR00448 76 VFKPELGEIVEGEVIEIVEFGAFVSLG--PFDGLFHVSQVTDD---YCYYDPKESALIGKETKKVLDEGDKVRARIVALS 150 (179)
T ss_pred EEeccCCCEEEEEEEEEEeeEEEEEeC--CceEEEEcHHhCCC---ceEEccccceEEEccCCeEEcCCCEEEEEEEEEE
Confidence 344444 78999999999999999994 49999999998766 4677877778877777899999999999999998
Q ss_pred CCC---CCCceeEEe
Q 013634 427 PQP---NRPKLQLTL 438 (439)
Q Consensus 427 ~~~---~~~~i~l~l 438 (439)
... ...+|.+++
T Consensus 151 ~~~~~~~~~~I~lt~ 165 (179)
T TIGR00448 151 LKDRRPEGSKIGLTM 165 (179)
T ss_pred ccCCCCCcceEEEEe
Confidence 432 245677664
No 35
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.33 E-value=1.4e-06 Score=66.79 Aligned_cols=66 Identities=20% Similarity=0.187 Sum_probs=55.1
Q ss_pred eEEEEEEEEEEc-CeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRS-NGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~-~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
..+.|.|.++.+ +|++|.++. |.+|++|++++.++ |.. +....|++||.|+|+|.+++ +.
T Consensus 5 ~iv~G~V~~i~~~~g~~v~l~~-~~~Glvhis~~s~~----~~~----------~~~~~~~~Gd~v~~kV~~~~----~~ 65 (72)
T cd05704 5 AVTLGMVTKVIPHSGLTVQLPF-GKTGLVSIFHLSDS----YTE----------NPLEGFKPGKIVRCCILSKK----DG 65 (72)
T ss_pred CEEEEEEEEeeCCcEEEEECCC-CCEEEEEHHHhcCc----ccC----------CHHHhCCCCCEEEEEEEEec----CC
Confidence 678999999986 899999986 99999999998775 211 23467899999999999987 47
Q ss_pred ceeEEe
Q 013634 433 KLQLTL 438 (439)
Q Consensus 433 ~i~l~l 438 (439)
+|.||+
T Consensus 66 ~i~LSl 71 (72)
T cd05704 66 KYQLSL 71 (72)
T ss_pred EEEEEe
Confidence 899987
No 36
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.29 E-value=3.3e-06 Score=64.49 Aligned_cols=68 Identities=16% Similarity=0.283 Sum_probs=57.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|+++.++|++|.+.+ +++|++|.+++.++ +. .+....|++||.|+++|..+|.. +++
T Consensus 2 ~~v~g~V~~v~~~g~~v~l~~-~~~g~i~~~~~~~~----~~----------~~~~~~~~~Gd~v~~~v~~~d~~--~~~ 64 (73)
T cd05691 2 SIVTGKVTEVDAKGATVKLGD-GVEGFLRAAELSRD----RV----------EDATERFKVGDEVEAKITNVDRK--NRK 64 (73)
T ss_pred CEEEEEEEEEECCeEEEEeCC-CCEEEEEHHHCCCc----cc----------cCHHHccCCCCEEEEEEEEEeCC--CCE
Confidence 357899999999999999976 79999999998765 11 13456799999999999999975 788
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.|++
T Consensus 65 i~ls~ 69 (73)
T cd05691 65 ISLSI 69 (73)
T ss_pred EEEEE
Confidence 88886
No 37
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=98.23 E-value=5.3e-06 Score=62.31 Aligned_cols=67 Identities=21% Similarity=0.238 Sum_probs=55.2
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.+.|.|+++.++|++|.++. +.+|+++.+++.++ +. ....+.|++||.|+|+|.++|. ..+
T Consensus 2 ~~~~g~V~~v~~~G~~v~l~~-~~~g~l~~~~l~~~----~~----------~~~~~~~~~Gd~v~v~v~~~d~---~~~ 63 (68)
T cd04472 2 KIYEGKVVKIKDFGAFVEILP-GKDGLVHISELSDE----RV----------EKVEDVLKVGDEVKVKVIEVDD---RGR 63 (68)
T ss_pred CEEEEEEEEEEEeEEEEEeCC-CCEEEEEhHHcCCc----cc----------cCHHHccCCCCEEEEEEEEECC---CCc
Confidence 468999999999999999976 79999999988764 11 1235689999999999999984 678
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.||.
T Consensus 64 i~ls~ 68 (68)
T cd04472 64 ISLSR 68 (68)
T ss_pred EEeeC
Confidence 88873
No 38
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.22 E-value=5.2e-06 Score=62.33 Aligned_cols=67 Identities=18% Similarity=0.272 Sum_probs=55.5
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.+.|.|.++.++|++|.+.. +.+|++|.+++.++ +.. +....|++||.|+|+|..++. +++
T Consensus 2 ~~~~g~V~~i~~~g~~v~i~~-~~~g~l~~~~l~~~----~~~----------~~~~~~~~Gd~v~v~v~~~~~---~~~ 63 (69)
T cd05692 2 SVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHK----RVK----------DVKDVLKEGDKVKVKVLSIDA---RGR 63 (69)
T ss_pred CEEEEEEEEEEeeeEEEEECC-CCEEEEEhHHcCCc----ccC----------CHHHccCCCCEEEEEEEEECC---CCc
Confidence 468999999999999999976 89999999988764 111 234679999999999999984 578
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.|++
T Consensus 64 i~ls~ 68 (69)
T cd05692 64 ISLSI 68 (69)
T ss_pred EEEEE
Confidence 88876
No 39
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.21 E-value=5.7e-06 Score=62.09 Aligned_cols=66 Identities=17% Similarity=0.222 Sum_probs=54.3
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|+++.++|++|.+. +.+|++|.+++.+. + . .+....|++||.|+|+|.++|.. +++
T Consensus 3 ~~~~g~V~~v~~~g~~v~l~--~~~g~l~~~e~~~~----~-~---------~~~~~~~~~Gd~v~v~i~~vd~~--~~~ 64 (68)
T cd05688 3 DVVEGTVKSITDFGAFVDLG--GVDGLLHISDMSWG----R-V---------KHPSEVVNVGDEVEVKVLKIDKE--RKR 64 (68)
T ss_pred CEEEEEEEEEEeeeEEEEEC--CeEEEEEhHHCCCc----c-c---------cCHhHEECCCCEEEEEEEEEECC--CCE
Confidence 46899999999999999995 69999999988632 1 1 13457799999999999999975 788
Q ss_pred eeEE
Q 013634 434 LQLT 437 (439)
Q Consensus 434 i~l~ 437 (439)
+.||
T Consensus 65 i~ls 68 (68)
T cd05688 65 ISLG 68 (68)
T ss_pred EecC
Confidence 8775
No 40
>PRK05807 hypothetical protein; Provisional
Probab=98.20 E-value=7.8e-06 Score=70.63 Aligned_cols=66 Identities=20% Similarity=0.266 Sum_probs=55.7
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.++|.|+++.++|+||.| + |.+|+||++++.+. |.. +....|++||.|+|+|..+|. ..+
T Consensus 7 ~vv~G~Vt~i~~~GafV~L-~-~~~Glvhiseis~~----~v~----------~~~~~~kvGd~V~VkV~~id~---~gk 67 (136)
T PRK05807 7 SILEGTVVNITNFGAFVEV-E-GKTGLVHISEVADT----YVK----------DIREHLKEQDKVKVKVISIDD---NGK 67 (136)
T ss_pred CEEEEEEEEEECCeEEEEE-C-CEEEEEEhhhcccc----ccc----------CccccCCCCCEEEEEEEEECC---CCc
Confidence 6899999999999999999 4 78999999998765 221 234679999999999999985 588
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 68 I~LSl 72 (136)
T PRK05807 68 ISLSI 72 (136)
T ss_pred EEEEE
Confidence 88886
No 41
>PRK08059 general stress protein 13; Validated
Probab=98.18 E-value=5.9e-06 Score=70.23 Aligned_cols=68 Identities=18% Similarity=0.244 Sum_probs=57.9
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|+++.++|++|.+.. +++|++|+++++.+ +. .+....|++||.|+|+|.++|.. +++
T Consensus 9 ~iv~G~V~~i~~~G~fV~i~~-~~~Gli~~sel~~~----~~----------~~~~~~~~vGD~I~vkI~~id~~--~~~ 71 (123)
T PRK08059 9 SVVTGKVTGIQPYGAFVALDE-ETQGLVHISEITHG----FV----------KDIHDFLSVGDEVKVKVLSVDEE--KGK 71 (123)
T ss_pred CEEEEEEEEEecceEEEEECC-CCEEEEEHHHCCcc----cc----------cCHHHcCCCCCEEEEEEEEEECC--CCe
Confidence 689999999999999999976 89999999998764 21 13356799999999999999965 789
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.||+
T Consensus 72 i~lsl 76 (123)
T PRK08059 72 ISLSI 76 (123)
T ss_pred EEEEE
Confidence 99886
No 42
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=98.14 E-value=1.5e-05 Score=61.85 Aligned_cols=60 Identities=13% Similarity=0.202 Sum_probs=52.2
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.++|.|.++.++|++|.+.+ +.+|++|.+++. ..|++||.++|+|.++ .+ +++
T Consensus 18 ~~~~g~V~~i~~~G~fV~l~~-~~~Glv~~se~~----------------------~~~~iGd~v~v~I~~i-~e--~~~ 71 (77)
T cd04473 18 KLYKGKVNGVAKYGVFVDLND-HVRGLIHRSNLL----------------------RDYEVGDEVIVQVTDI-PE--NGN 71 (77)
T ss_pred CEEEEEEEeEecceEEEEECC-CcEEEEEchhcc----------------------CcCCCCCEEEEEEEEE-CC--CCc
Confidence 789999999999999999987 799999987542 3489999999999998 54 899
Q ss_pred eeEEeC
Q 013634 434 LQLTLI 439 (439)
Q Consensus 434 i~l~l~ 439 (439)
|.|++.
T Consensus 72 i~l~~~ 77 (77)
T cd04473 72 IDLIPV 77 (77)
T ss_pred EEEEEC
Confidence 999864
No 43
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.14 E-value=1.4e-05 Score=61.46 Aligned_cols=63 Identities=16% Similarity=0.124 Sum_probs=54.4
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
....|.|.++.++|++|.+..-|++|+++.+++++. ..+++||.+.++|.++|.+ +++
T Consensus 6 ~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~~~~--------------------~~~~~Gq~v~~~V~~vd~~--~~~ 63 (74)
T cd05694 6 MVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF--------------------SKLKVGQLLLCVVEKVKDD--GRV 63 (74)
T ss_pred CEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHCCcc--------------------cccCCCCEEEEEEEEEECC--CCE
Confidence 468999999999999999953489999999887531 5689999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.||+
T Consensus 64 v~ls~ 68 (74)
T cd05694 64 VSLSA 68 (74)
T ss_pred EEEEE
Confidence 99986
No 44
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.14 E-value=4.3e-06 Score=86.69 Aligned_cols=68 Identities=21% Similarity=0.306 Sum_probs=59.8
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
....|+|+.+.++|+||++.+ |+||+||++++++.. . ......+++||.|.|+|.+||++ +||
T Consensus 279 ~~v~G~Vt~i~~~GafVei~~-GvEGlvhvSEisw~~-------------~-~~P~evv~~Gq~V~V~Vl~id~e--~rR 341 (541)
T COG0539 279 DKVEGKVTNLTDYGAFVEIEE-GVEGLVHVSEISWTK-------------K-NVPSEVVKVGQEVEVKVLDIDPE--RRR 341 (541)
T ss_pred CEEEEEEEEeecCcEEEEecC-Cccceeechhhcccc-------------c-CCHHHhcccCCEEEEEEEeeCch--hce
Confidence 788999999999999999976 999999999998651 1 12567899999999999999987 999
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.|+|
T Consensus 342 IsL~i 346 (541)
T COG0539 342 ISLGL 346 (541)
T ss_pred EEeee
Confidence 99986
No 45
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.13 E-value=7.5e-06 Score=78.43 Aligned_cols=69 Identities=16% Similarity=0.168 Sum_probs=59.5
Q ss_pred eEEEEEEEEEEcCeEEEEEeCC-ceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKF-GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~-gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
+.+.|.|+++.++|++|.|.++ |++|++|++++.++ ++. +....+++||.|.|+|.++|.. ++
T Consensus 10 diV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~---~i~-----------~i~~~~kvGd~V~vkVi~VD~~--k~ 73 (262)
T PRK03987 10 ELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASG---WVK-----------NIRDHVKEGQKVVCKVIRVDPR--KG 73 (262)
T ss_pred CEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcc---ccc-----------CHHHhCCCCCEEEEEEEEEecc--cC
Confidence 6789999999999999999987 89999999998765 221 2356789999999999999976 88
Q ss_pred ceeEEe
Q 013634 433 KLQLTL 438 (439)
Q Consensus 433 ~i~l~l 438 (439)
+|.||+
T Consensus 74 ~I~LSl 79 (262)
T PRK03987 74 HIDLSL 79 (262)
T ss_pred eEEEEE
Confidence 999986
No 46
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.11 E-value=1.1e-05 Score=88.23 Aligned_cols=75 Identities=15% Similarity=0.147 Sum_probs=59.8
Q ss_pred HHHHhcCC-eEEE-EEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEE
Q 013634 346 LIYFRKRP-TDTE-ARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHME 423 (439)
Q Consensus 346 ~~~l~~~~-~~~~-g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~ 423 (439)
..++.... +.|+ |.|++|.++|+||+|.. |+||+||++++.++ ++. +....|++||.|+|+|.
T Consensus 746 ~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~-g~EGLVHISeLs~~---rv~-----------~~~dv~kvGD~V~VkVi 810 (891)
T PLN00207 746 SLTMVPTVGDIYRNCEIKSIAPYGAFVEIAP-GREGLCHISELSSN---WLA-----------KPEDAFKVGDRIDVKLI 810 (891)
T ss_pred HHhcCcCCCcEEECcEEEEEeccEEEEEeCC-CCEEEEEhhhcCCc---ccc-----------CHHHhcCCCCEEEEEEE
Confidence 33443334 7885 69999999999999975 89999999999865 221 23578999999999999
Q ss_pred EecCCCCCCceeEEe
Q 013634 424 VVEPQPNRPKLQLTL 438 (439)
Q Consensus 424 ~vd~~~~~~~i~l~l 438 (439)
++|. +++|.|++
T Consensus 811 ~ID~---~grI~LSl 822 (891)
T PLN00207 811 EVND---KGQLRLSR 822 (891)
T ss_pred EECC---CCcEEEEE
Confidence 9995 67899886
No 47
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=98.08 E-value=1.9e-05 Score=70.22 Aligned_cols=71 Identities=15% Similarity=0.144 Sum_probs=64.6
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQP 429 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~ 429 (439)
+..+|.|+.+.++|+||.+- -++|++|.+.+.++ .+.+|+..-.++++++++.+++||.|+++|..++...
T Consensus 83 EVV~GeVv~~~~~G~fV~ig--p~dglvh~sqi~dd---~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~~ 153 (183)
T COG1095 83 EVVEGEVVEVVEFGAFVRIG--PLDGLVHVSQIMDD---YIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKS 153 (183)
T ss_pred cEEEEEEEEEeecceEEEec--cccccccHhhccCc---ccccCcccceeeecccceEEecCCEEEEEEEEEeccc
Confidence 67899999999999999997 48999999999988 5888998888998888999999999999999988764
No 48
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.05 E-value=1.8e-05 Score=60.00 Aligned_cols=68 Identities=15% Similarity=0.137 Sum_probs=56.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|.++.++|++|.+.. +.+|+++.+++.+. +. .+....|++||.++++|.+++.. .++
T Consensus 2 ~iv~g~V~~i~~~~~~v~l~~-~~~g~l~~~e~~~~----~~----------~~~~~~~~~Gd~i~~~i~~~~~~--~~~ 64 (70)
T cd05687 2 DIVKGTVVSVDDDEVLVDIGY-KSEGIIPISEFSDD----PI----------ENGEDEVKVGDEVEVYVLRVEDE--EGN 64 (70)
T ss_pred CEEEEEEEEEeCCEEEEEeCC-CceEEEEHHHhCcc----cc----------CCHhHcCCCCCEEEEEEEEEECC--CCe
Confidence 357899999999999999965 89999999988653 11 12356799999999999999964 688
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 65 i~lS~ 69 (70)
T cd05687 65 VVLSK 69 (70)
T ss_pred EEEEe
Confidence 99986
No 49
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.05 E-value=1.8e-05 Score=82.24 Aligned_cols=67 Identities=18% Similarity=0.256 Sum_probs=58.9
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+..+|+|.+++++|+||.|. |++|+||++++++.. + .+....+++||+|+|+|.++|.+ +.+
T Consensus 194 ~vV~G~V~~It~~GafVdig--GvdGLlHiseiS~~r------------v--~~P~~vvkvGd~VkvkVi~~D~e--~~R 255 (541)
T COG0539 194 EVVEGVVKNITDYGAFVDIG--GVDGLLHISEISWKR------------V--DHPSEVVKVGDEVKVKVISLDEE--RGR 255 (541)
T ss_pred ceEEEEEEEeecCcEEEEec--CeeeEEehhhccccc------------c--CCHHHhcccCCEEEEEEEEEccC--CCe
Confidence 78899999999999999996 799999999998651 1 24578999999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.|||
T Consensus 256 VsLSl 260 (541)
T COG0539 256 VSLSL 260 (541)
T ss_pred EEEEe
Confidence 99986
No 50
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.05 E-value=2.2e-05 Score=59.00 Aligned_cols=68 Identities=21% Similarity=0.285 Sum_probs=57.3
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.+.|.|.++.++|++|.+.. +++|+++.+++.+. + ..+....|++||.|+|+|..++.. +++
T Consensus 4 ~~v~g~V~~v~~~g~~v~i~~-~~~g~l~~~~~~~~----~----------~~~~~~~~~~G~~v~~~V~~~~~~--~~~ 66 (72)
T smart00316 4 DVVEGTVTEITPFGAFVDLGN-GVEGLIPISELSDK----R----------VKDPEEVLKVGDEVKVKVLSVDEE--KGR 66 (72)
T ss_pred CEEEEEEEEEEccEEEEEeCC-CCEEEEEHHHCCcc----c----------cCCHHHeecCCCEEEEEEEEEeCC--CCE
Confidence 578999999999999999975 89999999988764 1 123456799999999999999965 799
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.|++
T Consensus 67 i~ls~ 71 (72)
T smart00316 67 IILSL 71 (72)
T ss_pred EEEEe
Confidence 99886
No 51
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=98.02 E-value=5.6e-05 Score=69.12 Aligned_cols=80 Identities=16% Similarity=0.222 Sum_probs=66.5
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCC--
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNR-- 431 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~-- 431 (439)
+.++|.|+++.++|++|.+. .++|+++.+.+.++ .+.+|+....+++++....|++||.|+|+|.+++....+
T Consensus 83 EVv~g~V~~v~~~Gi~V~lg--~~~g~v~~~~l~~~---~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~~~~ 157 (187)
T PRK08563 83 EVVEGEVVEVVEFGAFVRIG--PVDGLLHISQIMDD---YISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKERRPR 157 (187)
T ss_pred CEEEEEEEEEEccEEEEEEe--CceEEEEcHHcCCC---ceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccCCCC
Confidence 78999999999999999996 48999999998766 467777777787777788999999999999999975332
Q ss_pred -CceeEEe
Q 013634 432 -PKLQLTL 438 (439)
Q Consensus 432 -~~i~l~l 438 (439)
.+|.+|+
T Consensus 158 ~~~I~ls~ 165 (187)
T PRK08563 158 GSKIGLTM 165 (187)
T ss_pred CCEEEEEe
Confidence 3666654
No 52
>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=97.97 E-value=2.4e-05 Score=57.57 Aligned_cols=64 Identities=23% Similarity=0.381 Sum_probs=52.7
Q ss_pred EEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCceeE
Q 013634 357 EARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQL 436 (439)
Q Consensus 357 ~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l 436 (439)
.|.|.++.++|++|.+.. |.+|+++.+++.+.+ + .+....|++||.|+|+|.++|.. ++++.|
T Consensus 2 ~g~V~~v~~~g~~v~l~~-~~~g~~~~~~~~~~~---~-----------~~~~~~~~~G~~v~~~v~~~d~~--~~~i~l 64 (65)
T cd00164 2 TGKVVSITKFGVFVELED-GVEGLVHISELSDKF---V-----------KDPSEVFKVGDEVEVKVLEVDPE--KGRISL 64 (65)
T ss_pred EEEEEEEEeeeEEEEecC-CCEEEEEHHHCCCcc---c-----------cCHhhEeCCCCEEEEEEEEEcCC--cCEEec
Confidence 699999999999999975 899999999887641 1 13457899999999999999965 677766
Q ss_pred E
Q 013634 437 T 437 (439)
Q Consensus 437 ~ 437 (439)
|
T Consensus 65 s 65 (65)
T cd00164 65 S 65 (65)
T ss_pred C
Confidence 4
No 53
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.97 E-value=2.8e-05 Score=80.83 Aligned_cols=68 Identities=21% Similarity=0.256 Sum_probs=58.9
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|+++.++|+||.+++ |++|++|.+++.+. .+ ......|++||.|+|+|.++|.+ +++
T Consensus 295 ~vv~G~V~~I~~fGvFVeL~~-gieGLvh~SeLs~~---~v-----------~~~~~~~kvGd~V~VkIi~ID~e--~rr 357 (486)
T PRK07899 295 QIVPGKVTKLVPFGAFVRVEE-GIEGLVHISELAER---HV-----------EVPEQVVQVGDEVFVKVIDIDLE--RRR 357 (486)
T ss_pred CEEEEEEEEEeccEEEEEeCC-CcEEEEEHHHcCcc---cc-----------cCccceeCCCCEEEEEEEEEECC--CCE
Confidence 789999999999999999977 89999999998764 11 12357899999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 358 I~LSl 362 (486)
T PRK07899 358 ISLSL 362 (486)
T ss_pred EEEEE
Confidence 99987
No 54
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=97.88 E-value=6.2e-05 Score=56.57 Aligned_cols=65 Identities=14% Similarity=0.168 Sum_probs=51.8
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.++|.|..+.++|++|.+ + |++|+++.++++.. +.. +... .+||.++|+|.++|.. .++
T Consensus 2 ~iv~g~V~~v~~~G~~v~l-~-g~~gfip~s~~~~~----~~~----------~~~~--~vG~~i~~~i~~vd~~--~~~ 61 (67)
T cd04465 2 EIVEGKVTEKVKGGLIVDI-E-GVRAFLPASQVDLR----PVE----------DLDE--YVGKELKFKIIEIDRE--RNN 61 (67)
T ss_pred CEEEEEEEEEECCeEEEEE-C-CEEEEEEHHHCCCc----ccC----------ChHH--hCCCEEEEEEEEEeCC--CCE
Confidence 3579999999999999999 4 89999999988653 100 1111 3899999999999975 789
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||.
T Consensus 62 i~lS~ 66 (67)
T cd04465 62 IVLSR 66 (67)
T ss_pred EEEEc
Confidence 99885
No 55
>cd05693 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.82 E-value=2.7e-05 Score=63.63 Aligned_cols=84 Identities=17% Similarity=0.201 Sum_probs=58.8
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceee-----cCCeEEEEeeCCceEEeeCceEEEEEEEecCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYV-----DEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 428 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~-----d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~ 428 (439)
....|.|..+.++|++|.+|. |++|+++++++.+++..|-.- ..........+....|++||.|+++|.++|..
T Consensus 5 ~vV~G~V~~v~~~gl~v~L~~-g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~vGd~V~~kVi~~d~~ 83 (100)
T cd05693 5 MLVLGQVKEITKLDLVISLPN-GLTGYVPITNISDAYTERLEELDEESEEEDDEEELPDLEDLFSVGQLVRCKVVSLDKS 83 (100)
T ss_pred CEEEEEEEEEcCCCEEEECCC-CcEEEEEHHHhhHHHHHHHHHhhhhccccccccccCCHHHhccCCCEEEEEEEEccCC
Confidence 567999999999999999987 999999999987641000000 00000011112357799999999999999963
Q ss_pred C-CCCceeEEe
Q 013634 429 P-NRPKLQLTL 438 (439)
Q Consensus 429 ~-~~~~i~l~l 438 (439)
- ++++|.|||
T Consensus 84 ~~~~~~i~LSl 94 (100)
T cd05693 84 KSGKKRIELSL 94 (100)
T ss_pred cCCCcEEEEEe
Confidence 1 268999987
No 56
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.79 E-value=1.5e-05 Score=74.40 Aligned_cols=69 Identities=16% Similarity=0.112 Sum_probs=60.2
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCc-eEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFG-IEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~g-veg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
+..-|.|..|.++|++|.|.+|+ +||++|++.+... |. ++.+..++.|++|-++|.+||+. +.
T Consensus 13 EiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~---wV-----------knIrd~vkegqkvV~kVlrVd~~--rg 76 (269)
T COG1093 13 EIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASG---WV-----------KNIRDYVKEGQKVVAKVLRVDPK--RG 76 (269)
T ss_pred cEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHH---HH-----------HHHHHHhhcCCeEEEEEEEEcCC--CC
Confidence 56789999999999999999998 9999999998764 33 23467899999999999999986 99
Q ss_pred ceeEEe
Q 013634 433 KLQLTL 438 (439)
Q Consensus 433 ~i~l~l 438 (439)
.|+|||
T Consensus 77 ~IDLSl 82 (269)
T COG1093 77 HIDLSL 82 (269)
T ss_pred eEeeeh
Confidence 999997
No 57
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.75 E-value=8.4e-05 Score=82.23 Aligned_cols=71 Identities=20% Similarity=0.231 Sum_probs=59.6
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..++|.|+++.++|+||.|++ |++|++|++++.++ +..+ . .+..+.|++||.|+|+|.++|.. +++
T Consensus 754 ~iV~GkV~~v~~~GvFVeL~~-gVeGlI~~s~lsdd----~~~~------~-~~~~~~f~vGD~V~v~Vl~iD~~--~rk 819 (863)
T PRK12269 754 STVEGEVSSVTDFGIFVRVPG-GVEGLVRKQHLVEN----RDGD------P-GEALRKYAVGDRVKAVIVDMNVK--DRK 819 (863)
T ss_pred CEEEEEEEEEecCeEEEEcCC-CeEEEEEHHHcCCc----cccc------c-hhhccccCCCCEEEEEEEEEEcC--CCE
Confidence 789999999999999999988 99999999999875 2111 0 11246799999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 820 I~LSl 824 (863)
T PRK12269 820 VAFSV 824 (863)
T ss_pred EEEEE
Confidence 99987
No 58
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.74 E-value=0.00016 Score=75.30 Aligned_cols=67 Identities=21% Similarity=0.217 Sum_probs=57.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..++|+|+++.++|+||.|. |++|+||.+++++. .. .+....|++||.|+|+|..+|.. +++
T Consensus 210 ~iv~G~V~~i~~~G~FVdlg--gv~Glv~~Sels~~-----~v---------~~~~~~~kvGd~V~vkVl~iD~e--~~r 271 (486)
T PRK07899 210 QVRKGVVSSIVNFGAFVDLG--GVDGLVHVSELSWK-----HI---------DHPSEVVEVGQEVTVEVLDVDMD--RER 271 (486)
T ss_pred CEEEEEEEEEECCeEEEEEC--CEEEEEEHHHCCCc-----cc---------CCHHHhcCCCCEEEEEEEEEECC--CCE
Confidence 78999999999999999994 89999999998753 11 13356799999999999999976 789
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 272 I~LSl 276 (486)
T PRK07899 272 VSLSL 276 (486)
T ss_pred EEEEE
Confidence 98886
No 59
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.73 E-value=9.8e-05 Score=73.05 Aligned_cols=67 Identities=10% Similarity=0.212 Sum_probs=57.7
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..++|.|+++.++|+||.+. |++|++|.++++++ + . .+....|++||.|+|+|..+|.+ +++
T Consensus 198 ~vv~G~V~~I~~~G~fV~i~--gv~Gllhisels~~----~--~--------~~~~~~~~vGd~VkvkVl~iD~e--~~r 259 (318)
T PRK07400 198 EVVVGTVRGIKPYGAFIDIG--GVSGLLHISEISHE----H--I--------ETPHSVFNVNDEMKVMIIDLDAE--RGR 259 (318)
T ss_pred CEEEEEEEEEECCeEEEEEC--CEEEEEEHHHcccc----c--c--------cChhhccCCCCEEEEEEEEEeCC--CCE
Confidence 78999999999999999994 89999999999865 1 1 13467899999999999999976 889
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 260 I~LS~ 264 (318)
T PRK07400 260 ISLST 264 (318)
T ss_pred EEEEE
Confidence 99886
No 60
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.70 E-value=7.9e-05 Score=78.20 Aligned_cols=69 Identities=17% Similarity=0.296 Sum_probs=57.8
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|+++.++|+||.+.+ |++|+||++++++. .. + .+....|++||.|+|+|..+|.+ +++
T Consensus 294 ~~v~G~V~~v~~~G~fV~l~~-gv~Glvh~sels~~-----~~------~--~~~~~~~~~Gd~v~vkVl~iD~e--~~r 357 (491)
T PRK13806 294 DKVTGKVVRLAPFGAFVEILP-GIEGLVHVSEMSWT-----RR------V--NKPEDVVAPGDAVAVKIKDIDPA--KRR 357 (491)
T ss_pred CEEEEEEEEEeCceEEEEeCC-CcEEEEEHHHcCcc-----cc------c--CCHHHcCCCCCEEEEEEEEEEcc--CCE
Confidence 789999999999999999965 89999999988642 00 0 13456799999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 358 i~Ls~ 362 (491)
T PRK13806 358 ISLSL 362 (491)
T ss_pred EEEEE
Confidence 99986
No 61
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.69 E-value=8.7e-05 Score=77.88 Aligned_cols=68 Identities=16% Similarity=0.209 Sum_probs=58.4
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..++|.|+++.++|+||.+.+ |++|+||.+++.+.. . .+....+++||.|+|+|..+|.+ +++
T Consensus 381 ~~v~G~V~~i~~~G~FV~l~~-gv~Gli~~se~s~~~------~--------~~~~~~~~~Gd~v~~~V~~id~e--~~r 443 (491)
T PRK13806 381 TTVTGTVEKRAQFGLFVNLAP-GVTGLLPASVISRAG------K--------PATYEKLKPGDSVTLVVEEIDTA--KRK 443 (491)
T ss_pred CEEEEEEEEEecCceEEEcCC-CcEEEEEHHHcCccc------c--------cchhhcCCCCCEEEEEEEEEeCC--CCE
Confidence 789999999999999999976 999999999987541 0 13357789999999999999986 888
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.|++
T Consensus 444 i~Ls~ 448 (491)
T PRK13806 444 ISLAP 448 (491)
T ss_pred EEEEe
Confidence 99985
No 62
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.68 E-value=0.00014 Score=55.15 Aligned_cols=61 Identities=8% Similarity=0.132 Sum_probs=49.8
Q ss_pred EEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCC
Q 013634 355 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 428 (439)
Q Consensus 355 ~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~ 428 (439)
...|.|+.+.++|++|.++. |++|+++.+++.+. |.. ..+....|++||.|+++|.++|..
T Consensus 3 iV~g~V~~i~~~gi~v~l~~-~i~g~i~~~~i~~~----~~~--------~~~~~~~~~~Gd~i~~kVl~~d~~ 63 (70)
T cd05702 3 LVKAKVKSVKPTQLNVQLAD-NVHGRIHVSEVFDE----WPD--------GKNPLSKFKIGQKIKARVIGGHDA 63 (70)
T ss_pred EEEEEEEEEECCcEEEEeCC-CcEEEEEHHHhccc----ccc--------ccChhHhCCCCCEEEEEEEEEeCc
Confidence 57899999999999999986 99999999988754 210 013356789999999999999965
No 63
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.67 E-value=0.00032 Score=76.48 Aligned_cols=67 Identities=15% Similarity=0.169 Sum_probs=56.9
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.++|.|+++.++|+||.+.. |.+|++|++++.+.+ + .+....|++||.|+|+|.++|.. ++
T Consensus 623 ~v~~G~V~~I~~fGafVei~~-~~~GllhiSels~~~---v-----------~~~~~v~kvGD~V~VkV~~iD~~---gr 684 (693)
T PRK11824 623 EIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADER---V-----------EKVEDVLKEGDEVKVKVLEIDKR---GR 684 (693)
T ss_pred eEEEEEEEEEECCeEEEEECC-CCEEEEEeeeccCcc---c-----------cCccceeCCCCEEEEEEEEECCC---Cc
Confidence 789999999999999999976 899999999987541 1 13467899999999999999953 78
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 685 I~LS~ 689 (693)
T PRK11824 685 IRLSR 689 (693)
T ss_pred EEEEE
Confidence 88875
No 64
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=97.66 E-value=9.5e-05 Score=79.40 Aligned_cols=70 Identities=19% Similarity=0.148 Sum_probs=55.5
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.++|.|+++.++|+||.|.. |++|+||++++.+.. |+... .+....+++||.|+|+|.++|. +.|
T Consensus 649 ~i~~GkV~~I~dfGaFVel~~-G~eGLvHISeisdls--~~~rv--------~~~~dv~kvGd~V~VKVl~ID~---~gK 714 (719)
T TIGR02696 649 ERFLGTVVKTTAFGAFVSLLP-GKDGLLHISQIRKLA--GGKRV--------ENVEDVLSVGQKIQVEIADIDD---RGK 714 (719)
T ss_pred CEEEEEEEEEECceEEEEecC-CceEEEEhhhccccc--cccCc--------CCHHHcCCCCCEEEEEEEEECC---CCC
Confidence 789999999999999999975 899999999885320 12110 1346789999999999999993 678
Q ss_pred eeEE
Q 013634 434 LQLT 437 (439)
Q Consensus 434 i~l~ 437 (439)
|.|+
T Consensus 715 I~L~ 718 (719)
T TIGR02696 715 LSLV 718 (719)
T ss_pred eeec
Confidence 8775
No 65
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.63 E-value=0.00011 Score=81.39 Aligned_cols=69 Identities=17% Similarity=0.255 Sum_probs=57.4
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..++|.|.++.++|+||.+.+ |++|+||.+++++. ... ......|++||.|+|+|.++|.+ +++
T Consensus 667 ~~v~G~V~~i~~~G~fV~l~~-gV~GlIh~sels~~------~~~-------~~~~~~~kvGq~VkvkVl~ID~e--~rr 730 (863)
T PRK12269 667 ARFTRRIVKVTNAGAFIEMEE-GIDGFLHVDDLSWV------KRT-------RPADHELEVGKEIECMVIECDPQ--ARR 730 (863)
T ss_pred CEEEEEEEEEecceEEEEeCC-CcEEEEEhHHhhcc------ccc-------cchhhccCCCCEEEEEEEEEecc--CCE
Confidence 789999999999999999976 99999999988642 110 11235799999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 731 I~LS~ 735 (863)
T PRK12269 731 IRLGV 735 (863)
T ss_pred EEEEe
Confidence 99986
No 66
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.62 E-value=0.00014 Score=57.44 Aligned_cols=71 Identities=8% Similarity=0.034 Sum_probs=54.8
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+...|.|+++.++|++|.++. +++|++|.+++... .+... ..+....+++||.|+++|.+++.+ ++
T Consensus 8 diV~g~V~~i~~~g~~v~i~~-~~~G~l~~se~~~~---~~~~~-------~~~~~~~l~vGd~i~~~V~~~~~~---~~ 73 (86)
T cd05789 8 DVVIGRVTEVGFKRWKVDINS-PYDAVLPLSEVNLP---RTDED-------ELNMRSYLDEGDLIVAEVQSVDSD---GS 73 (86)
T ss_pred CEEEEEEEEECCCEEEEECCC-CeEEEEEHHHccCC---CCccc-------hHHHHhhCCCCCEEEEEEEEECCC---CC
Confidence 678999999999999999975 89999999988642 00000 012345789999999999999853 78
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.||+
T Consensus 74 i~LS~ 78 (86)
T cd05789 74 VSLHT 78 (86)
T ss_pred EEEEe
Confidence 88875
No 67
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=97.54 E-value=0.00038 Score=55.44 Aligned_cols=63 Identities=13% Similarity=-0.077 Sum_probs=49.4
Q ss_pred eEEEEEEEEEEcC--eEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCC
Q 013634 354 TDTEARIVKIRSN--GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 428 (439)
Q Consensus 354 ~~~~g~V~~v~~~--g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~ 428 (439)
..+.|.|+++.++ |+||.+.+ |.+|++|++++++. .|.. . .+....+++||.|.|+|......
T Consensus 9 ~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~seis~~---~~~~------v--~~~~~~~~~Gd~v~VqV~~~~~~ 73 (88)
T cd04453 9 NIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDILPA---YFKK------H--KKIAKLLKEGQEILVQVVKEPIG 73 (88)
T ss_pred CEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHcCch---hccc------c--CCHHHcCCCCCEEEEEEEEecCC
Confidence 6899999999996 99999987 89999999988642 0100 0 12356799999999999986654
No 68
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.51 E-value=0.00019 Score=76.87 Aligned_cols=69 Identities=19% Similarity=0.188 Sum_probs=58.8
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..++|.|.++.++|+||.+++ |++|++|++++.+. +. +.+....|++||.|+|+|..+|.. +++
T Consensus 375 ~~v~g~V~~v~~~G~fV~l~~-~v~g~i~~s~l~~~----~~---------~~~~~~~~~~Gd~v~v~Il~vd~~--~~~ 438 (565)
T PRK06299 375 DVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDISWD----KK---------GEEAVELYKKGDEVEAVVLKVDVE--KER 438 (565)
T ss_pred CEEEEEEEEEecceEEEECCC-CCEEEEEHHHcCcc----cc---------ccChHhhCCCCCEEEEEEEEEeCC--CCE
Confidence 789999999999999999976 89999999998753 11 123467899999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 439 i~ls~ 443 (565)
T PRK06299 439 ISLGI 443 (565)
T ss_pred EEEEE
Confidence 99886
No 69
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.43 E-value=0.0004 Score=70.88 Aligned_cols=68 Identities=21% Similarity=0.262 Sum_probs=57.5
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|+++.++|+||.+++ |++|++|.+++.+.. + .+....|++||.|+|+|..+|.+ +++
T Consensus 279 ~~v~g~V~~i~~~G~fV~l~~-gi~Glv~~se~~~~~------------~--~~~~~~~~~Gd~v~v~V~~id~e--~~~ 341 (390)
T PRK06676 279 DVIEGTVKRLTDFGAFVEVLP-GVEGLVHISQISHKH------------I--ATPSEVLEEGQEVKVKVLEVNEE--EKR 341 (390)
T ss_pred cEEEEEEEEEeCceEEEEECC-CCeEEEEhHHcCccc------------c--CChhhccCCCCEEEEEEEEEECC--CCE
Confidence 789999999999999999976 899999999886431 1 12356799999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 342 i~ls~ 346 (390)
T PRK06676 342 ISLSI 346 (390)
T ss_pred EEEEE
Confidence 99986
No 70
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=97.42 E-value=0.00041 Score=73.52 Aligned_cols=68 Identities=18% Similarity=0.270 Sum_probs=59.2
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..++|.|+++.++|+||.+++ |++|+||.+++.++ +. .+....|++||.|+|+|..+|.+ +++
T Consensus 448 ~~v~g~V~~v~~~G~fV~l~~-~~~Glv~~s~l~~~----~~----------~~~~~~~~~Gd~v~~~V~~id~~--~~~ 510 (516)
T TIGR00717 448 SVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSEN----RD----------EDKTDEIKVGDEVEAKVVDIDKK--NRK 510 (516)
T ss_pred eEEEEEEEEEecceEEEEcCC-CeEEEEEHHHcCcc----cc----------ccccccCCCCCEEEEEEEEEeCC--CCE
Confidence 789999999999999999987 89999999999865 11 13467899999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.|++
T Consensus 511 i~ls~ 515 (516)
T TIGR00717 511 VSLSV 515 (516)
T ss_pred EEEEE
Confidence 99986
No 71
>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=97.41 E-value=0.00073 Score=50.80 Aligned_cols=62 Identities=13% Similarity=0.109 Sum_probs=50.5
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+..+|.|.++.++|++|.+. +.+|+++.+++.. +..+++||.|+|.|.+++......+
T Consensus 5 ~iV~G~V~~~~~~~~~vdig--~~eg~lp~~e~~~--------------------~~~~~~Gd~v~v~v~~v~~~~~~~~ 62 (67)
T cd04455 5 EIVTGIVKRVDRGNVIVDLG--KVEAILPKKEQIP--------------------GESYRPGDRIKAYVLEVRKTSKGPQ 62 (67)
T ss_pred CEEEEEEEEEcCCCEEEEcC--CeEEEeeHHHCCC--------------------CCcCCCCCEEEEEEEEEecCCCCCE
Confidence 56799999999999999995 4999999876642 2357999999999999997644567
Q ss_pred eeEE
Q 013634 434 LQLT 437 (439)
Q Consensus 434 i~l~ 437 (439)
|.||
T Consensus 63 i~lS 66 (67)
T cd04455 63 IILS 66 (67)
T ss_pred EEEe
Confidence 7776
No 72
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.33 E-value=0.00054 Score=74.40 Aligned_cols=68 Identities=21% Similarity=0.289 Sum_probs=58.3
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|.++.++|+||.+++ |++|++|.+++.+.. + .+....|++||.|+|+|.++|.+ +++
T Consensus 564 ~~v~g~V~~i~~~G~fV~l~~-~i~Gli~~sel~~~~------------~--~~~~~~~kvGd~V~vkV~~id~e--~~r 626 (647)
T PRK00087 564 SIVLGKVVRIAPFGAFVELEP-GVDGLVHISQISWKR------------I--DKPEDVLSEGEEVKAKILEVDPE--EKR 626 (647)
T ss_pred eEEEEEEEEEECCeEEEEECC-CCEEEEEhhhcCccc------------c--CCHhhcCCCCCEEEEEEEEEeCC--CCE
Confidence 789999999999999999976 899999999887541 1 23456799999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.|++
T Consensus 627 I~lsl 631 (647)
T PRK00087 627 IRLSI 631 (647)
T ss_pred EEEEE
Confidence 99986
No 73
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=97.32 E-value=0.0014 Score=59.05 Aligned_cols=72 Identities=13% Similarity=0.111 Sum_probs=58.3
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQP 429 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~ 429 (439)
+..+|.|+++.+.|++|.+.. ++++|+.+.++++ ..|+.+++...+.+++.+..++.||.|+++|..+..+.
T Consensus 83 EVv~g~V~~v~~~G~~v~~Gp--~~ifI~~~~l~~~--~~fd~~~~~~~~~~~~~~~~i~~g~~VR~rV~~v~~~~ 154 (176)
T PTZ00162 83 EVLDAIVTDVNKLGFFAQAGP--LKAFVSRSAIPPD--FVYDSDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDA 154 (176)
T ss_pred CEEEEEEEEEecceEEEEeeC--eEEEEcHHHCCCc--cEECCCCCcceEecCCCcEEECCCCEEEEEEEEEEecC
Confidence 789999999999999999964 5699999999765 23444445567765666899999999999999887653
No 74
>TIGR00717 rpsA ribosomal protein S1. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
Probab=97.32 E-value=0.00045 Score=73.18 Aligned_cols=69 Identities=17% Similarity=0.225 Sum_probs=58.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|+++.++|+||.++. |++|+||++++.+. +.. ......|++||.|.|+|..+|.. +++
T Consensus 361 ~~v~g~V~~v~~~G~fV~l~~-~v~glv~~s~ls~~----~~~---------~~~~~~~~~G~~V~~~Vl~vd~~--~~~ 424 (516)
T TIGR00717 361 DRVTGKIKKITDFGAFVELEG-GIDGLIHLSDISWD----KDG---------READHLYKKGDEIEAVVLAVDKE--KKR 424 (516)
T ss_pred CEEEEEEEEEecceEEEECCC-CCEEEEEHHHCcCc----ccC---------CCHhHccCCCCEEEEEEEEEeCc--CCE
Confidence 789999999999999999976 99999999998754 111 12357899999999999999976 788
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 425 i~ls~ 429 (516)
T TIGR00717 425 ISLGV 429 (516)
T ss_pred EEEee
Confidence 98886
No 75
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=97.32 E-value=0.00088 Score=72.95 Aligned_cols=65 Identities=15% Similarity=0.183 Sum_probs=54.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.++|.|+++.++|+||.+.. |.+|++|++++.+. ++ .+....|++||.|+|+|.++|. +.+
T Consensus 620 ~i~~G~V~~I~~~GafVei~~-g~~GllHiSei~~~---~v-----------~~~~~~~kvGD~V~VkVi~id~---~gk 681 (684)
T TIGR03591 620 KIYEGKVVRIMDFGAFVEILP-GKDGLVHISEIANE---RV-----------EKVEDVLKEGDEVKVKVLEIDK---QGR 681 (684)
T ss_pred cEEEEEEEEEeCCEEEEEECC-CcEEEEEHHHcCCC---cc-----------cChhhccCCCCEEEEEEEEECC---CCC
Confidence 789999999999999999975 89999999998754 11 1346789999999999999995 455
Q ss_pred eeE
Q 013634 434 LQL 436 (439)
Q Consensus 434 i~l 436 (439)
|.|
T Consensus 682 i~L 684 (684)
T TIGR03591 682 IKL 684 (684)
T ss_pred ccC
Confidence 543
No 76
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.26 E-value=0.0016 Score=64.56 Aligned_cols=64 Identities=14% Similarity=0.197 Sum_probs=53.2
Q ss_pred CeEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 353 PTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 353 ~~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
....+|.|+++.++|++|.+. |++|+||.+.+++. .... ..+|+.|+|+|..+|.+ ++
T Consensus 119 ~~~V~g~V~~~~~~G~~V~l~--Gv~gfip~s~ls~~-----------------~~~~-~~vG~~i~~kVl~id~~--~~ 176 (318)
T PRK07400 119 DATVRSEVFATNRGGALVRIE--GLRGFIPGSHISTR-----------------KPKE-ELVGEELPLKFLEVDEE--RN 176 (318)
T ss_pred CCEEEEEEEEEECCeEEEEEC--CEEEEEEHHHcCcc-----------------CCcc-ccCCCEEEEEEEEEEcc--cC
Confidence 478899999999999999994 99999999988742 1112 34999999999999976 78
Q ss_pred ceeEEe
Q 013634 433 KLQLTL 438 (439)
Q Consensus 433 ~i~l~l 438 (439)
+|.||+
T Consensus 177 ~i~lS~ 182 (318)
T PRK07400 177 RLVLSH 182 (318)
T ss_pred EEEEEh
Confidence 988885
No 77
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.18 E-value=0.0017 Score=66.36 Aligned_cols=67 Identities=18% Similarity=0.259 Sum_probs=56.1
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..++|.|.++.++|+||.+. |++|+||.+++.+. +. .+....|++||.|+|+|..+|.. +++
T Consensus 194 ~~v~g~V~~v~~~G~fV~l~--~v~g~v~~sels~~----~~----------~~~~~~~~vGd~i~~~Vl~vd~~--~~~ 255 (390)
T PRK06676 194 DVVEGTVARLTDFGAFVDIG--GVDGLVHISELSHE----RV----------EKPSEVVSVGQEVEVKVLSIDWE--TER 255 (390)
T ss_pred CEEEEEEEEEecceEEEEeC--CeEEEEEHHHcCcc----cc----------CCHHHhcCCCCEEEEEEEEEeCC--CCE
Confidence 78999999999999999994 79999999998753 11 13356789999999999999975 788
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 256 i~lS~ 260 (390)
T PRK06676 256 ISLSL 260 (390)
T ss_pred EEEEE
Confidence 88875
No 78
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.17 E-value=0.00075 Score=72.35 Aligned_cols=69 Identities=20% Similarity=0.288 Sum_probs=57.2
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|+++.++|++|.++. |++|++|.++++++. . ..+....+++||.|+|+|..+|.. +++
T Consensus 288 ~~v~g~V~~i~~~G~fV~l~~-~v~Glv~~sel~~~~-----~--------~~~~~~~~~~G~~v~v~V~~id~~--~~~ 351 (565)
T PRK06299 288 SKVKGKVTNITDYGAFVELEE-GIEGLVHVSEMSWTK-----K--------NKHPSKVVSVGQEVEVMVLEIDEE--KRR 351 (565)
T ss_pred CEEEEEEEEEeCCeEEEEeCC-CCEEEEEHHHcCccc-----c--------ccCHHHhcCCCCEEEEEEEEEcCC--CCE
Confidence 789999999999999999975 899999999986431 0 012345689999999999999976 789
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 352 i~ls~ 356 (565)
T PRK06299 352 ISLGL 356 (565)
T ss_pred EEEeh
Confidence 99885
No 79
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=97.13 E-value=0.0037 Score=49.74 Aligned_cols=68 Identities=9% Similarity=0.034 Sum_probs=54.4
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecC--CeEEEEeeCCceEEeeCceEEEEEEEecCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDE--QQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 428 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~--~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~ 428 (439)
+..+|+|+++.+.|++|.+. .++++++-..++++ +.+++ +...+.+ +....++.||.|+++|..+..+
T Consensus 3 EVi~g~V~~v~~~G~~v~~G--pl~~f~~~~~ip~~----~~~~~~~~~~~~~~-~~~~~i~~g~~VR~rV~~v~~~ 72 (88)
T cd04462 3 EVVDAIVTSVNKTGFFAEVG--PLSIFISRHLIPSD----MEFDPNASPPCFTS-NEDIVIKKDTEVRLKIIGTRVD 72 (88)
T ss_pred cEEEEEEEEEeccEEEEEEc--CceEEEEeeecCcc----ceECCcCCCCeEeC-CCcEEECCCCEEEEEEEEEEEc
Confidence 57899999999999999996 47889999888765 44443 3335653 3578999999999999998765
No 80
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.10 E-value=0.0016 Score=50.92 Aligned_cols=67 Identities=9% Similarity=-0.105 Sum_probs=54.5
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
....|.|+++.+++++|.+.. +.+|.++.+++... +. .+....+++||.|.++|.+++.. ++
T Consensus 8 diV~G~V~~v~~~~~~V~i~~-~~~g~l~~~~~~~~----~~----------~~~~~~~~~GD~i~~~V~~~~~~---~~ 69 (82)
T cd04454 8 DIVIGIVTEVNSRFWKVDILS-RGTARLEDSSATEK----DK----------KEIRKSLQPGDLILAKVISLGDD---MN 69 (82)
T ss_pred CEEEEEEEEEcCCEEEEEeCC-CceEEeechhccCc----ch----------HHHHhcCCCCCEEEEEEEEeCCC---CC
Confidence 678999999999999999965 89999999988653 10 12356689999999999999852 77
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.||+
T Consensus 70 i~LS~ 74 (82)
T cd04454 70 VLLTT 74 (82)
T ss_pred EEEEE
Confidence 88886
No 81
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.87 E-value=0.0022 Score=67.74 Aligned_cols=67 Identities=15% Similarity=0.212 Sum_probs=56.4
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.|.|.|+.+.++|+||++.. |-+|+||++.+.... . ++....+++||.|.|++..+|. +.+
T Consensus 621 ~iy~G~V~ri~~fGaFv~l~~-gkdgl~hiS~~~~~r------------v--~kv~dvlk~Gd~v~Vkv~~iD~---~Gr 682 (692)
T COG1185 621 EVYEGTVVRIVDFGAFVELLP-GKDGLVHISQLAKER------------V--EKVEDVLKEGDEVKVKVIEIDK---QGR 682 (692)
T ss_pred cEEEEEEEEEeecceEEEecC-CcceeEEehhhhhhh------------h--hcccceeecCceEEEEEeeecc---cCC
Confidence 689999999999999999977 899999999887541 1 2446889999999999999996 467
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
++|++
T Consensus 683 i~ls~ 687 (692)
T COG1185 683 IRLSI 687 (692)
T ss_pred cccee
Confidence 77765
No 82
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=96.78 E-value=0.0019 Score=69.43 Aligned_cols=68 Identities=19% Similarity=0.230 Sum_probs=58.7
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
...+|+|.+|..+|+||.|. ..-+|.||++.+.+. |.. ++...+++||.|+|+|.+||.. +.+
T Consensus 660 m~leg~Vrnv~~fgafVdIg-v~qDglvHis~ls~~----fv~----------~P~~vv~vGdiV~v~V~~vD~~--r~r 722 (780)
T COG2183 660 MILEGTVRNVVDFGAFVDIG-VHQDGLVHISQLSDK----FVK----------DPNEVVKVGDIVKVKVIEVDTA--RKR 722 (780)
T ss_pred CEEEEEEEEeeeccceEEec-cccceeeeHHHhhhh----hcC----------ChHHhcccCCEEEEEEEEEecc--cCe
Confidence 46799999999999999995 488999999999886 333 3478899999999999999976 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.|++
T Consensus 723 I~Lsm 727 (780)
T COG2183 723 IALSM 727 (780)
T ss_pred eeeEe
Confidence 99886
No 83
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=96.72 E-value=0.016 Score=60.11 Aligned_cols=71 Identities=11% Similarity=0.091 Sum_probs=56.1
Q ss_pred HHHHHhcC-CeEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEE
Q 013634 345 TLIYFRKR-PTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHME 423 (439)
Q Consensus 345 ~~~~l~~~-~~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~ 423 (439)
...-++.+ .+...|+|.++.++|++|.+. |++|+++.++.. .+..|++||+|+|.|.
T Consensus 126 i~~eyk~~~GeIV~G~V~ri~~~giiVDLg--gvea~LP~sE~i--------------------p~E~~~~GdrIka~I~ 183 (470)
T PRK09202 126 VYEEYKDRVGEIITGVVKRVERGNIIVDLG--RAEAILPRKEQI--------------------PRENFRPGDRVRAYVY 183 (470)
T ss_pred HHHHHHhhcCCEEEEEEEEEecCCEEEEEC--CeEEEecHHHcC--------------------CCccCCCCCEEEEEEE
Confidence 33344433 378899999999999999993 899999977642 3567899999999999
Q ss_pred EecCCCCCCceeEE
Q 013634 424 VVEPQPNRPKLQLT 437 (439)
Q Consensus 424 ~vd~~~~~~~i~l~ 437 (439)
+|+.....++|.||
T Consensus 184 ~Vd~~~kg~qIilS 197 (470)
T PRK09202 184 EVRKEARGPQIILS 197 (470)
T ss_pred EEecCCCCCeEEEE
Confidence 99986444588887
No 84
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=96.52 E-value=0.0055 Score=66.64 Aligned_cols=67 Identities=15% Similarity=0.202 Sum_probs=56.4
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+.+.|.|.++.++|+||.+ . |++|++|.+++.+. +. .+....|++||.|+|+|.++|.. +++
T Consensus 479 ~iV~g~V~~v~~~G~fV~l-~-gv~Gll~~sels~~----~~----------~~~~~~~~vGd~V~vkV~~id~~--~~~ 540 (647)
T PRK00087 479 DVVEGEVKRLTDFGAFVDI-G-GVDGLLHVSEISWG----RV----------EKPSDVLKVGDEIKVYILDIDKE--NKK 540 (647)
T ss_pred CEEEEEEEEEeCCcEEEEE-C-CEEEEEEHHHcCcc----cc----------CCHHHhcCCCCEEEEEEEEEECC--CCE
Confidence 7899999999999999999 3 89999999998753 11 13456799999999999999975 788
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 541 I~lS~ 545 (647)
T PRK00087 541 LSLSL 545 (647)
T ss_pred EEEEe
Confidence 88875
No 85
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=96.39 E-value=0.035 Score=55.71 Aligned_cols=68 Identities=10% Similarity=0.083 Sum_probs=54.0
Q ss_pred HHhcCCeEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecC
Q 013634 348 YFRKRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEP 427 (439)
Q Consensus 348 ~l~~~~~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~ 427 (439)
|-.+..+...|+|.++.++|++|.+. |++|+++.++.. .+..|++||.|+|.|.+|+.
T Consensus 130 f~~k~GeiV~G~V~~~~~~~~~Vdlg--~vEa~LP~~E~i--------------------p~e~~~~Gd~Ika~V~~V~~ 187 (362)
T PRK12327 130 FSEREGDIVTGVVQRRDNRFVYVNLG--KIEAVLPPAEQI--------------------PGETYKHGDRIKVYVVKVEK 187 (362)
T ss_pred HHHhcCCEEEEEEEEEeCCcEEEEeC--CeEEEecHHHcC--------------------CCCCCCCCCEEEEEEEEEec
Confidence 33344478899999999999999984 699999875432 24568999999999999997
Q ss_pred CCCCCceeEE
Q 013634 428 QPNRPKLQLT 437 (439)
Q Consensus 428 ~~~~~~i~l~ 437 (439)
....++|.||
T Consensus 188 ~~kgp~IivS 197 (362)
T PRK12327 188 TTKGPQIFVS 197 (362)
T ss_pred CCCCCeEEEE
Confidence 7556778877
No 86
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=96.19 E-value=0.0079 Score=46.49 Aligned_cols=64 Identities=16% Similarity=0.195 Sum_probs=51.0
Q ss_pred EEEEEEcCeEEEEEeCCceEEEEE-cccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCceeEE
Q 013634 359 RIVKIRSNGFIVFVPKFGIEGPVY-LTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLT 437 (439)
Q Consensus 359 ~V~~v~~~g~~V~l~~~gveg~v~-~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~ 437 (439)
.|..+.+.|+.|.|.+||+||++- .+++..+ .+ ++-.+.+ +|-.+.|+|..+|.. |.=|+||
T Consensus 22 ~Vv~i~d~~~YV~LleY~iegmIl~~selsr~---ri-----------rsi~kll-VGk~e~v~ViRVDk~--KGYIDLs 84 (86)
T PHA02858 22 GIVFVKDNIFYVKLIDYGLEALIVNYVNVNAD---RA-----------EKLKKKL-VGKTINVQVIRTDKL--KGYIDVR 84 (86)
T ss_pred EEEEEeccEEEEEEecCccceEEecHHHHhHH---HH-----------Hhhhhhh-cCCeeEEEEEEECCC--CCEEEeE
Confidence 667889999999999999999987 6665543 11 1235666 999999999999976 8899998
Q ss_pred eC
Q 013634 438 LI 439 (439)
Q Consensus 438 l~ 439 (439)
.+
T Consensus 85 ~~ 86 (86)
T PHA02858 85 HV 86 (86)
T ss_pred cC
Confidence 64
No 87
>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=96.02 E-value=0.072 Score=53.17 Aligned_cols=69 Identities=12% Similarity=0.148 Sum_probs=53.9
Q ss_pred HHHhcCCeEEEEEEEEEEcCe-EEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEe
Q 013634 347 IYFRKRPTDTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 425 (439)
Q Consensus 347 ~~l~~~~~~~~g~V~~v~~~g-~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~v 425 (439)
.|-.+..+..+|+|.++.++| ++|.+. |++|+++.++... +..|++||.|+|.|.+|
T Consensus 126 ey~~k~GeiV~G~V~~v~~~g~v~VdiG--~~ea~LP~~E~ip--------------------~E~~~~Gd~ik~~V~~V 183 (341)
T TIGR01953 126 EFSSKEGEIISGTVKRVNRRGNLYVELG--KTEGILPKKEQIP--------------------GEKFRIGDRIKAYVYEV 183 (341)
T ss_pred HHHhhcCCEEEEEEEEEecCCcEEEEEC--CeEEEecHHHcCC--------------------CcCCCCCCEEEEEEEEE
Confidence 343334478899999999988 588883 8999999876532 33499999999999999
Q ss_pred cCCCCCCceeEE
Q 013634 426 EPQPNRPKLQLT 437 (439)
Q Consensus 426 d~~~~~~~i~l~ 437 (439)
+.....++|.||
T Consensus 184 ~~~~kg~qIivS 195 (341)
T TIGR01953 184 RKTAKGPQIILS 195 (341)
T ss_pred EcCCCCCeEEEE
Confidence 976556788887
No 88
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=96.00 E-value=0.016 Score=52.92 Aligned_cols=66 Identities=11% Similarity=0.084 Sum_probs=52.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeC---------CceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEE
Q 013634 354 TDTEARIVKIRSNGFIVFVPK---------FGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV 424 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~---------~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~ 424 (439)
....|.|+++.++|++|.+.. .+++|++|.+++.+. +. .+....|++||.|.++|.+
T Consensus 66 diV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~----~~----------~~~~~~~~~GD~V~akV~~ 131 (189)
T PRK09521 66 DIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDG----YV----------ESLTDAFKIGDIVRAKVIS 131 (189)
T ss_pred CEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChh----hh----------hhHHhccCCCCEEEEEEEe
Confidence 688999999999999999963 368999999987653 10 1225678999999999998
Q ss_pred ecCCCCCCceeEEe
Q 013634 425 VEPQPNRPKLQLTL 438 (439)
Q Consensus 425 vd~~~~~~~i~l~l 438 (439)
++ +++.||+
T Consensus 132 i~-----~~i~LS~ 140 (189)
T PRK09521 132 YT-----DPLQLST 140 (189)
T ss_pred cC-----CcEEEEE
Confidence 87 4577664
No 89
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.67 E-value=0.035 Score=52.61 Aligned_cols=71 Identities=11% Similarity=0.065 Sum_probs=55.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
....|.|+++.+++++|.+.. +.+|++|++++.+. +...|+ .+....|++||.|.++|.+++.+ ++
T Consensus 65 DiViG~V~~i~~~~~~vdI~~-~~~g~L~~s~i~~~---~~~~d~-------~~~~~~~~~GDlV~akV~~i~~~---~~ 130 (235)
T PRK04163 65 DLVIGKVTDVTFSGWEVDINS-PYKAYLPVSEVLGR---PVNVEG-------TDLRKYLDIGDYIIAKVKDVDRT---RD 130 (235)
T ss_pred CEEEEEEEEEeCceEEEEeCC-CceeEEEHHHcCCC---ccccch-------hhhHhhCCCCCEEEEEEEEECCC---Cc
Confidence 688999999999999999976 68999999988754 111121 23456799999999999999864 34
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
+.||+
T Consensus 131 ~~LS~ 135 (235)
T PRK04163 131 VVLTL 135 (235)
T ss_pred EEEEE
Confidence 77764
No 90
>cd05699 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=95.34 E-value=0.039 Score=41.85 Aligned_cols=67 Identities=16% Similarity=0.019 Sum_probs=52.4
Q ss_pred EEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceE-EEEEEEecCCCCCCc
Q 013634 355 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTV-NIHMEVVEPQPNRPK 433 (439)
Q Consensus 355 ~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V-~V~v~~vd~~~~~~~ 433 (439)
..+|.|+.-+++++.|.+.+.|+.|+++...+.|. + ..+ +...+.+++||++ ++-+. +.. +|.
T Consensus 3 lV~~~V~EKt~D~l~v~l~~~~l~a~l~~~HLsD~----~--~k~------~~~~~klrvG~~L~~~lvL--~~~--~r~ 66 (72)
T cd05699 3 LVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDH----V--SNC------PLLWHCLQEGDTIPNLMCL--SNY--KGR 66 (72)
T ss_pred eEEEEEEEEcCCcEEEEecCCCcEEEEEccccCCc----h--hhC------HHHHhhhhcCCCccceEEE--ecc--ccE
Confidence 46899999999999999999999999999988864 1 111 1235789999999 78777 443 788
Q ss_pred eeEE
Q 013634 434 LQLT 437 (439)
Q Consensus 434 i~l~ 437 (439)
|.|+
T Consensus 67 i~lt 70 (72)
T cd05699 67 IILT 70 (72)
T ss_pred EEEe
Confidence 7776
No 91
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=94.82 E-value=0.074 Score=55.07 Aligned_cols=60 Identities=18% Similarity=0.137 Sum_probs=50.8
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 428 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~ 428 (439)
..++|.|+.+.+.|++|+++. |.+|++|.++++.. |. .+....+.+||.|+|+..+.|+.
T Consensus 670 ~vy~~tIt~~rd~G~~V~l~p-~~~~Llh~sqL~~e---~i-----------akpsd~levGq~I~vk~ie~d~~ 729 (760)
T KOG1067|consen 670 GVYTATITEIRDTGVMVELYP-MQQGLLHNSQLDQE---KI-----------AKPSDLLEVGQEIQVKYIERDPR 729 (760)
T ss_pred eEEEEEEeeecccceEEEecC-Cchhhccchhcccc---cc-----------cChHHHHhhcceeEEEEEeecCc
Confidence 467999999999999999988 99999999999864 21 13455699999999999999974
No 92
>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=93.48 E-value=0.53 Score=35.33 Aligned_cols=62 Identities=13% Similarity=0.134 Sum_probs=46.0
Q ss_pred eEEEEEEEEEEcCe-EEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~~g-~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
-.++|+|+...+++ +.|.+++ |.+-..|++..- ++..-.+..||.|.|++..-|+. +.
T Consensus 5 ie~~G~V~e~L~~~~f~V~l~n-g~~vla~i~GKm------------------r~~rI~I~~GD~V~Ve~spyd~t--kg 63 (68)
T TIGR00008 5 IEMEGKVTESLPNAMFRVELEN-GHEVLAHISGKI------------------RMHYIRILPGDKVKVELSPYDLT--RG 63 (68)
T ss_pred EEEEEEEEEECCCCEEEEEECC-CCEEEEEecCcc------------------hhccEEECCCCEEEEEECcccCC--cE
Confidence 35799999998877 4578865 888888886532 12356789999999999887754 66
Q ss_pred ceeE
Q 013634 433 KLQL 436 (439)
Q Consensus 433 ~i~l 436 (439)
+|..
T Consensus 64 rIi~ 67 (68)
T TIGR00008 64 RITY 67 (68)
T ss_pred eEEe
Confidence 6643
No 93
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=93.39 E-value=0.43 Score=41.73 Aligned_cols=70 Identities=9% Similarity=-0.008 Sum_probs=46.3
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 428 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~ 428 (439)
+..+|+|+.|.+.|+|+.... ++.++.--..+.+ .+|++.++......++ ...+++|+.|+++|......
T Consensus 83 EVvdgvV~~Vnk~G~F~~~GP--l~~f~sshl~ppd--~~f~p~~n~P~f~~~d-~s~I~~~~~VR~kiigtr~~ 152 (170)
T KOG3298|consen 83 EVVDGVVTKVNKMGVFARSGP--LEVFYSSHLKPPD--YEFDPGENPPNFQTED-ESVIQKGVEVRLKIIGTRVD 152 (170)
T ss_pred cEEEEEEEEEeeeeEEEeccc--eEeeeecccCCCC--cccCCCCCCCcccccc-cceeeeCcEEEEEEEEEEEe
Confidence 788999999999999999965 4444432223333 2454444433333222 23899999999999887654
No 94
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=93.09 E-value=0.081 Score=60.10 Aligned_cols=68 Identities=21% Similarity=0.329 Sum_probs=58.6
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|.|..+.++|++|.++. |++|+.+.+...++ |.. +....+.+|++|.++|.++|.+ +++
T Consensus 601 ~~~~G~l~~~~~~g~~V~F~g-~lsGf~p~s~~sd~----~v~----------~~~ehf~vGqTv~~~i~nvd~e--k~r 663 (1710)
T KOG1070|consen 601 KITKGTLCAIKENGAFVTFTG-GLSGFAPVSEMSDD----FVL----------SDSEHFPVGQTVRAKIVNVDDE--KRR 663 (1710)
T ss_pred ceEEEEEeeeccCCeEEEecC-ccccccchhhhhhh----hhc----------ChhhhcccccEEEEEEEecCch--hce
Confidence 578999999999999999998 99999999988876 322 3467799999999999999987 899
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.+++
T Consensus 664 m~l~~ 668 (1710)
T KOG1070|consen 664 MPLGL 668 (1710)
T ss_pred eehhh
Confidence 98865
No 95
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=92.41 E-value=1.5 Score=45.00 Aligned_cols=70 Identities=21% Similarity=0.331 Sum_probs=51.8
Q ss_pred HHhcCCeEEEEEEEEEEcCeEEEEEe-CCc---eEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEE
Q 013634 348 YFRKRPTDTEARIVKIRSNGFIVFVP-KFG---IEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHME 423 (439)
Q Consensus 348 ~l~~~~~~~~g~V~~v~~~g~~V~l~-~~g---veg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~ 423 (439)
|-.+..+...|+|..+.+.++.|.+. .+| +||.++-++.- .+..|+.||.|+|-|.
T Consensus 148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqi--------------------p~E~y~~Gdrika~i~ 207 (449)
T PRK12329 148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQL--------------------PNDNYRANATFKVFLK 207 (449)
T ss_pred HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcC--------------------CCCcCCCCCEEEEEEE
Confidence 33334488999999999998888883 234 78888765421 3567999999999999
Q ss_pred EecCCC-CCCceeEE
Q 013634 424 VVEPQP-NRPKLQLT 437 (439)
Q Consensus 424 ~vd~~~-~~~~i~l~ 437 (439)
.|+... ..++|.||
T Consensus 208 ~V~~~~~kGpqIilS 222 (449)
T PRK12329 208 EVSEGPRRGPQLFVS 222 (449)
T ss_pred EeecCCCCCCEEEEE
Confidence 998763 34778776
No 96
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=92.24 E-value=1.2 Score=34.94 Aligned_cols=63 Identities=10% Similarity=0.168 Sum_probs=47.3
Q ss_pred eEEEEEEEEEEcCeE-EEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRSNGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~-~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
-.++|+|+.+.+++. .|.++. |.+-..|++..- ++..-.+..||.|.|++..-|+. +.
T Consensus 7 ie~~G~V~e~Lp~~~frV~Len-G~~vla~isGKm------------------R~~rIrIl~GD~V~VE~spYDlt--kG 65 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLEN-GVEVGAYASGRM------------------RKHRIRILAGDRVTLELSPYDLT--KG 65 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeCC-CCEEEEEeccce------------------eeeeEEecCCCEEEEEECcccCC--ce
Confidence 568999999988775 467754 888888876431 12356789999999999988865 77
Q ss_pred ceeEE
Q 013634 433 KLQLT 437 (439)
Q Consensus 433 ~i~l~ 437 (439)
+|...
T Consensus 66 RIiyR 70 (87)
T PRK12442 66 RINFR 70 (87)
T ss_pred eEEEE
Confidence 77654
No 97
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=91.22 E-value=1 Score=36.01 Aligned_cols=69 Identities=12% Similarity=0.033 Sum_probs=49.8
Q ss_pred eEEEEEEEEEEcCeEEEEE--------eCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEe
Q 013634 354 TDTEARIVKIRSNGFIVFV--------PKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 425 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l--------~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~v 425 (439)
...-|.|+++....+.|.+ +. ...|.+|.++.... ..++. +-...|++||.|+.+|.+.
T Consensus 8 DiVig~V~~v~~~~~~v~I~~v~~~~l~~-~~~g~l~~~dv~~~-----~~d~~-------~~~~~f~~GDiV~AkVis~ 74 (92)
T cd05791 8 SIVIARVTRINPRFAKVDILCVGGRPLKE-SFRGVIRKEDIRAT-----EKDKV-------EMYKCFRPGDIVRAKVISL 74 (92)
T ss_pred CEEEEEEEEEcCCEEEEEEEEecCeecCC-CcccEEEHHHcccc-----ccchH-------HHHhhcCCCCEEEEEEEEc
Confidence 5678999999999999998 44 56788888776532 11110 1256789999999999987
Q ss_pred cCCCCCCceeEEe
Q 013634 426 EPQPNRPKLQLTL 438 (439)
Q Consensus 426 d~~~~~~~i~l~l 438 (439)
+. .+.+.||+
T Consensus 75 ~~---~~~~~Lst 84 (92)
T cd05791 75 GD---ASSYYLST 84 (92)
T ss_pred CC---CCCcEEEe
Confidence 74 35566664
No 98
>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=91.14 E-value=2.8 Score=35.42 Aligned_cols=71 Identities=11% Similarity=0.004 Sum_probs=50.8
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEe-eCCceEEeeCceEEEEEEEecC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVK-MDGNLSYSVLQTVNIHMEVVEP 427 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~-~~~~~~~~iGd~V~V~v~~vd~ 427 (439)
+...|.|.+-.+.|+.|.| .|-=+-+|+-+.|... ..|+.+++...+.- +...-.+..|+.|+++|.++..
T Consensus 5 Evl~g~I~~~~~~Gi~vsl-gFFddI~IP~~~L~~p--s~fd~~~~~W~W~~~~~~~l~~d~ge~IRFRV~~~~f 76 (122)
T PF08292_consen 5 EVLTGKIKSSTAEGIRVSL-GFFDDIFIPPSLLPEP--SRFDEEEQAWVWEYDEEQELFFDIGEEIRFRVESEIF 76 (122)
T ss_dssp -EEEEEEEEEETTEEEEEE-CCEEEEEEECCCC-TT--EEEECCCTEEEEEESSSEEEEE-TT-EEEEEEEEEEE
T ss_pred CEEEEEEEecCCCcEEEEe-cccccEEECHHHCCCC--CccCccCCEEEEECCCCceeEccCCCEEEEEEeEEEE
Confidence 5789999999999999999 5666778888888754 24554555555544 4446688999999999988775
No 99
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=91.01 E-value=2.7 Score=42.28 Aligned_cols=70 Identities=14% Similarity=0.135 Sum_probs=52.6
Q ss_pred HHHHhcCCeEEEEEEEEEEcC-eEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEE
Q 013634 346 LIYFRKRPTDTEARIVKIRSN-GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV 424 (439)
Q Consensus 346 ~~~l~~~~~~~~g~V~~v~~~-g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~ 424 (439)
-.|..+..+...|+|.++... +++|.+. +.+|.++-++.- .+..|+.||.|+|-|.+
T Consensus 132 ~ey~~~~Geiv~g~V~r~~~~~~i~vdlg--~~ea~LP~~eqi--------------------p~E~~~~Gdrik~~i~~ 189 (374)
T PRK12328 132 EKYKKKVGKIVFGTVVRVDNEENTFIEID--EIRAVLPMKNRI--------------------KGEKFKVGDVVKAVLKR 189 (374)
T ss_pred HHHHHhcCcEEEEEEEEEecCCCEEEEcC--CeEEEeCHHHcC--------------------CCCcCCCCCEEEEEEEE
Confidence 344444458899999999864 5788885 689988765321 35679999999999999
Q ss_pred ecCCCC-CCceeEE
Q 013634 425 VEPQPN-RPKLQLT 437 (439)
Q Consensus 425 vd~~~~-~~~i~l~ 437 (439)
|+.... .++|.||
T Consensus 190 V~~~~k~gp~IilS 203 (374)
T PRK12328 190 VKIDKNNGILIELS 203 (374)
T ss_pred EecCCCCCCEEEEE
Confidence 998754 3688877
No 100
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=90.77 E-value=0.8 Score=43.60 Aligned_cols=59 Identities=19% Similarity=0.229 Sum_probs=50.0
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
+..+|+|-+....|.||.+ +-+.-|+||-++. ...+++|++++++|..+.. .++
T Consensus 157 q~v~~tVYr~~~~G~fv~~-e~~~~GfIh~sEr----------------------~~~prlG~~l~~rVi~~re---Dg~ 210 (287)
T COG2996 157 QEVDATVYRLLESGTFVIT-ENGYLGFIHKSER----------------------FAEPRLGERLTARVIGVRE---DGK 210 (287)
T ss_pred CeeeeEEEEEeccceEEEE-cCCeEEEEcchhh----------------------cccccCCceEEEEEEEEcc---CCe
Confidence 6789999999999999999 5599999986542 2457999999999999986 588
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.||+
T Consensus 211 lnLSl 215 (287)
T COG2996 211 LNLSL 215 (287)
T ss_pred eeccc
Confidence 88886
No 101
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=90.64 E-value=0.77 Score=52.65 Aligned_cols=68 Identities=13% Similarity=0.167 Sum_probs=57.2
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
....|.|..+.+.|+|+.+-. ++++++.++++.+.+... .++.|.+|+.|..+|..++.. .++
T Consensus 1164 ~iv~G~V~nv~~~glfi~ls~-~v~a~v~is~~~ds~~k~--------------w~k~~~~gklv~~rv~~ve~~--s~r 1226 (1710)
T KOG1070|consen 1164 DIVRGFVKNVETKGLFIALSR-KVEAFVPISGLSDSFEKE--------------WEKHLPVGKLVTGRVLSVEED--SKR 1226 (1710)
T ss_pred ceeEEEEEEecCCcEEEEEcc-ceEEEEEccccccchhhh--------------hhccCCccceeeeEEEEeecc--Cce
Confidence 678999999999999999965 999999999887753222 257899999999999999976 678
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|.|+|
T Consensus 1227 iel~L 1231 (1710)
T KOG1070|consen 1227 IELSL 1231 (1710)
T ss_pred EEEEE
Confidence 88876
No 102
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=88.30 E-value=0.36 Score=50.43 Aligned_cols=62 Identities=13% Similarity=0.255 Sum_probs=51.4
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPK 433 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~ 433 (439)
..+.|+|.++.++|+||.+.+ .+.|++|-+++.++ ..|.+||.+-|++..|.++ ++.
T Consensus 124 ~~Y~g~v~~v~~~GvFv~Ln~-~v~GL~~~~d~~~~--------------------~~~~vgdeiiV~v~~vr~~--~ge 180 (715)
T COG1107 124 KYYKGIVSRVEKYGVFVELNS-HVRGLIHRRDLGGD--------------------PDYAVGDEIIVQVSDVRPE--KGE 180 (715)
T ss_pred eeeeccccchhhhcceeecCh-hhhccccccccCCC--------------------CCCCCCCeEEEEeeccCCC--CCc
Confidence 578999999999999999987 78888887665432 4579999999999999876 788
Q ss_pred eeEEe
Q 013634 434 LQLTL 438 (439)
Q Consensus 434 i~l~l 438 (439)
|+|.-
T Consensus 181 idf~~ 185 (715)
T COG1107 181 IDFEP 185 (715)
T ss_pred cceee
Confidence 87763
No 103
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=87.56 E-value=4.6 Score=30.89 Aligned_cols=62 Identities=13% Similarity=0.224 Sum_probs=45.4
Q ss_pred eEEEEEEEEEEcCe-EEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~~g-~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
..+.|+|..+.+++ |.|++.+ |.+-.-|+++.-. ...-.+..||.|.|++...|.. +.
T Consensus 7 ~e~~g~V~e~L~~~~f~v~~ed-g~~~~ahI~GKmr------------------~~~i~I~~GD~V~Ve~~~~d~~--kg 65 (75)
T COG0361 7 IEMEGTVIEMLPNGRFRVELEN-GHERLAHISGKMR------------------KNRIRILPGDVVLVELSPYDLT--KG 65 (75)
T ss_pred cEEEEEEEEecCCCEEEEEecC-CcEEEEEccCcch------------------heeEEeCCCCEEEEEecccccc--cc
Confidence 46789999988776 5688765 8888888765321 2245689999999999988754 66
Q ss_pred ceeE
Q 013634 433 KLQL 436 (439)
Q Consensus 433 ~i~l 436 (439)
+|..
T Consensus 66 ~I~~ 69 (75)
T COG0361 66 RIVY 69 (75)
T ss_pred cEEE
Confidence 6654
No 104
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=84.46 E-value=2.7 Score=43.26 Aligned_cols=68 Identities=10% Similarity=0.010 Sum_probs=46.4
Q ss_pred eEEEEEEEEEEcC--eEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEE
Q 013634 354 TDTEARIVKIRSN--GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV 424 (439)
Q Consensus 354 ~~~~g~V~~v~~~--g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~ 424 (439)
..|.|.|.++.++ |+||.+.. |-.|++|++++.... ++.+......-...+....++.||.|-|+|.+
T Consensus 27 nIY~GrV~~i~p~l~aAFVdiG~-~k~gfL~~~d~~~~~--~~~~~~~~~~~~~~~i~~~l~~G~~IlVQV~K 96 (414)
T TIGR00757 27 NIYKGRVTRILPSLQAAFVDIGL-EKNGFLHASDIGPNY--ECLAPAEAKREAGPSISELLRPGQSVLVQVVK 96 (414)
T ss_pred CEEEEEEeeecCCCceEEEEcCC-CceEEEEHHHcCchh--hccccccccccccCCHHHhCcCCCEEEEEEee
Confidence 6899999999998 99999975 899999999985431 11111000000000223468999999999987
No 105
>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=81.14 E-value=6.7 Score=30.95 Aligned_cols=59 Identities=8% Similarity=-0.052 Sum_probs=45.6
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 428 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~ 428 (439)
...-|+|+++...++.|.|.. ...+.++...+++- .++.+..+++||.|-.+|..++..
T Consensus 8 D~VIG~V~~~~~~~~~VdI~s-~~~a~L~~~~f~ga---------------tk~~rp~L~~GDlV~ArV~~~~~~ 66 (86)
T cd05790 8 DHVIGIVVAKAGDFFKVDIGG-SEPASLSYLAFEGA---------------TKRNRPNLNVGDLVYARVVKANRD 66 (86)
T ss_pred CEEEEEEEEEcCCeEEEEcCC-CcceEechHHcccc---------------cccccccCCCCCEEEEEEEecCCC
Confidence 567899999999999999976 46788887654321 124567899999999999998864
No 106
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=80.53 E-value=11 Score=27.53 Aligned_cols=48 Identities=13% Similarity=0.085 Sum_probs=27.4
Q ss_pred EEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 356 TEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 356 ~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
....|+++.++|+++...+ +-+-+++.++. ...+++||.|+|-|..-.
T Consensus 5 ~~L~V~~~~~~g~fL~~~~-~~~vlLp~~e~----------------------~~~~~~Gd~v~VFvY~D~ 52 (61)
T PF13509_consen 5 NTLKVVDKNEFGYFLDDGE-GKEVLLPKSEV----------------------PEPLKVGDEVEVFVYLDK 52 (61)
T ss_dssp ----EEEE-SSEEEEEETT--EEEEEEGGG----------------------------TTSEEEEEEEE-T
T ss_pred cceEEEEEeCCEEEEECCC-CCEEEechHHc----------------------CCCCCCCCEEEEEEEECC
Confidence 4678999999999987644 45666665433 245899999999998633
No 107
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=72.70 E-value=11 Score=35.43 Aligned_cols=64 Identities=14% Similarity=0.082 Sum_probs=49.3
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 428 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~ 428 (439)
...-|.|.++...+..|.|-. -..+.+++++.... .++.++ .+.+..+++||.|-.+|..+|..
T Consensus 66 D~VIG~I~~v~~~~W~VDI~s-p~~A~L~ls~~~~r---~~~~~~-------~~~r~~l~vGD~v~AkV~~vd~~ 129 (239)
T COG1097 66 DVVIGKIIEVGPSGWKVDIGS-PYPALLSLSDFLRR---KFENAE-------KDLRPFLNVGDLVYAKVVDVDRD 129 (239)
T ss_pred CEEEEEEEEEcccceEEEcCC-ccceEeehhhhhcc---cccccc-------cccccccccCCEEEEEEEEccCC
Confidence 567899999999999999965 46788999887432 222222 23467899999999999999974
No 108
>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=69.46 E-value=8.8 Score=29.98 Aligned_cols=59 Identities=10% Similarity=-0.006 Sum_probs=33.8
Q ss_pred eEEEEEEEEEEcCeEEEEEeCC-----------------ceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCc
Q 013634 354 TDTEARIVKIRSNGFIVFVPKF-----------------GIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQ 416 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~-----------------gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd 416 (439)
....|.|+.++...+.|.+-.. .+.|.++.++.... +.|. -+..+-|+.||
T Consensus 6 diV~~rVtrv~~~~a~v~Il~v~~~~~~~~~~~~~~l~~~f~GiIR~~DVR~t-----e~Dk-------v~~~~~FrpGD 73 (82)
T PF10447_consen 6 DIVIARVTRVNPRQAKVEILCVEGKGNDSINAGDRPLKEPFQGIIRKQDVRAT-----EKDK-------VKMYDCFRPGD 73 (82)
T ss_dssp -EEEEEEEEE-SSEEEEEEEES----------SSS----SS-S-EEEEGGGT------SS-----------GGGT--SSS
T ss_pred CEEEEEEEEEeccEEEEEEEEEEeccccccccCCcccccccEEEEEeeeeccc-----ccch-------hhHHhccCCCC
Confidence 4678999999999999888654 34444444443321 0110 01256789999
Q ss_pred eEEEEEEE
Q 013634 417 TVNIHMEV 424 (439)
Q Consensus 417 ~V~V~v~~ 424 (439)
.|+.+|.+
T Consensus 74 IVrA~ViS 81 (82)
T PF10447_consen 74 IVRARVIS 81 (82)
T ss_dssp EEEEEEEE
T ss_pred EEEEEEee
Confidence 99999975
No 109
>PRK15464 cold shock-like protein CspH; Provisional
Probab=69.41 E-value=13 Score=27.99 Aligned_cols=53 Identities=8% Similarity=-0.111 Sum_probs=37.3
Q ss_pred EEEEEEEEEc-CeE-EEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 356 TEARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 356 ~~g~V~~v~~-~g~-~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
..|+|..... .|+ |+.-++-|-+.++|++.+... ..+.++.||+|+..+..-+
T Consensus 5 ~~G~Vk~fn~~KGfGFI~~~~g~~DvFvH~s~l~~~------------------g~~~l~~G~~V~f~v~~~~ 59 (70)
T PRK15464 5 MTGIVKTFDRKSGKGFIIPSDGRKEVQVHISAFTPR------------------DAEVLIPGLRVEFCRVNGL 59 (70)
T ss_pred ceEEEEEEECCCCeEEEccCCCCccEEEEehhehhc------------------CCCCCCCCCEEEEEEEECC
Confidence 4788888765 343 455566567899999887532 2356899999999987643
No 110
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=68.42 E-value=1.8 Score=40.92 Aligned_cols=76 Identities=14% Similarity=0.213 Sum_probs=55.4
Q ss_pred HHHHhcC-C---eEEEEEEEEEEcCeEEEEEeCCc-eEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEE
Q 013634 346 LIYFRKR-P---TDTEARIVKIRSNGFIVFVPKFG-IEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNI 420 (439)
Q Consensus 346 ~~~l~~~-~---~~~~g~V~~v~~~g~~V~l~~~g-veg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V 420 (439)
|+|..++ | ...-+.|..|.+-|+.|.|-+|+ +||+|-++.|+.. ++ ++..+.+++|-.=-|
T Consensus 6 cR~ye~kyPev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELSrR----------RI----RSI~klirVGr~E~v 71 (304)
T KOG2916|consen 6 CRFYENKYPEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELSRR----------RI----RSIQKLIRVGRNEPV 71 (304)
T ss_pred eehhhccCCCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHHHH----------HH----HHHHHHHhcCCcceE
Confidence 5555544 4 34556677788899999997665 9999999988643 11 233567889988888
Q ss_pred EEEEecCCCCCCceeEE
Q 013634 421 HMEVVEPQPNRPKLQLT 437 (439)
Q Consensus 421 ~v~~vd~~~~~~~i~l~ 437 (439)
.|..||.+ |.=|+||
T Consensus 72 vVlrVDke--kGYIDLS 86 (304)
T KOG2916|consen 72 VVLRVDKE--KGYIDLS 86 (304)
T ss_pred EEEEEcCC--CCceech
Confidence 88999976 8888876
No 111
>PRK15463 cold shock-like protein CspF; Provisional
Probab=62.09 E-value=23 Score=26.72 Aligned_cols=53 Identities=6% Similarity=-0.080 Sum_probs=36.5
Q ss_pred EEEEEEEEEc-CeE-EEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 356 TEARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 356 ~~g~V~~v~~-~g~-~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
..|+|..... .|+ |+.-++-+-+.++|++.+... ..+.++.||+|+..+..-+
T Consensus 5 ~~G~Vk~fn~~kGfGFI~~~~g~~DvFvH~sal~~~------------------g~~~l~~G~~V~f~v~~~~ 59 (70)
T PRK15463 5 MTGIVKTFDGKSGKGLITPSDGRKDVQVHISALNLR------------------DAEELTTGLRVEFCRINGL 59 (70)
T ss_pred ceEEEEEEeCCCceEEEecCCCCccEEEEehhhhhc------------------CCCCCCCCCEEEEEEEECC
Confidence 4788888765 343 444455467889999887642 2456789999999876533
No 112
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=60.13 E-value=64 Score=24.31 Aligned_cols=61 Identities=13% Similarity=0.182 Sum_probs=36.2
Q ss_pred eEEEEEEEEEEcC-eEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRSN-GFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~~-g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
-+.+|.|+...++ -+.|.+++ |..-.++++.. + + +......+||.|.|++...+.. +.
T Consensus 7 ~~~~G~Vi~~~~~~~y~V~~~~-g~~~~c~~~Gk-------l-------r----~~~i~i~vGD~V~ve~~~~~~~--~g 65 (72)
T PRK00276 7 IEMEGTVVEALPNAMFRVELEN-GHEVLAHISGK-------M-------R----KNYIRILPGDKVTVELSPYDLT--KG 65 (72)
T ss_pred EEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEccc-------e-------e----eCCcccCCCCEEEEEEcccCCC--eE
Confidence 4568999988876 45565533 54444443321 1 1 1234478999999998665543 44
Q ss_pred cee
Q 013634 433 KLQ 435 (439)
Q Consensus 433 ~i~ 435 (439)
.|.
T Consensus 66 ~Iv 68 (72)
T PRK00276 66 RIT 68 (72)
T ss_pred EEE
Confidence 544
No 113
>PRK10811 rne ribonuclease E; Reviewed
Probab=55.54 E-value=23 Score=40.09 Aligned_cols=67 Identities=12% Similarity=0.006 Sum_probs=45.6
Q ss_pred eEEEEEEEEEEc--CeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 354 TDTEARIVKIRS--NGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 354 ~~~~g~V~~v~~--~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
.+|.|.|.+|-+ +++||.|.. |..|++++++....+ | ... ...-...+.+..++.||.|-|+|.+-.
T Consensus 40 nIYkGkVenIvPGInAAFVDIG~-gknGFL~L~Di~~~~---f-~~~-~~~~~~~~i~~~Lk~GqeILVQV~KEa 108 (1068)
T PRK10811 40 NIYKGKITRIEPSLEAAFVDYGA-ERHGFLPLKEIAREY---F-PAN-YSAHGRPNIKDVLREGQEVIVQIDKEE 108 (1068)
T ss_pred ceEEEEEecccCCcceeEEEecC-CcceEEEhhhccccc---c-ccc-cccccccccccccCCCCEEEEEEeecc
Confidence 689999999876 589999986 999999998875431 1 110 000000012456889999999998743
No 114
>KOG1856 consensus Transcription elongation factor SPT6 [RNA processing and modification]
Probab=54.20 E-value=16 Score=41.59 Aligned_cols=59 Identities=15% Similarity=0.150 Sum_probs=44.6
Q ss_pred EEEEEEEEEEcCe---EEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCC
Q 013634 355 DTEARIVKIRSNG---FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQ 428 (439)
Q Consensus 355 ~~~g~V~~v~~~g---~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~ 428 (439)
...+.|.+|.... +.|.+.. |+.|+|+.+++++. . + ++....+++|+.|.++|..+|..
T Consensus 988 iV~~~V~~vt~rr~~Cv~v~ld~-G~~g~i~~~~~Sd~---~---------v--~~p~~~v~vgq~v~~kvi~id~e 1049 (1299)
T KOG1856|consen 988 IVPVTVTKVTHRRGICVRVRLDC-GVTGFILAKNLSDR---D---------V--RRPENRVKVGQTVYCKVIKIDKE 1049 (1299)
T ss_pred eEEEeeeEEEecccceeEEEecC-CCceeeeccccChh---h---------c--cCHHHhhccCceEEEEeeeeeHh
Confidence 4566777887766 6678865 99999999888763 1 1 24556778999999999999954
No 115
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=53.25 E-value=56 Score=24.90 Aligned_cols=52 Identities=12% Similarity=0.075 Sum_probs=34.2
Q ss_pred EEEEEEEEc-CeE-EEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 357 EARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 357 ~g~V~~v~~-~g~-~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
+|+|..... .|+ ||.-++-|-+.++|++.+... ..+.++.||.|+..+..-.
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~gg~dVFvH~s~i~~~------------------g~~~l~~G~~V~f~~~~~~ 56 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD------------------GYRTLKAGQSVQFDVHQGP 56 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCCCCccEEEEEeecccc------------------CCCCCCCCCEEEEEEEECC
Confidence 467776654 343 455555568899999887542 2356788888888876533
No 116
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=53.23 E-value=90 Score=25.35 Aligned_cols=62 Identities=6% Similarity=-0.007 Sum_probs=44.1
Q ss_pred eEEEEEEEEEEcCeEE-EEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRSNGFI-VFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~-V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
....|.|+....++.| |.+++ |.+-++++... + +..-.++.||.|.|.+..-+.. +.
T Consensus 21 ~e~~g~V~~~lG~~~~~V~~~d-G~~~la~i~GK-------~------------Rk~IwI~~GD~VlVe~~~~~~~--kg 78 (100)
T PRK04012 21 GEVFGVVEQMLGANRVRVRCMD-GVERMGRIPGK-------M------------KKRMWIREGDVVIVAPWDFQDE--KA 78 (100)
T ss_pred CEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEchh-------h------------cccEEecCCCEEEEEecccCCC--EE
Confidence 5789999998887754 67765 88888877542 1 2246789999999998776643 66
Q ss_pred ceeEE
Q 013634 433 KLQLT 437 (439)
Q Consensus 433 ~i~l~ 437 (439)
.|...
T Consensus 79 ~Iv~r 83 (100)
T PRK04012 79 DIIWR 83 (100)
T ss_pred EEEEE
Confidence 66543
No 117
>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=52.60 E-value=83 Score=24.16 Aligned_cols=59 Identities=10% Similarity=0.032 Sum_probs=40.5
Q ss_pred EEEEEEEEEcCe-EEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCCce
Q 013634 356 TEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRPKL 434 (439)
Q Consensus 356 ~~g~V~~v~~~g-~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i 434 (439)
..|.|+...+++ +.|.+++ |.+-+++++.. + +..-.++.||.|.|.+..-|.. +.+|
T Consensus 2 ~~g~V~~~~g~~~~~V~~~~-g~~~la~i~gK-------~------------rk~iwI~~GD~V~Ve~~~~d~~--kg~I 59 (77)
T cd05793 2 EYGQVEKMLGNGRLEVRCFD-GKKRLCRIRGK-------M------------RKRVWINEGDIVLVAPWDFQDD--KADI 59 (77)
T ss_pred EEEEEEEEcCCCEEEEEECC-CCEEEEEEchh-------h------------cccEEEcCCCEEEEEeccccCC--EEEE
Confidence 468899887776 4577765 88888777542 1 2246789999999998765533 5555
Q ss_pred eE
Q 013634 435 QL 436 (439)
Q Consensus 435 ~l 436 (439)
..
T Consensus 60 v~ 61 (77)
T cd05793 60 IY 61 (77)
T ss_pred EE
Confidence 43
No 118
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=52.30 E-value=59 Score=23.67 Aligned_cols=51 Identities=10% Similarity=-0.061 Sum_probs=33.8
Q ss_pred EEEEEEEEEc--CeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEE
Q 013634 356 TEARIVKIRS--NGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEV 424 (439)
Q Consensus 356 ~~g~V~~v~~--~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~ 424 (439)
+.|+|..... .--|+.-++-+-+-++|.+++... .-..++.||.|+..+..
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~------------------~~~~l~~G~~V~F~~~~ 53 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGN------------------GFRSLKEGDRVEFEVEE 53 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSS------------------SSTS--TTSEEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEecccccccc------------------ccccCCCCCEEEEEEEE
Confidence 3688888775 223455555455788998887653 12567899999999887
No 119
>PF02599 CsrA: Global regulator protein family; InterPro: IPR003751 The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay []. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis [].; GO: 0003723 RNA binding, 0006109 regulation of carbohydrate metabolic process, 0006402 mRNA catabolic process; PDB: 1Y00_B 2JPP_A 1T3O_A 1VPZ_A.
Probab=51.85 E-value=39 Score=24.11 Aligned_cols=29 Identities=10% Similarity=0.075 Sum_probs=21.9
Q ss_pred eeCCceEEeeCceEEEEEEEecCCCCCCceeEE
Q 013634 405 KMDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLT 437 (439)
Q Consensus 405 ~~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~ 437 (439)
.++.+..+.+||.|+|+|.+++ ..+++|-
T Consensus 5 sRk~gE~I~Ig~~I~I~Vl~i~----~~~Vklg 33 (54)
T PF02599_consen 5 SRKVGESIVIGDDIEITVLEIS----GGQVKLG 33 (54)
T ss_dssp EEETT-EEEETTTEEEEEEEEE----TTEEEEE
T ss_pred EccCCCEEEECCCEEEEEEEEc----CCEEEEE
Confidence 3577889999999999999998 3445543
No 120
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=50.99 E-value=87 Score=24.15 Aligned_cols=49 Identities=12% Similarity=0.042 Sum_probs=34.3
Q ss_pred EEEEEEEEcCe-EEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEe
Q 013634 357 EARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 425 (439)
Q Consensus 357 ~g~V~~v~~~g-~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~v 425 (439)
-|.|+....++ +.|++++ |.+-++++... + +..-.++.||.|.|....-
T Consensus 3 i~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK-------~------------Rk~iwI~~GD~VlV~~~~~ 52 (78)
T cd04456 3 IVRVLRMLGNNRHEVECAD-GQRRLVSIPGK-------L------------RKNIWIKRGDFLIVDPIEE 52 (78)
T ss_pred EEEEEEECCCCEEEEEECC-CCEEEEEEchh-------h------------ccCEEEcCCCEEEEEeccc
Confidence 47788877666 5578876 88888877542 1 2236678999999987654
No 121
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria []. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=50.06 E-value=28 Score=26.07 Aligned_cols=22 Identities=18% Similarity=0.401 Sum_probs=17.9
Q ss_pred EEEEEEEECCCCceeEEEEEEe
Q 013634 67 AFSVIWELTPEAEIISTRYTKS 88 (439)
Q Consensus 67 a~s~~~~l~~~G~i~~~~~~~s 88 (439)
.+.+.+.||++|+|.++++..|
T Consensus 17 ~v~v~~~I~~~G~v~~~~v~~s 38 (79)
T PF03544_consen 17 TVVVEFTIDPDGRVSDVRVIQS 38 (79)
T ss_dssp EEEEEEEEETTTEEEEEEEEEE
T ss_pred EEEEEEEEeCCCCEEEEEEEEc
Confidence 5677889999999999876544
No 122
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=49.92 E-value=72 Score=23.85 Aligned_cols=54 Identities=11% Similarity=0.062 Sum_probs=36.3
Q ss_pred EEEEEEEEEEc-CeE-EEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 355 DTEARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 355 ~~~g~V~~v~~-~g~-~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
...|+|..... .|+ |+.-++-|-+-++|++.+... ..+.++.||.|+..+..-+
T Consensus 3 ~~~G~Vk~f~~~kGyGFI~~~~g~~dvfvH~s~l~~~------------------g~~~l~~G~~V~f~~~~~~ 58 (69)
T PRK09507 3 KIKGNVKWFNESKGFGFITPEDGSKDVFVHFSAIQTN------------------GFKTLAEGQRVEFEITNGA 58 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEeeccccc------------------CCCCCCCCCEEEEEEEECC
Confidence 45788887664 333 455555457889999877532 2356789999999877543
No 123
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=49.85 E-value=33 Score=23.08 Aligned_cols=33 Identities=24% Similarity=0.203 Sum_probs=27.6
Q ss_pred eEEEEEEEEEE-cCeEEEEEeCCceEEEEEcccC
Q 013634 354 TDTEARIVKIR-SNGFIVFVPKFGIEGPVYLTPR 386 (439)
Q Consensus 354 ~~~~g~V~~v~-~~g~~V~l~~~gveg~v~~~~l 386 (439)
..+.|.|.++. +..+.|++.++|-...|..+++
T Consensus 13 ~wyra~V~~~~~~~~~~V~f~DyG~~~~v~~~~l 46 (48)
T cd04508 13 KWYRAKITSILSDGKVEVFFVDYGNTEVVPLSDL 46 (48)
T ss_pred eEEEEEEEEECCCCcEEEEEEcCCCcEEEeHHHc
Confidence 57899999998 6668999999999888877654
No 124
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=49.78 E-value=43 Score=29.51 Aligned_cols=51 Identities=20% Similarity=0.164 Sum_probs=39.3
Q ss_pred hCCceeecCcceEEEecCCCCCeeeeEeeccchHHHHHHHHHHHHHHHHHHH
Q 013634 134 ERGALTLASAEVKFQIDTETHDPLDIGMYQIREANQMVEEFMLAANVSVAEQ 185 (439)
Q Consensus 134 ~~Gal~~~~~~~~~~~d~~~~~~~~v~~~~~~~a~~lVeE~MilAN~~vA~~ 185 (439)
+.+.+.+...+.-+.+-+ +|.+.--.+.+..+|..+.+|+|-.+|+++|+-
T Consensus 63 kk~~l~~~kgerIitiy~-sGkVsm~~ikdedEAkeilgel~d~ineA~~kg 113 (193)
T COG4871 63 KKNILILQKGERIITIYG-SGKVSMTMIKDEDEAKEILGELMDIINEAIAKG 113 (193)
T ss_pred ccceEEEeeccEEEEEcc-CCeEEeeeecCHHHHHHHHHHHHHHHHHHHHcc
Confidence 457788887777777754 365544446678899999999999999998874
No 125
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=48.76 E-value=27 Score=26.83 Aligned_cols=25 Identities=28% Similarity=0.448 Sum_probs=16.9
Q ss_pred CceeEEEEEEEECCCCceeEEEEEE
Q 013634 63 VERLAFSVIWELTPEAEIISTRYTK 87 (439)
Q Consensus 63 ~~r~a~s~~~~l~~~G~i~~~~~~~ 87 (439)
.......|.++||++|+|.++++.+
T Consensus 23 ~~~~~~~V~i~i~~dG~v~~~~i~~ 47 (85)
T PF13103_consen 23 SGGLSVTVRITIDPDGRVISVRIVK 47 (85)
T ss_dssp -TT--EEEEEEE-TTSBEEEEEEEE
T ss_pred CCCcEEEEEEEECCCCCEEEEEEec
Confidence 3456678888999999998877654
No 126
>CHL00010 infA translation initiation factor 1
Probab=47.37 E-value=1.2e+02 Score=23.20 Aligned_cols=61 Identities=10% Similarity=0.157 Sum_probs=34.7
Q ss_pred eEEEEEEEEEEc-CeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRS-NGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~-~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
-...|+|+.... .-+.|.+++ |..-.++++.. + + +......+||.|.|++...+.. +.
T Consensus 7 ~~~~G~Vik~lg~~~y~V~~~~-g~~~~c~~rGk-------l-------r----~~~i~~~vGD~V~ve~~~~~~~--~g 65 (78)
T CHL00010 7 IEMEGLVTESLPNGMFRVRLDN-GCQVLGYISGK-------I-------R----RNSIRILPGDRVKVELSPYDLT--KG 65 (78)
T ss_pred EEEEEEEEEEcCCCEEEEEeCC-CCEEEEEeccc-------e-------e----cCCcccCCCCEEEEEEcccCCC--eE
Confidence 356899999885 445565533 54333443221 1 0 1134468899999997655533 44
Q ss_pred cee
Q 013634 433 KLQ 435 (439)
Q Consensus 433 ~i~ 435 (439)
.|.
T Consensus 66 ~Ii 68 (78)
T CHL00010 66 RII 68 (78)
T ss_pred EEE
Confidence 443
No 127
>PRK01712 carbon storage regulator; Provisional
Probab=47.26 E-value=51 Score=24.45 Aligned_cols=28 Identities=7% Similarity=0.055 Sum_probs=22.2
Q ss_pred eCCceEEeeCceEEEEEEEecCCCCCCceeEE
Q 013634 406 MDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLT 437 (439)
Q Consensus 406 ~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~ 437 (439)
++.+..+.+||-++|+|..++. .+++|.
T Consensus 6 Rk~gE~I~Igd~I~I~V~~i~~----~~VrlG 33 (64)
T PRK01712 6 RKVGESLMIGDDIEVTVLGVKG----NQVRIG 33 (64)
T ss_pred ccCCCEEEeCCCEEEEEEEEeC----CEEEEE
Confidence 5678889999999999999883 455554
No 128
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=45.36 E-value=65 Score=29.19 Aligned_cols=56 Identities=11% Similarity=0.155 Sum_probs=40.4
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceE-----------EEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEE
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIE-----------GPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHM 422 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gve-----------g~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v 422 (439)
...-|.|+++....+.|++- +++ |-+|+++..+. | .++....|++||.|+.+|
T Consensus 66 diV~grV~~v~~~~a~V~i~--~ve~~~r~~~~~~~~~ihvs~~~~~----~----------~~~~~d~f~~GDivrA~V 129 (188)
T COG1096 66 DIVYGRVTDVREQRALVRIV--GVEGKERELATSGAADIHVSQVRDG----Y----------VEKLSDAFRIGDIVRARV 129 (188)
T ss_pred CEEEEEEeeccceEEEEEEE--EEecccccCCCCceeeEEEEecccc----c----------ccccccccccccEEEEEE
Confidence 67889999999999888874 343 44566555443 1 123457899999999999
Q ss_pred EEe
Q 013634 423 EVV 425 (439)
Q Consensus 423 ~~v 425 (439)
.+.
T Consensus 130 is~ 132 (188)
T COG1096 130 IST 132 (188)
T ss_pred Eec
Confidence 875
No 129
>TIGR01352 tonB_Cterm TonB family C-terminal domain. This model represents the C-terminal of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to help span the periplasm.
Probab=44.59 E-value=40 Score=24.79 Aligned_cols=21 Identities=14% Similarity=0.243 Sum_probs=17.1
Q ss_pred EEEEEEEECCCCceeEEEEEE
Q 013634 67 AFSVIWELTPEAEIISTRYTK 87 (439)
Q Consensus 67 a~s~~~~l~~~G~i~~~~~~~ 87 (439)
...+.+.|+++|+|.+.++.+
T Consensus 11 ~v~v~~~i~~~G~v~~~~i~~ 31 (74)
T TIGR01352 11 TVVVRFTVDADGRVTSVSVLK 31 (74)
T ss_pred EEEEEEEECCCCCEEEEEEEE
Confidence 366788999999999988753
No 130
>PRK00568 carbon storage regulator; Provisional
Probab=43.67 E-value=58 Score=25.03 Aligned_cols=28 Identities=14% Similarity=0.213 Sum_probs=22.1
Q ss_pred eCCceEEeeCceEEEEEEEecCCCCCCceeEE
Q 013634 406 MDGNLSYSVLQTVNIHMEVVEPQPNRPKLQLT 437 (439)
Q Consensus 406 ~~~~~~~~iGd~V~V~v~~vd~~~~~~~i~l~ 437 (439)
++.+..+.+||-|+++|..+. ..+++|-
T Consensus 6 RK~gEsI~Igd~I~I~Vl~i~----g~~VrlG 33 (76)
T PRK00568 6 RKVNEGIVIDDNIHIKVISID----RGSVRLG 33 (76)
T ss_pred eeCCCeEEeCCCeEEEEEEEc----CCEEEEE
Confidence 567888999999999999888 3455543
No 131
>cd05701 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=43.08 E-value=61 Score=23.97 Aligned_cols=59 Identities=14% Similarity=0.036 Sum_probs=39.7
Q ss_pred EEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecC
Q 013634 355 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEP 427 (439)
Q Consensus 355 ~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~ 427 (439)
.+.|+|-.+.+.-+.|.|.+-|--..++++.--++ -|.+| .+.+++|+.+.|++...+.
T Consensus 3 ~htA~VQh~~kdfAvvSL~~t~~L~a~p~~sHLNd---tfrf~-----------seklkvG~~l~v~lk~~~~ 61 (69)
T cd05701 3 RHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLND---TFRFD-----------SEKLSVGQCLDVTLKDPNC 61 (69)
T ss_pred ccchhhhhhhhceEEEEeeccccEEEEEchhhccc---ccccc-----------ceeeeccceEEEEEecCcc
Confidence 35667777777777888877666566666543222 23332 4778999999999987654
No 132
>PRK14998 cold shock-like protein CspD; Provisional
Probab=42.41 E-value=75 Score=24.12 Aligned_cols=52 Identities=12% Similarity=0.064 Sum_probs=34.4
Q ss_pred EEEEEEEEc-CeE-EEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 357 EARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 357 ~g~V~~v~~-~g~-~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
.|+|..... .|+ |+.-++-|-+.++|++.+... ..+.++.|++|+..+..-+
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~g~~dVFvH~s~l~~~------------------g~~~l~~G~~V~f~~~~~~ 56 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEGGGEDIFAHYSTIQMD------------------GYRTLKAGQSVRFDVHQGP 56 (73)
T ss_pred CeEEEEEeCCCceEEEecCCCCccEEEEeeeeccc------------------CCCCCCCCCEEEEEEEECC
Confidence 467776654 343 455555567889999877532 2366788999888876543
No 133
>COG1551 CsrA RNA-binding global regulator CsrA [Signal transduction mechanisms]
Probab=41.91 E-value=61 Score=24.47 Aligned_cols=22 Identities=9% Similarity=0.018 Sum_probs=19.6
Q ss_pred eCCceEEeeCceEEEEEEEecC
Q 013634 406 MDGNLSYSVLQTVNIHMEVVEP 427 (439)
Q Consensus 406 ~~~~~~~~iGd~V~V~v~~vd~ 427 (439)
++.+..+.+||-|+|+|..++-
T Consensus 6 Rk~~Esi~IgddI~itVl~i~g 27 (73)
T COG1551 6 RKVGESIMIGDDIEITVLSIKG 27 (73)
T ss_pred eecCceEEecCCeEEEEEEEcC
Confidence 5678899999999999999984
No 134
>PRK10943 cold shock-like protein CspC; Provisional
Probab=41.78 E-value=90 Score=23.29 Aligned_cols=53 Identities=11% Similarity=0.081 Sum_probs=35.7
Q ss_pred EEEEEEEEEEc-CeE-EEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEe
Q 013634 355 DTEARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 425 (439)
Q Consensus 355 ~~~g~V~~v~~-~g~-~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~v 425 (439)
...|+|..... .|+ |+.-++-|-+-++|++.+... ..+.+..||.|+..+..-
T Consensus 3 ~~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~------------------g~~~l~~G~~V~f~~~~~ 57 (69)
T PRK10943 3 KIKGQVKWFNESKGFGFITPADGSKDVFVHFSAIQGN------------------GFKTLAEGQNVEFEIQDG 57 (69)
T ss_pred ccceEEEEEeCCCCcEEEecCCCCeeEEEEhhHcccc------------------CCCCCCCCCEEEEEEEEC
Confidence 35788887765 343 444445467889999887542 235678999999887653
No 135
>PRK11712 ribonuclease G; Provisional
Probab=41.23 E-value=67 Score=33.87 Aligned_cols=69 Identities=10% Similarity=-0.008 Sum_probs=44.5
Q ss_pred eEEEEEEEEEEc--CeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEe
Q 013634 354 TDTEARIVKIRS--NGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 425 (439)
Q Consensus 354 ~~~~g~V~~v~~--~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~v 425 (439)
..|.|.|.+|-+ +++||.+.. +-.|++|+++..... ++..+...-.....+....++.||.|-|+|.+-
T Consensus 40 nIY~G~V~~v~pg~~AAFVdIG~-~k~gFL~~~d~~~~~--~~~~~~~~~~~~~~~i~~~l~~Gq~iLVQV~Ke 110 (489)
T PRK11712 40 NIYKGRVSRVLPGMQAAFVDIGL-DKAAFLHASDIVPHT--ECVAGEEQKQFVVRDISELVRQGQDIMVQVVKD 110 (489)
T ss_pred cEEEEEEeecCCCCceeEEeeCC-CccEEEEhhhccchh--hhcccccccccccccHHHhccCCCEEEEEEEeC
Confidence 579999999877 579999975 999999999874320 111110000000001234589999999999873
No 136
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=40.26 E-value=57 Score=22.78 Aligned_cols=34 Identities=26% Similarity=0.261 Sum_probs=28.6
Q ss_pred eEEEEEEEEEEc-CeEEEEEeCCceEEEEEcccCC
Q 013634 354 TDTEARIVKIRS-NGFIVFVPKFGIEGPVYLTPRG 387 (439)
Q Consensus 354 ~~~~g~V~~v~~-~g~~V~l~~~gveg~v~~~~l~ 387 (439)
..+.|.|+++.+ ..+.|.+.++|-...|...++.
T Consensus 17 ~wyra~I~~~~~~~~~~V~f~D~G~~~~v~~~~l~ 51 (57)
T smart00333 17 EWYRARIIKVDGEQLYEVFFIDYGNEEVVPPSDLR 51 (57)
T ss_pred CEEEEEEEEECCCCEEEEEEECCCccEEEeHHHee
Confidence 578999999998 7899999999998888776553
No 137
>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=37.07 E-value=93 Score=23.10 Aligned_cols=52 Identities=10% Similarity=-0.007 Sum_probs=34.7
Q ss_pred EEEEEEEEc-CeE-EEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 357 EARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 357 ~g~V~~v~~-~g~-~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
.|+|..... .|+ |+.-++-|-+.++|.+.+... ..+.++.||.|+..+..-+
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~~~~~------------------g~~~l~~G~~V~f~~~~~~ 56 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEGVDGDIFAHYSTIQMD------------------GYRTLKAGQKVQFEVVQGP 56 (68)
T ss_pred CeEEEEEeCCCCeEEEecCCCCccEEEEHHHhhhc------------------CCCCCCCCCEEEEEEEECC
Confidence 467776553 343 455555567889999887532 2366789999999877644
No 138
>TIGR00202 csrA carbon storage regulator (csrA). Modulates the expression of genes in the glycogen biosynthesis and gluconeogenesis pathways by accelerating the 5'-to-3' degradation of these transcripts through selective RNA binding. The N-terminal end of the sequence (AA 11-45) contains the KH motif which is characteristic of a set of RNA-binding proteins.
Probab=34.79 E-value=1e+02 Score=23.25 Aligned_cols=22 Identities=14% Similarity=0.098 Sum_probs=19.1
Q ss_pred eCCceEEeeCceEEEEEEEecC
Q 013634 406 MDGNLSYSVLQTVNIHMEVVEP 427 (439)
Q Consensus 406 ~~~~~~~~iGd~V~V~v~~vd~ 427 (439)
++.+..+.+||.++|+|..+..
T Consensus 6 Rk~gE~I~Igd~I~I~Vl~i~g 27 (69)
T TIGR00202 6 RKVNESIQIGDDIEVKVLSVKG 27 (69)
T ss_pred ccCCCEEEeCCCEEEEEEEEcC
Confidence 5678899999999999998873
No 139
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=34.22 E-value=1.5e+02 Score=26.10 Aligned_cols=62 Identities=8% Similarity=0.191 Sum_probs=42.2
Q ss_pred eEEEEEEEEEEcCe-EEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~~g-~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
...-|.|+....++ +.|.+.. |..-++|++..- +..-.+..||.|.|.+..-+.. +-
T Consensus 32 gq~~g~V~~~LGn~~f~V~c~d-G~~rLa~I~GKm-------------------RK~IWI~~GD~VlVel~~yd~~--Kg 89 (155)
T PTZ00329 32 GQEYAQVLRMLGNGRLEAYCFD-GVKRLCHIRGKM-------------------RKRVWINIGDIILVSLRDFQDS--KA 89 (155)
T ss_pred CcEEEEEEEEcCCCEEEEEECC-CCEEEEEeeccc-------------------eeeEEecCCCEEEEeccCCCCC--EE
Confidence 45678888888777 4567765 888888876431 1235679999999988655533 55
Q ss_pred ceeEE
Q 013634 433 KLQLT 437 (439)
Q Consensus 433 ~i~l~ 437 (439)
.|...
T Consensus 90 dIi~R 94 (155)
T PTZ00329 90 DVILK 94 (155)
T ss_pred EEEEE
Confidence 55543
No 140
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=34.08 E-value=2.3e+02 Score=22.11 Aligned_cols=61 Identities=15% Similarity=0.119 Sum_probs=41.2
Q ss_pred eEEEEEEEEEEcCe-EEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~~g-~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
....|.|+....++ +.|.+++ |.+-++++... + +..-.++.||.|.|.+..-+. .+.
T Consensus 5 ~q~~g~V~~~lG~~~~~V~~~d-G~~~la~ipgK-------~------------Rk~iwI~~GD~VlVe~~~~~~--~kg 62 (83)
T smart00652 5 GQEIAQVVKMLGNGRLEVMCAD-GKERLARIPGK-------M------------RKKVWIRRGDIVLVDPWDFQD--VKA 62 (83)
T ss_pred CcEEEEEEEEcCCCEEEEEECC-CCEEEEEEchh-------h------------cccEEEcCCCEEEEEecCCCC--CEE
Confidence 45788999887776 4577765 88888877542 1 224667999999998765443 244
Q ss_pred ceeE
Q 013634 433 KLQL 436 (439)
Q Consensus 433 ~i~l 436 (439)
.|..
T Consensus 63 ~Iv~ 66 (83)
T smart00652 63 DIIY 66 (83)
T ss_pred EEEE
Confidence 5543
No 141
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=33.36 E-value=2e+02 Score=21.47 Aligned_cols=53 Identities=15% Similarity=0.082 Sum_probs=35.6
Q ss_pred EEEEEEEEEc-CeE-EEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 356 TEARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 356 ~~g~V~~v~~-~g~-~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
..|+|..... .|+ |+.-++-|-+-++|++.+... ..+.++.||.|+..+..-+
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvfvH~s~l~~~------------------g~~~l~~G~~V~f~~~~~~ 59 (70)
T PRK10354 5 MTGIVKWFNADKGFGFITPDDGSKDVFVHFSAIQND------------------GYKSLDEGQKVSFTIESGA 59 (70)
T ss_pred ceEEEEEEeCCCCcEEEecCCCCccEEEEEeecccc------------------CCCCCCCCCEEEEEEEECC
Confidence 3688877654 332 455555457889999887542 2356789999999877644
No 142
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=33.35 E-value=1.3e+02 Score=27.50 Aligned_cols=33 Identities=15% Similarity=0.313 Sum_probs=25.0
Q ss_pred cCCeEEEEEEEEEEcCeEEEEEeCCceEEEEEc
Q 013634 351 KRPTDTEARIVKIRSNGFIVFVPKFGIEGPVYL 383 (439)
Q Consensus 351 ~~~~~~~g~V~~v~~~g~~V~l~~~gveg~v~~ 383 (439)
......+|.|+.|.+..+.++-..++=.-.|++
T Consensus 37 ~n~~tiEGrVvEV~~~~i~iesk~yn~~v~i~~ 69 (213)
T PRK06763 37 SNFSTIEGRVVEVDNGVIVIKSKQYEEPVSVYI 69 (213)
T ss_pred cccceeeeEEEEEeCCEEEEEeccCCCceEEEe
Confidence 344688999999999999999887665544443
No 143
>PRK09890 cold shock protein CspG; Provisional
Probab=32.15 E-value=2.2e+02 Score=21.29 Aligned_cols=53 Identities=13% Similarity=0.045 Sum_probs=35.5
Q ss_pred EEEEEEEEEc-CeE-EEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 356 TEARIVKIRS-NGF-IVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 356 ~~g~V~~v~~-~g~-~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
..|+|..... .|+ |+.-++-|-+-++|++.+... ..+.++.||.|+..+..-+
T Consensus 5 ~~G~Vk~f~~~kGfGFI~~~~g~~dvFvH~s~l~~~------------------~~~~l~~G~~V~f~~~~~~ 59 (70)
T PRK09890 5 MTGLVKWFNADKGFGFITPDDGSKDVFVHFTAIQSN------------------EFRTLNENQKVEFSIEQGQ 59 (70)
T ss_pred ceEEEEEEECCCCcEEEecCCCCceEEEEEeeeccC------------------CCCCCCCCCEEEEEEEECC
Confidence 4788888764 333 444455457889998877542 2356789999999876544
No 144
>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=31.42 E-value=1.5e+02 Score=21.30 Aligned_cols=51 Identities=14% Similarity=0.022 Sum_probs=34.6
Q ss_pred EEEEEEEEc-Ce-EEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEe
Q 013634 357 EARIVKIRS-NG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVV 425 (439)
Q Consensus 357 ~g~V~~v~~-~g-~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~v 425 (439)
.|+|..... .| -|+.-++-|-+-++|.+.+... ....++.||.|+..+..-
T Consensus 2 ~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~------------------~~~~~~~G~~V~f~~~~~ 54 (65)
T cd04458 2 TGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGD------------------GFRSLEEGDRVEFELEEG 54 (65)
T ss_pred cEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhcc------------------CCCcCCCCCEEEEEEEEC
Confidence 477777665 23 3455555577888888776532 246679999999988764
No 145
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=27.10 E-value=1.3e+02 Score=25.80 Aligned_cols=21 Identities=14% Similarity=-0.061 Sum_probs=14.7
Q ss_pred eEEEEEEEEEEcCe--EEEEEeC
Q 013634 354 TDTEARIVKIRSNG--FIVFVPK 374 (439)
Q Consensus 354 ~~~~g~V~~v~~~g--~~V~l~~ 374 (439)
.-+.|++++..... ..|.+++
T Consensus 23 ~yYPa~~~~~~~~~~~~~V~Fed 45 (131)
T PF08605_consen 23 KYYPATCVGSGVDRDRSLVRFED 45 (131)
T ss_pred eEeeEEEEeecCCCCeEEEEEec
Confidence 56688888875544 6777766
No 146
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=26.04 E-value=1.1e+02 Score=22.41 Aligned_cols=52 Identities=13% Similarity=0.130 Sum_probs=34.6
Q ss_pred EEEEEEEEEEcCe-EEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 355 DTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 355 ~~~g~V~~v~~~g-~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
...|.|+....++ +.|.+++ |.+-.+++... + +..-.++.||.|.|.+..-|
T Consensus 4 e~~~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK-------~------------r~~iwI~~GD~V~V~~~~~d 56 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECED-GEERLARIPGK-------F------------RKRIWIKRGDFVLVEPSPYD 56 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETT-SEEEEEEE-HH-------H------------HTCC---TTEEEEEEESTTC
T ss_pred EEEEEEEEECCCCEEEEEeCC-CCEEEEEeccc-------e------------eeeEecCCCCEEEEEecccC
Confidence 5678999888776 5577765 88888887542 1 33456899999999885444
No 147
>PLN00208 translation initiation factor (eIF); Provisional
Probab=25.97 E-value=2.6e+02 Score=24.37 Aligned_cols=61 Identities=8% Similarity=0.139 Sum_probs=41.2
Q ss_pred eEEEEEEEEEEcCe-EEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEecCCCCCC
Q 013634 354 TDTEARIVKIRSNG-FIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVEPQPNRP 432 (439)
Q Consensus 354 ~~~~g~V~~v~~~g-~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd~~~~~~ 432 (439)
...-|.|+....++ +.|.+.+ |..-+++++.. + +..-.++.||.|.|.+..-+.. +-
T Consensus 32 gq~~g~V~~~lGn~~~~V~c~d-G~~rLa~IpGK-------m------------RKrIWI~~GD~VlVel~~~d~~--Kg 89 (145)
T PLN00208 32 GQEYAQVLRMLGNGRCEALCID-GTKRLCHIRGK-------M------------RKKVWIAAGDIILVGLRDYQDD--KA 89 (145)
T ss_pred CcEEEEEEEEcCCCEEEEEECC-CCEEEEEEecc-------c------------eeeEEecCCCEEEEEccCCCCC--EE
Confidence 45678888887776 4567765 88888887542 1 1245679999999997665543 55
Q ss_pred ceeE
Q 013634 433 KLQL 436 (439)
Q Consensus 433 ~i~l 436 (439)
.|..
T Consensus 90 dIv~ 93 (145)
T PLN00208 90 DVIL 93 (145)
T ss_pred EEEE
Confidence 5543
No 148
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=22.46 E-value=57 Score=25.54 Aligned_cols=64 Identities=17% Similarity=0.288 Sum_probs=32.1
Q ss_pred CcccCCCCHhhHHHHhcCceEEcCCCcccCCCcc-ccccccCCCCCCceeEEEEEEEECCCCceeEEEEEEeE
Q 013634 18 TNFVHPGTPLDDEASKRGTSVYLVERRIDMLPKP-LTEDICSLRADVERLAFSVIWELTPEAEIISTRYTKSV 89 (439)
Q Consensus 18 s~~v~~~s~ld~eA~~R~~svYlp~~~~pMLP~~-Ls~~~~SL~~~~~r~a~s~~~~l~~~G~i~~~~~~~s~ 89 (439)
.+-|++|..|.....+.|-+. .....|+-.. -...+-.|.||+ ++.|.+|++|++...++..+.
T Consensus 4 ~~~V~~GDtLs~iF~~~gls~---~dl~~v~~~~~~~k~L~~L~pGq-----~l~f~~d~~g~L~~L~~~~~~ 68 (85)
T PF04225_consen 4 EYTVKSGDTLSTIFRRAGLSA---SDLYAVLEADGEAKPLTRLKPGQ-----TLEFQLDEDGQLTALRYERSP 68 (85)
T ss_dssp EEE--TT--HHHHHHHTT--H---HHHHHHHHHGGGT--GGG--TT------EEEEEE-TTS-EEEEEEEEET
T ss_pred EEEECCCCcHHHHHHHcCCCH---HHHHHHHhccCccchHhhCCCCC-----EEEEEECCCCCEEEEEEEcCC
Confidence 356888999988888887432 1123333222 122355689996 567799999999877665543
No 149
>COG5428 Uncharacterized conserved small protein [Function unknown]
Probab=22.24 E-value=1.1e+02 Score=22.95 Aligned_cols=21 Identities=5% Similarity=0.259 Sum_probs=17.4
Q ss_pred EEEEEECCCCceeEEEEEEeE
Q 013634 69 SVIWELTPEAEIISTRYTKSV 89 (439)
Q Consensus 69 s~~~~l~~~G~i~~~~~~~s~ 89 (439)
.+.+++|.+|+|..++|..+-
T Consensus 31 di~Idide~GkV~GiEi~~As 51 (69)
T COG5428 31 DILIDIDENGKVIGIEIWNAS 51 (69)
T ss_pred cEEEEecCCCcEEEEEEEchh
Confidence 357899999999999887763
No 150
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=22.14 E-value=5.4e+02 Score=23.37 Aligned_cols=71 Identities=14% Similarity=-0.014 Sum_probs=43.3
Q ss_pred eEEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEe-----eCCceEEeeCceEEEEEEEecC
Q 013634 354 TDTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVK-----MDGNLSYSVLQTVNIHMEVVEP 427 (439)
Q Consensus 354 ~~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~-----~~~~~~~~iGd~V~V~v~~vd~ 427 (439)
+...|.|.+-+..|+.|.|. +-=+-+|+-..+.... .|.+++....+.- .+..-.+.+|..|+.+|.+...
T Consensus 83 EVi~gki~~cs~eG~rvtl~-FFdDI~IP~~~L~~p~--~f~~~e~vWVWey~~Edg~~~~Ly~D~~e~IRFRV~~e~f 158 (202)
T KOG3297|consen 83 EVITGKIKECSEEGLRVTLG-FFDDIFIPKEMLPEPC--VFEPDEQVWVWEYEQEDGPGTKLYFDVGEEIRFRVEDESF 158 (202)
T ss_pred eEEEEEeecCCccceEEEEE-eeeceeechhhCCCCc--ccccccEEEEEEecccCCCCceeEecCCCeEEEEEeeecc
Confidence 34566666667788887775 3335566666665541 3444443333321 2345578999999999988743
No 151
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=22.00 E-value=1.9e+02 Score=20.48 Aligned_cols=33 Identities=15% Similarity=0.051 Sum_probs=24.9
Q ss_pred eEEEEEEEEEEc-CeEEEEEeC--CceEEEEEcccC
Q 013634 354 TDTEARIVKIRS-NGFIVFVPK--FGIEGPVYLTPR 386 (439)
Q Consensus 354 ~~~~g~V~~v~~-~g~~V~l~~--~gveg~v~~~~l 386 (439)
..+.|+|+.+.+ ..+.|+++. .|.+-.++.+++
T Consensus 18 ~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~L 53 (61)
T smart00743 18 SWWEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDL 53 (61)
T ss_pred EEEEEEEEEECCCCEEEEEECCCCcccEEEEeHHHc
Confidence 568999999988 668888887 666666665554
No 152
>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=21.91 E-value=1.7e+02 Score=20.85 Aligned_cols=14 Identities=14% Similarity=0.242 Sum_probs=12.0
Q ss_pred eEEEEEEEEEEcCe
Q 013634 354 TDTEARIVKIRSNG 367 (439)
Q Consensus 354 ~~~~g~V~~v~~~g 367 (439)
..+.|.|..+...|
T Consensus 5 N~l~g~V~~ie~~g 18 (64)
T PF03459_consen 5 NQLPGTVESIENLG 18 (64)
T ss_dssp EEEEEEEEEEEESS
T ss_pred cEEEEEEEEEEECC
Confidence 46899999999888
No 153
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=20.45 E-value=74 Score=24.97 Aligned_cols=33 Identities=15% Similarity=0.231 Sum_probs=22.1
Q ss_pred EEEEECCCCceeEEEEEEeEEecCceecHHHHHHHh
Q 013634 70 VIWELTPEAEIISTRYTKSVIKSCAALSYVEAQARM 105 (439)
Q Consensus 70 ~~~~l~~~G~i~~~~~~~s~I~s~~~ltY~~v~~~l 105 (439)
|.+++|.+|+|++.+|.++..+ ..+-+++.+.+
T Consensus 32 V~V~v~g~g~v~~i~i~~~~~~---~~~~~~L~~~I 64 (93)
T PF02575_consen 32 VTVTVNGNGEVVDIEIDPSALR---PLDPEELEDLI 64 (93)
T ss_dssp EEEEEETTS-EEEEEE-GGGGC---TS-HHHHHHHH
T ss_pred EEEEEecCceEEEEEEehHhhc---cCCHHHHHHHH
Confidence 5669999999999999988775 24555555544
No 154
>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=20.06 E-value=3.6e+02 Score=19.82 Aligned_cols=49 Identities=16% Similarity=0.188 Sum_probs=33.7
Q ss_pred EEEEEEEEEEcCeEEEEEeCCceEEEEEcccCCCCCCCceeecCCeEEEEeeCCceEEeeCceEEEEEEEec
Q 013634 355 DTEARIVKIRSNGFIVFVPKFGIEGPVYLTPRGQKGSGDWYVDEQQQKIVKMDGNLSYSVLQTVNIHMEVVE 426 (439)
Q Consensus 355 ~~~g~V~~v~~~g~~V~l~~~gveg~v~~~~l~~~~~~~~~~d~~~~~l~~~~~~~~~~iGd~V~V~v~~vd 426 (439)
..+|+|..|.+....+-|.+ |-. + .++.+ |. -..++.|.+|.|....++
T Consensus 4 ~veG~I~~id~~~~titLdD-Gks---y--~lp~e----f~-------------~~~L~~G~kV~V~yd~~~ 52 (61)
T PF07076_consen 4 DVEGTIKSIDPETMTITLDD-GKS---Y--KLPEE----FD-------------FDGLKPGMKVVVFYDEVD 52 (61)
T ss_pred cceEEEEEEcCCceEEEecC-CCE---E--ECCCc----cc-------------ccccCCCCEEEEEEEccC
Confidence 46899999999999988876 421 1 12221 22 245789999999887766
Done!