Query 030455
Match_columns 177
No_of_seqs 151 out of 1127
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 13:59:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030455.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030455hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3297 DNA-directed RNA polym 100.0 1.6E-51 3.6E-56 316.7 16.5 172 1-177 1-199 (202)
2 PTZ00162 DNA-directed RNA poly 100.0 1.4E-47 3E-52 300.2 19.0 157 1-175 1-172 (176)
3 COG1095 RPB7 DNA-directed RNA 100.0 4.5E-47 9.8E-52 294.5 17.9 161 1-177 1-176 (183)
4 TIGR00448 rpoE DNA-directed RN 100.0 1.6E-46 3.4E-51 295.2 19.5 161 1-177 1-176 (179)
5 PRK08563 DNA-directed RNA poly 100.0 5.8E-44 1.3E-48 282.1 18.3 161 1-177 1-176 (187)
6 KOG3298 DNA-directed RNA polym 100.0 6.1E-36 1.3E-40 226.6 17.2 155 1-174 1-170 (170)
7 PF08292 RNA_pol_Rbc25: RNA po 100.0 1.3E-33 2.7E-38 208.8 12.6 109 64-177 1-122 (122)
8 cd04462 S1_RNAPII_Rpb7 S1_RNAP 99.9 8.8E-21 1.9E-25 133.0 11.4 88 66-172 1-88 (88)
9 cd04330 RNAP_III_Rpc25_N RNAP_ 99.8 4.3E-21 9.2E-26 132.3 7.7 65 2-66 1-80 (80)
10 cd04329 RNAP_II_Rpb7_N RNAP_II 99.8 8.7E-21 1.9E-25 130.8 7.7 65 2-66 1-80 (80)
11 cd00655 RNAP_Rpb7_N_like RNAP_ 99.8 9.5E-21 2.1E-25 130.6 7.6 65 2-66 1-80 (80)
12 cd04331 RNAP_E_N RNAP_E_N: Rpo 99.8 3.8E-20 8.2E-25 127.6 7.7 64 2-65 1-79 (80)
13 cd04460 S1_RpoE S1_RpoE: RpoE, 99.5 3.2E-14 6.9E-19 101.4 8.8 93 68-176 1-93 (99)
14 PF03876 SHS2_Rpb7-N: SHS2 dom 99.4 3.1E-13 6.7E-18 90.5 6.5 55 8-62 1-70 (70)
15 cd04328 RNAP_I_Rpa43_N RNAP_I_ 99.3 1E-11 2.3E-16 87.0 7.7 64 1-66 8-89 (89)
16 cd04471 S1_RNase_R S1_RNase_R: 99.2 2.2E-10 4.7E-15 78.2 10.1 71 66-143 1-73 (83)
17 PRK11642 exoribonuclease R; Pr 99.2 3.2E-11 6.9E-16 113.5 7.6 84 57-147 634-719 (813)
18 TIGR00358 3_prime_RNase VacB a 99.0 7.7E-10 1.7E-14 102.3 7.8 83 57-146 563-647 (654)
19 TIGR02063 RNase_R ribonuclease 99.0 1.3E-09 2.7E-14 101.7 8.6 83 57-146 618-702 (709)
20 PF00575 S1: S1 RNA binding do 99.0 5.9E-09 1.3E-13 69.7 8.4 65 63-145 1-66 (74)
21 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 98.9 8.6E-09 1.9E-13 71.2 7.4 84 62-174 2-86 (86)
22 cd05708 S1_Rrp5_repeat_sc12 S1 98.7 1.4E-07 3E-12 63.2 9.1 73 66-170 2-76 (77)
23 cd05686 S1_pNO40 S1_pNO40: pNO 98.7 9E-08 2E-12 64.3 8.0 62 64-143 1-64 (73)
24 cd04454 S1_Rrp4_like S1_Rrp4_l 98.7 9.9E-08 2.1E-12 65.4 8.1 80 62-174 2-82 (82)
25 cd05706 S1_Rrp5_repeat_sc10 S1 98.7 2.4E-07 5.2E-12 61.8 9.6 63 65-145 2-65 (73)
26 PRK05054 exoribonuclease II; P 98.7 6.3E-08 1.4E-12 89.5 7.7 84 57-146 550-637 (644)
27 COG0557 VacB Exoribonuclease R 98.6 4E-08 8.7E-13 91.7 5.5 83 57-146 613-697 (706)
28 cd04452 S1_IF2_alpha S1_IF2_al 98.6 6.6E-07 1.4E-11 59.9 9.4 64 64-145 1-67 (76)
29 PRK08582 hypothetical protein; 98.6 5.1E-07 1.1E-11 68.3 9.5 64 62-143 1-65 (139)
30 cd05689 S1_RPS1_repeat_ec4 S1_ 98.6 6.5E-07 1.4E-11 59.5 8.5 63 66-145 3-66 (72)
31 cd04461 S1_Rrp5_repeat_hs8_sc7 98.6 4.4E-07 9.5E-12 62.3 7.7 64 64-145 12-76 (83)
32 cd05698 S1_Rrp5_repeat_hs6_sc5 98.5 4.9E-07 1.1E-11 59.7 7.5 60 67-144 1-61 (70)
33 cd05697 S1_Rrp5_repeat_hs5 S1_ 98.5 7.2E-07 1.6E-11 59.0 7.7 61 67-145 1-62 (69)
34 TIGR02062 RNase_B exoribonucle 98.5 2.2E-07 4.8E-12 85.8 6.4 82 57-146 546-633 (639)
35 PRK05807 hypothetical protein; 98.5 1.1E-06 2.3E-11 66.3 9.0 63 63-143 2-64 (136)
36 PRK07252 hypothetical protein; 98.5 1.4E-06 2.9E-11 64.4 9.2 64 65-146 2-66 (120)
37 cd05690 S1_RPS1_repeat_ec5 S1_ 98.5 1E-06 2.2E-11 57.9 7.6 63 67-146 1-64 (69)
38 cd05696 S1_Rrp5_repeat_hs4 S1_ 98.5 1.4E-06 3E-11 58.3 8.2 61 67-145 1-64 (71)
39 PRK04163 exosome complex RNA-b 98.5 8.7E-07 1.9E-11 72.5 8.5 85 62-175 59-144 (235)
40 cd05705 S1_Rrp5_repeat_hs14 S1 98.4 1.1E-06 2.3E-11 59.4 7.1 66 65-145 2-68 (74)
41 cd05691 S1_RPS1_repeat_ec6 S1_ 98.4 2E-06 4.4E-11 56.9 8.2 61 67-145 1-62 (73)
42 cd05707 S1_Rrp5_repeat_sc11 S1 98.4 1.1E-06 2.5E-11 57.8 6.7 61 67-145 1-62 (68)
43 cd05688 S1_RPS1_repeat_ec3 S1_ 98.4 1.9E-06 4.1E-11 56.1 7.6 62 66-145 1-62 (68)
44 smart00316 S1 Ribosomal protei 98.4 3.2E-06 7E-11 54.8 8.6 61 66-144 2-63 (72)
45 cd05684 S1_DHX8_helicase S1_DH 98.4 3.7E-06 7.9E-11 57.0 9.0 59 67-142 1-63 (79)
46 COG0539 RpsA Ribosomal protein 98.4 9.7E-07 2.1E-11 79.6 7.9 63 66-146 192-254 (541)
47 cd05692 S1_RPS1_repeat_hs4 S1_ 98.4 2.5E-06 5.3E-11 55.4 7.5 59 67-143 1-60 (69)
48 COG1098 VacB Predicted RNA bin 98.4 4.4E-07 9.6E-12 66.8 3.9 64 62-143 1-65 (129)
49 cd05703 S1_Rrp5_repeat_hs12_sc 98.3 3.9E-06 8.6E-11 56.4 7.9 63 67-145 1-64 (73)
50 cd05685 S1_Tex S1_Tex: The C-t 98.3 2.3E-06 5E-11 55.5 6.4 61 67-145 1-62 (68)
51 cd05704 S1_Rrp5_repeat_hs13 S1 98.3 2.3E-06 5E-11 57.3 5.6 60 65-142 2-63 (72)
52 PRK08059 general stress protei 98.3 7.5E-06 1.6E-10 60.6 8.8 65 64-146 5-70 (123)
53 cd05695 S1_Rrp5_repeat_hs3 S1_ 98.2 7E-06 1.5E-10 54.1 7.3 59 67-145 1-60 (66)
54 KOG4134 DNA-dependent RNA poly 98.2 1.7E-05 3.7E-10 63.9 9.8 99 6-105 31-146 (253)
55 cd05687 S1_RPS1_repeat_ec1_hs1 98.2 1.6E-05 3.6E-10 52.4 8.1 58 67-142 1-59 (70)
56 PRK09521 exosome complex RNA-b 98.2 6.4E-06 1.4E-10 65.2 6.9 80 61-175 59-149 (189)
57 cd04472 S1_PNPase S1_PNPase: P 98.1 1.1E-05 2.3E-10 52.5 6.4 59 67-143 1-60 (68)
58 PTZ00248 eukaryotic translatio 98.1 1E-05 2.2E-10 68.9 7.9 65 64-146 15-82 (319)
59 PRK07400 30S ribosomal protein 98.1 1.9E-05 4.2E-10 67.4 9.4 64 64-145 194-257 (318)
60 TIGR03591 polynuc_phos polyrib 98.1 2.6E-06 5.6E-11 79.4 3.6 116 9-143 553-678 (684)
61 cd05694 S1_Rrp5_repeat_hs2_sc2 98.1 4.5E-05 9.8E-10 51.5 8.8 55 65-143 3-59 (74)
62 PRK03987 translation initiatio 98.0 2E-05 4.4E-10 65.6 8.1 65 64-146 6-73 (262)
63 PLN00207 polyribonucleotide nu 98.0 1.1E-05 2.4E-10 76.5 7.0 67 59-143 746-814 (891)
64 cd05702 S1_Rrp5_repeat_hs11_sc 98.0 4.1E-05 8.8E-10 50.7 6.8 61 67-143 1-62 (70)
65 cd04453 S1_RNase_E S1_RNase_E: 97.9 4.6E-05 1E-09 53.2 6.8 67 63-144 4-73 (88)
66 cd05693 S1_Rrp5_repeat_hs1_sc1 97.9 3.3E-05 7.3E-10 55.2 6.0 72 65-143 2-82 (100)
67 cd04465 S1_RPS1_repeat_ec2_hs2 97.9 0.00011 2.3E-09 48.2 7.9 57 67-143 1-57 (67)
68 PHA02945 interferon resistance 97.9 0.00011 2.5E-09 51.0 8.0 64 64-146 9-75 (88)
69 cd04473 S1_RecJ_like S1_RecJ_l 97.9 9E-05 1.9E-09 50.2 7.3 53 63-141 13-66 (77)
70 PRK07899 rpsA 30S ribosomal pr 97.9 6.9E-05 1.5E-09 67.4 8.5 63 66-146 208-270 (486)
71 cd05791 S1_CSL4 S1_CSL4: CSL4, 97.8 9.3E-05 2E-09 52.1 7.0 82 62-174 2-92 (92)
72 COG2183 Tex Transcriptional ac 97.8 4.7E-05 1E-09 71.0 6.7 65 65-147 657-722 (780)
73 PRK11824 polynucleotide phosph 97.8 0.00013 2.9E-09 68.2 9.4 64 62-143 617-681 (693)
74 PRK07899 rpsA 30S ribosomal pr 97.8 0.00014 3.1E-09 65.4 9.1 64 66-147 293-357 (486)
75 PRK12269 bifunctional cytidyla 97.7 0.00016 3.4E-09 69.1 9.0 67 65-146 751-818 (863)
76 cd04455 S1_NusA S1_NusA: N-uti 97.7 0.00018 3.9E-09 47.4 6.7 55 65-143 2-56 (67)
77 TIGR02696 pppGpp_PNP guanosine 97.7 9.4E-05 2E-09 69.0 7.2 66 63-142 644-710 (719)
78 PRK06676 rpsA 30S ribosomal pr 97.7 0.00018 3.9E-09 62.6 8.3 65 64-146 190-254 (390)
79 PRK13806 rpsA 30S ribosomal pr 97.7 0.00018 4E-09 64.7 8.5 65 65-146 291-356 (491)
80 cd00164 S1_like S1_like: Ribos 97.7 0.0002 4.3E-09 45.3 6.2 57 70-144 1-58 (65)
81 PRK13806 rpsA 30S ribosomal pr 97.7 0.0002 4.4E-09 64.5 8.3 63 66-146 379-442 (491)
82 PRK06299 rpsA 30S ribosomal pr 97.6 0.00025 5.5E-09 64.6 7.9 65 65-146 372-437 (565)
83 TIGR00717 rpsA ribosomal prote 97.5 0.00041 8.9E-09 62.5 8.5 63 65-145 445-508 (516)
84 COG0539 RpsA Ribosomal protein 97.5 0.00039 8.5E-09 63.0 7.2 65 65-147 276-341 (541)
85 PRK07400 30S ribosomal protein 97.4 0.00068 1.5E-08 57.9 8.1 64 64-145 29-93 (318)
86 PRK06676 rpsA 30S ribosomal pr 97.4 0.00098 2.1E-08 58.1 9.1 65 65-147 276-341 (390)
87 PRK09202 nusA transcription el 97.4 0.00046 1E-08 61.9 6.9 61 62-146 130-190 (470)
88 PRK12269 bifunctional cytidyla 97.4 0.00086 1.9E-08 64.2 9.0 63 66-146 493-555 (863)
89 PRK06299 rpsA 30S ribosomal pr 97.4 0.00083 1.8E-08 61.3 8.6 65 64-146 199-263 (565)
90 TIGR00717 rpsA ribosomal prote 97.4 0.00085 1.8E-08 60.4 8.3 64 66-146 359-423 (516)
91 COG1097 RRP4 RNA-binding prote 97.3 0.0015 3.2E-08 53.5 8.4 85 62-175 60-145 (239)
92 PRK00087 4-hydroxy-3-methylbut 97.3 0.0012 2.5E-08 61.5 8.9 64 65-146 561-625 (647)
93 cd05790 S1_Rrp40 S1_Rrp40: Rrp 97.3 0.0024 5.2E-08 44.5 8.2 63 62-143 2-65 (86)
94 PRK00087 4-hydroxy-3-methylbut 97.2 0.0012 2.6E-08 61.3 8.1 64 65-146 476-539 (647)
95 PF03293 Pox_RNA_pol: Poxvirus 97.0 0.063 1.4E-06 40.5 13.8 120 6-141 7-144 (160)
96 COG1093 SUI2 Translation initi 97.0 0.00062 1.3E-08 56.3 3.3 66 64-147 9-77 (269)
97 PRK12327 nusA transcription el 97.0 0.0021 4.6E-08 55.9 6.7 95 11-145 95-189 (362)
98 TIGR01953 NusA transcription t 96.8 0.0044 9.6E-08 53.5 6.9 60 62-145 127-187 (341)
99 COG1185 Pnp Polyribonucleotide 96.3 0.0094 2E-07 55.3 6.4 63 62-142 615-678 (692)
100 PRK12328 nusA transcription el 95.7 0.032 6.8E-07 48.7 6.6 95 11-145 99-194 (374)
101 COG1096 Predicted RNA-binding 95.3 0.13 2.7E-06 40.8 8.0 87 62-174 60-148 (188)
102 PF10447 EXOSC1: Exosome compo 95.1 0.088 1.9E-06 36.3 5.8 24 64-87 2-25 (82)
103 PRK12329 nusA transcription el 93.9 0.18 3.9E-06 45.0 6.5 59 62-144 148-212 (449)
104 TIGR00757 RNaseEG ribonuclease 92.5 0.34 7.5E-06 42.9 6.1 75 63-143 22-99 (414)
105 PF13509 S1_2: S1 domain; PDB: 92.1 0.17 3.6E-06 32.6 2.9 36 66-101 1-36 (61)
106 KOG3409 Exosomal 3'-5' exoribo 90.6 1.6 3.5E-05 34.3 7.3 64 63-142 65-137 (193)
107 PHA02858 EIF2a-like PKR inhibi 89.2 0.74 1.6E-05 31.9 4.0 65 62-146 12-79 (86)
108 KOG1067 Predicted RNA-binding 88.4 0.81 1.7E-05 42.2 4.8 63 66-146 668-731 (760)
109 KOG1004 Exosomal 3'-5' exoribo 87.3 8 0.00017 31.4 9.3 94 52-174 51-145 (230)
110 KOG1070 rRNA processing protei 84.0 4.8 0.0001 40.9 7.9 85 65-167 508-608 (1710)
111 KOG1070 rRNA processing protei 83.9 1.7 3.7E-05 43.9 4.8 63 66-146 599-662 (1710)
112 COG4776 Rnb Exoribonuclease II 83.0 0.84 1.8E-05 41.1 2.2 73 64-146 559-637 (645)
113 COG1107 Archaea-specific RecJ- 81.5 1.5 3.3E-05 40.5 3.3 58 65-146 121-179 (715)
114 cd05699 S1_Rrp5_repeat_hs7 S1_ 76.5 5 0.00011 26.9 3.8 57 67-139 1-60 (72)
115 PF10246 MRP-S35: Mitochondria 75.2 13 0.00029 26.6 5.9 59 62-145 19-78 (104)
116 PRK11712 ribonuclease G; Provi 72.9 9.6 0.00021 34.7 5.9 76 63-144 35-113 (489)
117 PRK10811 rne ribonuclease E; R 67.2 20 0.00044 35.4 6.9 72 64-144 36-110 (1068)
118 cd04486 YhcR_OBF_like YhcR_OBF 64.9 39 0.00085 22.6 6.3 25 119-143 36-60 (78)
119 COG2996 Predicted RNA-bindinin 64.1 22 0.00047 30.0 5.7 52 66-143 155-207 (287)
120 KOG2916 Translation initiation 55.6 11 0.00024 31.6 2.7 36 64-99 14-52 (304)
121 PF11604 CusF_Ec: Copper bindi 48.5 30 0.00064 22.7 3.4 55 72-142 1-57 (70)
122 PF03504 Chlam_OMP6: Chlamydia 48.2 34 0.00074 23.7 3.7 39 94-138 48-91 (95)
123 PRK09838 periplasmic copper-bi 47.1 55 0.0012 23.8 4.9 55 70-140 45-101 (115)
124 PF01938 TRAM: TRAM domain; I 42.5 46 0.00099 20.7 3.5 30 57-86 28-60 (61)
125 KOG4078 Putative mitochondrial 41.9 37 0.0008 25.9 3.4 63 58-145 74-137 (173)
126 PF07238 PilZ: PilZ domain; I 39.9 94 0.002 20.3 5.1 35 53-87 8-42 (102)
127 TIGR02866 CoxB cytochrome c ox 33.0 80 0.0017 24.9 4.3 21 124-144 117-137 (201)
128 COG2996 Predicted RNA-bindinin 28.5 82 0.0018 26.6 3.7 38 64-101 71-109 (287)
129 PF02237 BPL_C: Biotin protein 28.4 1.1E+02 0.0023 18.3 3.4 19 66-84 11-29 (48)
130 PRK12327 nusA transcription el 27.3 3.6E+02 0.0078 23.6 7.7 57 22-79 118-187 (362)
131 PF01835 A2M_N: MG2 domain; I 26.9 81 0.0018 21.3 3.0 20 125-144 8-27 (99)
132 PF14326 DUF4384: Domain of un 25.3 1.6E+02 0.0035 19.5 4.2 14 127-140 2-15 (83)
133 PF00394 Cu-oxidase: Multicopp 23.4 2.1E+02 0.0044 21.4 4.9 22 124-145 60-81 (159)
134 PF11396 DUF2874: Protein of u 22.7 98 0.0021 19.0 2.6 38 21-58 7-44 (61)
135 COG1622 CyoA Heme/copper-type 21.7 1.7E+02 0.0036 24.2 4.4 29 115-143 122-156 (247)
136 TIGR01433 CyoA cytochrome o ub 21.1 1.6E+02 0.0035 23.8 4.1 21 124-144 139-159 (226)
137 COG0621 MiaB 2-methylthioadeni 21.1 3.2E+02 0.0069 24.6 6.2 21 66-86 415-435 (437)
138 PRK12328 nusA transcription el 20.3 3.7E+02 0.008 23.7 6.4 53 27-80 127-193 (374)
No 1
>KOG3297 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=1.6e-51 Score=316.67 Aligned_cols=172 Identities=48% Similarity=0.922 Sum_probs=162.9
Q ss_pred CeEEEEeeeeEEECCCCCCccHHHHHHHHHHhHhcCc---------------ccccceeeeCCCCeeeEEEEEEEeeccC
Q 030455 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDK---------------EIEGGFVYPGEGASTHTVKFRLVVFRPF 65 (177)
Q Consensus 1 MF~~~~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k---------------~i~~g~I~~g~G~~~~~V~f~~~~f~p~ 65 (177)
||++.+++|+|+|||++|.+++.++|+++|++||+|| ++++|+|.||||+++.+|.||+++||||
T Consensus 1 MF~Lsel~D~VrI~P~qf~~~~~~ai~~eL~~k~anKvl~nvGLCI~vyDi~~v~e~~v~pGDGas~~~V~FR~vVFrPF 80 (202)
T KOG3297|consen 1 MFYLSELEDTVRIPPSQFEKPLEDAIKEELNRKLANKVLPNVGLCICVYDILEVEEGIVLPGDGASYARVWFRVVVFRPF 80 (202)
T ss_pred CeeehhcccceecChHHhCchHHHHHHHHHHHHHHhhhcccccEEEEEeEeeeecceEEecCCCceEEEEEEEEEEEecc
Confidence 9999999999999999999999999999999999999 7899999999999999999999999999
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeC-----CeeeEEcCCCEEEEEEEE
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFG-----DTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~-----~~~~~~~~G~~VRvrV~~ 140 (177)
+|||+.|+|+++++.|+.++|||||++++|.++||+++.| +++++. |+|.|+ .++++++.|..|||||.+
T Consensus 81 ~gEVi~gki~~cs~eG~rvtl~FFdDI~IP~~~L~~p~~f--~~~e~v---WVWey~~Edg~~~~Ly~D~~e~IRFRV~~ 155 (202)
T KOG3297|consen 81 VGEVITGKIKECSEEGLRVTLGFFDDIFIPKEMLPEPCVF--EPDEQV---WVWEYEQEDGPGTKLYFDVGEEIRFRVED 155 (202)
T ss_pred cceEEEEEeecCCccceEEEEEeeeceeechhhCCCCccc--ccccEE---EEEEecccCCCCceeEecCCCeEEEEEee
Confidence 9999999999999999999999999999999999999999 998888 999997 578999999999999999
Q ss_pred EeCCCCcccc-------cCCCCCCCCeEEEEEecCCCCccccCC
Q 030455 141 VNYPSIPIEQ-------AEGSKPFAPMVINGSIDYDGLGPVSWW 177 (177)
Q Consensus 141 v~~~~~~~~~-------~~~~~~~~~~~i~gs~~~~gLG~i~Ww 177 (177)
..|.+.+.+. .+..+..+||.++|||+++|||++|||
T Consensus 156 e~f~d~~p~~~~~~~t~~e~~e~~~py~l~gs~~~~GLG~lsWW 199 (202)
T KOG3297|consen 156 ESFVDVSPEGNSTAITGAEDPEKESPYTLLGSMNEDGLGPLSWW 199 (202)
T ss_pred ecccccCccccccccccccccccCCCeEEEEEecCCCCccchhh
Confidence 9998876432 344567889999999999999999999
No 2
>PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional
Probab=100.00 E-value=1.4e-47 Score=300.17 Aligned_cols=157 Identities=24% Similarity=0.380 Sum_probs=149.6
Q ss_pred CeEEEEeeeeEEECCCCCCccHHHHHHHHHHhHhcCc---------------ccccceeeeCCCCeeeEEEEEEEeeccC
Q 030455 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDK---------------EIEGGFVYPGEGASTHTVKFRLVVFRPF 65 (177)
Q Consensus 1 MF~~~~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k---------------~i~~g~I~~g~G~~~~~V~f~~~~f~p~ 65 (177)
||++++++|+|+|||++|+++++++|+++|+++|+|| ++++|+|.||||+++|+|+|+|++||||
T Consensus 1 MF~~~~l~d~v~i~P~~f~~~~~~~i~~~L~~~~egkv~~~~GliV~v~di~~i~~G~I~~gdG~~~~~V~FraivFrPf 80 (176)
T PTZ00162 1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQDGTGMIVVNVKYQAIVFKPF 80 (176)
T ss_pred CcEEEEEEEEEEECHHHcCccHHHHHHHHHHHHHCCCCcCcccEEEEEEEeeEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence 9999999999999999999999999999999999998 8899999999999999999999999999
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
+||+++|+|++++++|+|+++||++ +++|.+++|+++.| |++++. |+|..++++++++.|+.||+||++++++.
T Consensus 81 ~gEVv~g~V~~v~~~G~~v~~Gp~~-ifI~~~~l~~~~~f--d~~~~~---~~~~~~~~~~~i~~g~~VR~rV~~v~~~~ 154 (176)
T PTZ00162 81 KDEVLDAIVTDVNKLGFFAQAGPLK-AFVSRSAIPPDFVY--DSDSAY---PCYISSDGQIQIKPNTEVRLRLQGVRYDA 154 (176)
T ss_pred CCCEEEEEEEEEecceEEEEeeCeE-EEEcHHHCCCccEE--CCCCCc---ceEecCCCcEEECCCCEEEEEEEEEEecC
Confidence 9999999999999999999999998 99999999999999 999888 99998888999999999999999999854
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCcccc
Q 030455 146 IPIEQAEGSKPFAPMVINGSIDYDGLGPVS 175 (177)
Q Consensus 146 ~~~~~~~~~~~~~~~~i~gs~~~~gLG~i~ 175 (177)
. + +.++|||++||||+++
T Consensus 155 ~-----~-------~~~i~T~~~~~LG~~~ 172 (176)
T PTZ00162 155 S-----N-------LFAIATINSDYLGPIE 172 (176)
T ss_pred C-----C-------cEEEEEecCCCcCccc
Confidence 2 2 6999999999999974
No 3
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=100.00 E-value=4.5e-47 Score=294.46 Aligned_cols=161 Identities=30% Similarity=0.497 Sum_probs=151.2
Q ss_pred CeEEEEeeeeEEECCCCCCccHHHHHHHHHHhHhcCc---------------ccccceeeeCCCCeeeEEEEEEEeeccC
Q 030455 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDK---------------EIEGGFVYPGEGASTHTVKFRLVVFRPF 65 (177)
Q Consensus 1 MF~~~~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k---------------~i~~g~I~~g~G~~~~~V~f~~~~f~p~ 65 (177)
||++++++|+|+|||++|+++++++++++|++||+|| ++++|+|.+|||++||+|+|+|++|+|+
T Consensus 1 My~l~~~~d~VripP~~fg~~~~~~v~~~L~~k~eG~~~~~~G~~v~V~~v~~igeG~I~~GDG~~y~~V~f~al~fkP~ 80 (183)
T COG1095 1 MYKLVELEDTVRIPPSYFGEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPF 80 (183)
T ss_pred CcEEEEEeeEEEeCHHHcCccHHHHHHHHHHHHhcceEccccCEEEEEEEeeEeeccEEecCCCcEEEEEEEEEEEEEec
Confidence 9999999999999999999999999999999999998 8899999999999999999999999999
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
.||+++|.|++++++|+||++||+++++|.++.++|++.| |++. |.|.+++++++++.||.||+||+++++..
T Consensus 81 ~gEVV~GeVv~~~~~G~fV~igp~dglvh~sqi~dd~~~~--d~~~-----~~~~g~~tk~~i~~gd~VR~RIv~~s~~~ 153 (183)
T COG1095 81 RGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDDYIDY--DEKN-----KVLIGEETKRVLKVGDKVRARIVGVSLKS 153 (183)
T ss_pred cccEEEEEEEEEeecceEEEeccccccccHhhccCccccc--Cccc-----ceeeecccceEEecCCEEEEEEEEEeccc
Confidence 9999999999999999999999999999999999997777 8765 56999999999999999999999999976
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCccccCC
Q 030455 146 IPIEQAEGSKPFAPMVINGSIDYDGLGPVSWW 177 (177)
Q Consensus 146 ~~~~~~~~~~~~~~~~i~gs~~~~gLG~i~Ww 177 (177)
++. .+ ..|.+||++||||+++||
T Consensus 154 ~~~--~~-------~~I~lTmrq~~LGklew~ 176 (183)
T COG1095 154 RRP--RE-------SKIGLTMRQPGLGKLEWI 176 (183)
T ss_pred Ccc--cc-------ceEEEEeccccCCcchhh
Confidence 522 12 699999999999999998
No 4
>TIGR00448 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE.
Probab=100.00 E-value=1.6e-46 Score=295.18 Aligned_cols=161 Identities=32% Similarity=0.504 Sum_probs=151.0
Q ss_pred CeEEEEeeeeEEECCCCCCccHHHHHHHHHHhHhcCc---------------ccccceeeeCCCCeeeEEEEEEEeeccC
Q 030455 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDK---------------EIEGGFVYPGEGASTHTVKFRLVVFRPF 65 (177)
Q Consensus 1 MF~~~~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k---------------~i~~g~I~~g~G~~~~~V~f~~~~f~p~ 65 (177)
||++++++|+|+|||++|+++++++|+++|++||+|| ++++|+|.||||+++|+|+|+|++|+|+
T Consensus 1 Mf~~~~l~d~v~i~P~~~~~~~~~~i~~~l~~~~~gk~~~~~G~~i~v~di~~i~~g~i~~gdG~~~~~V~f~~i~f~p~ 80 (179)
T TIGR00448 1 MYILSKIADTVRIPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVIPGDGSAYHNVTFRALVFKPE 80 (179)
T ss_pred CeEEEEEeeEEEECHHHhCccHHHHHHHHHHHHhcCcCcCCcCEEEEEEEeEEecCCEEECCCCCEEEEEEEEEEEEecc
Confidence 9999999999999999999999999999999999998 7899999999999999999999999999
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
+||+++|+|++++++|+|+++||+++++++++++++++.| |++++. |+| ++++.+|+.||.|||||.++++++
T Consensus 81 ~gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~--d~~~~~---~~~--~~~~~~~~~Gd~VrvrV~~v~~~~ 153 (179)
T TIGR00448 81 LGEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYY--DPKESA---LIG--KETKKVLDEGDKVRARIVALSLKD 153 (179)
T ss_pred CCCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEE--ccccce---EEE--ccCCeEEcCCCEEEEEEEEEEccC
Confidence 9999999999999999999999999999999999999999 999998 665 677899999999999999999976
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCccccCC
Q 030455 146 IPIEQAEGSKPFAPMVINGSIDYDGLGPVSWW 177 (177)
Q Consensus 146 ~~~~~~~~~~~~~~~~i~gs~~~~gLG~i~Ww 177 (177)
. .++ ..+|.|||++||||+++|+
T Consensus 154 ~---~~~------~~~I~lt~k~~~LG~~~w~ 176 (179)
T TIGR00448 154 R---RPE------GSKIGLTMRQPLLGKLEWI 176 (179)
T ss_pred C---CCC------cceEEEEeccCcCCccccc
Confidence 4 111 1488999999999999996
No 5
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=100.00 E-value=5.8e-44 Score=282.14 Aligned_cols=161 Identities=25% Similarity=0.406 Sum_probs=149.3
Q ss_pred CeEEEEeeeeEEECCCCCCccHHHHHHHHHHhHhcCc---------------ccccceeeeCCCCeeeEEEEEEEeeccC
Q 030455 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDK---------------EIEGGFVYPGEGASTHTVKFRLVVFRPF 65 (177)
Q Consensus 1 MF~~~~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k---------------~i~~g~I~~g~G~~~~~V~f~~~~f~p~ 65 (177)
||++++++|+|+|||++|+++++++|.++|+++|+|| ++++|+|.||||+++|+|+|+|++|+|+
T Consensus 1 MF~~~~l~d~v~i~P~~~~~~~~~~i~~~l~~~~~~k~~~~~G~~v~v~di~~i~~g~i~~gdg~~~~~v~f~~lvf~P~ 80 (187)
T PRK08563 1 MYKLVKLEDVVRIPPEMFGEDLEEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPE 80 (187)
T ss_pred CeEEEEEeEEEEECHHHcCccHHHHHHHHHHHHhhCcCcCCcCEEEEEEEeEEecccEEecCCCCcEEEEEEEEEEEecc
Confidence 9999999999999999999999999999999999998 7899999999999999999999999999
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
+||+++|+|++++++|+|+++|++++++++++++++++.| |++++. | .+++.+.+|+.||.|||||.++++.+
T Consensus 81 ~GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~--d~~~~~---~--~~~~~~~~i~~Gd~VrvrV~~v~~~~ 153 (187)
T PRK08563 81 LQEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISY--DPKNGR---L--IGKESKRVLKVGDVVRARIVAVSLKE 153 (187)
T ss_pred CCCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEE--ccccce---E--EEccCCeEEcCCCEEEEEEEEEEccc
Confidence 9999999999999999999999999999999999998999 999888 4 45677889999999999999999854
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCccccCC
Q 030455 146 IPIEQAEGSKPFAPMVINGSIDYDGLGPVSWW 177 (177)
Q Consensus 146 ~~~~~~~~~~~~~~~~i~gs~~~~gLG~i~Ww 177 (177)
. .+. ...|.+||++||||+++||
T Consensus 154 ~---~~~------~~~I~ls~~~~~LG~~~w~ 176 (187)
T PRK08563 154 R---RPR------GSKIGLTMRQPGLGKLEWI 176 (187)
T ss_pred C---CCC------CCEEEEEecCCCCCcHHHH
Confidence 3 110 1389999999999999999
No 6
>KOG3298 consensus DNA-directed RNA polymerase subunit E' [Transcription]
Probab=100.00 E-value=6.1e-36 Score=226.60 Aligned_cols=155 Identities=26% Similarity=0.442 Sum_probs=141.6
Q ss_pred CeEEEEeeeeEEECCCCCCccHHHHHHHHHHhHhcCc---------------ccccceeeeCCCCeeeEEEEEEEeeccC
Q 030455 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDK---------------EIEGGFVYPGEGASTHTVKFRLVVFRPF 65 (177)
Q Consensus 1 MF~~~~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k---------------~i~~g~I~~g~G~~~~~V~f~~~~f~p~ 65 (177)
||+...++..+.++|++|+.++++.|++.|.+..++| +|++|+|.+++|.+.|+|+|+|++||||
T Consensus 1 mff~~~l~~~i~l~p~~~gp~~~~~l~~~L~~~veg~ctg~~Gyvi~vt~ld~Ig~g~I~~~~G~v~FpVky~av~Fkpf 80 (170)
T KOG3298|consen 1 MFFHKDLDLNICLHPSYFGPNLQAILKRKLLAEVEGKCTGKYGYVIAVTTLDNIGEGRIRPGTGFVTFPVKYKAVTFKPF 80 (170)
T ss_pred CcceeeeeeeeeecccccCchHHHHHHHHHHHHhhccccccccEEEEEEEhhhccCCccccCCceEEEEEEEEEEEEeec
Confidence 9999999999999999999999999999999877766 8999999999999999999999999999
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
+||+++|+|+++++.|+|++.||+ .+++.+++.|+.++| ++.++. +++..++.. .|++|+.||++|+++++..
T Consensus 81 KGEVvdgvV~~Vnk~G~F~~~GPl-~~f~sshl~ppd~~f--~p~~n~---P~f~~~d~s-~I~~~~~VR~kiigtr~~~ 153 (170)
T KOG3298|consen 81 KGEVVDGVVTKVNKMGVFARSGPL-EVFYSSHLKPPDYEF--DPGENP---PNFQTEDES-VIQKGVEVRLKIIGTRVDE 153 (170)
T ss_pred CCcEEEEEEEEEeeeeEEEeccce-EeeeecccCCCCccc--CCCCCC---Ccccccccc-eeeeCcEEEEEEEEEEEee
Confidence 999999999999999999999999 588999999999999 888775 556655444 9999999999999999843
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCccc
Q 030455 146 IPIEQAEGSKPFAPMVINGSIDYDGLGPV 174 (177)
Q Consensus 146 ~~~~~~~~~~~~~~~~i~gs~~~~gLG~i 174 (177)
.+ +.++||+++|+||++
T Consensus 154 -----~~-------i~algtl~~D~LG~i 170 (170)
T KOG3298|consen 154 -----TE-------IFALGTLKGDYLGPI 170 (170)
T ss_pred -----ee-------EEEEEEecCcccccC
Confidence 32 999999999999986
No 7
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=100.00 E-value=1.3e-33 Score=208.83 Aligned_cols=109 Identities=49% Similarity=0.965 Sum_probs=85.1
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEe-CCeeeEEcCCCEEEEEEEEEe
Q 030455 64 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEF-GDTKYVIDGLDEIKFRVLSVN 142 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~-~~~~~~~~~G~~VRvrV~~v~ 142 (177)
||+||++.|+|+++++.||+|+||||++|+||.++|++++.| |++.+. |+|.+ +++.++|+.|+.|||||.++.
T Consensus 1 PF~gEvl~g~I~~~~~~Gi~vslgFFddI~IP~~~L~~ps~f--d~~~~~---W~W~~~~~~~l~~d~ge~IRFRV~~~~ 75 (122)
T PF08292_consen 1 PFVGEVLTGKIKSSTAEGIRVSLGFFDDIFIPPSLLPEPSRF--DEEEQA---WVWEYDEEQELFFDIGEEIRFRVESEI 75 (122)
T ss_dssp --TT-EEEEEEEEEETTEEEEEECCEEEEEEECCCC-TTEEE--ECCCTE---EEEEESSSEEEEE-TT-EEEEEEEEEE
T ss_pred CCCCCEEEEEEEecCCCcEEEEecccccEEECHHHCCCCCcc--CccCCE---EEEECCCCceeEccCCCEEEEEEeEEE
Confidence 899999999999999999999999999999999999999999 999999 99999 899999999999999999999
Q ss_pred CCCCccc------------ccCCCCCCCCeEEEEEecCCCCccccCC
Q 030455 143 YPSIPIE------------QAEGSKPFAPMVINGSIDYDGLGPVSWW 177 (177)
Q Consensus 143 ~~~~~~~------------~~~~~~~~~~~~i~gs~~~~gLG~i~Ww 177 (177)
|.+.+.. .....+.+|||.|+|||+++|||+++||
T Consensus 76 f~d~~p~~~~~~~~~~~~~~~~~~~~~~Py~I~gs~~~~GLG~~sWW 122 (122)
T PF08292_consen 76 FPDVPPTPPPSAEASGEEEEEEEDEPKPPYQIIGSINEDGLGLVSWW 122 (122)
T ss_dssp E---------------------------SEEEEEEB-STT-EEGGGC
T ss_pred EecCCCCCcccccccccccccccccCCCCeEEEEEecCCCCcccccC
Confidence 9765421 1234567999999999999999999999
No 8
>cd04462 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination.
Probab=99.85 E-value=8.8e-21 Score=133.03 Aligned_cols=88 Identities=20% Similarity=0.342 Sum_probs=74.8
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
+|||++|+|++++++|+|+++||++.+|+.. ++|+++.| |++.+. |+|. .+++++++.|+.|||||.+++++.
T Consensus 1 kgEVi~g~V~~v~~~G~~v~~Gpl~~f~~~~-~ip~~~~~--~~~~~~---~~~~-~~~~~~i~~g~~VR~rV~~v~~~~ 73 (88)
T cd04462 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRH-LIPSDMEF--DPNASP---PCFT-SNEDIVIKKDTEVRLKIIGTRVDA 73 (88)
T ss_pred CCcEEEEEEEEEeccEEEEEEcCceEEEEee-ecCccceE--CCcCCC---CeEe-CCCcEEECCCCEEEEEEEEEEEcc
Confidence 6999999999999999999999997655554 44666888 987777 8887 447899999999999999999842
Q ss_pred CcccccCCCCCCCCeEEEEEecCCCCc
Q 030455 146 IPIEQAEGSKPFAPMVINGSIDYDGLG 172 (177)
Q Consensus 146 ~~~~~~~~~~~~~~~~i~gs~~~~gLG 172 (177)
.. +.++|||++||||
T Consensus 74 -----~~-------~~~igt~~~~~LG 88 (88)
T cd04462 74 -----TD-------IFAIGTIKDDYLG 88 (88)
T ss_pred -----Cc-------eEEEEEccCCCCC
Confidence 22 7999999999998
No 9
>cd04330 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis.
Probab=99.84 E-value=4.3e-21 Score=132.35 Aligned_cols=65 Identities=54% Similarity=0.976 Sum_probs=63.2
Q ss_pred eEEEEeeeeEEECCCCCCccHHHHHHHHHHhHhcCc---------------ccccceeeeCCCCeeeEEEEEEEeeccCC
Q 030455 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDK---------------EIEGGFVYPGEGASTHTVKFRLVVFRPFV 66 (177)
Q Consensus 2 F~~~~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k---------------~i~~g~I~~g~G~~~~~V~f~~~~f~p~~ 66 (177)
|++++++|+|+|||++|+++++++|+++|++||+|| ++++|+|.+|||+++|+|+|+|++||||+
T Consensus 1 F~~~~l~d~v~i~P~~fg~~~~~~i~~~L~~ky~gkv~~~~Gl~v~v~di~~i~eG~I~~gdG~~~~~V~Fr~lvFrPf~ 80 (80)
T cd04330 1 FILSEIEDTVRIPPSQFSRPLNDAIEDELNKKYANKVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80 (80)
T ss_pred CEEEEEEEEEEECHHHcCcCHHHHHHHHHHHHhCCcEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEECCC
Confidence 789999999999999999999999999999999998 78999999999999999999999999985
No 10
>cd04329 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter.
Probab=99.84 E-value=8.7e-21 Score=130.79 Aligned_cols=65 Identities=29% Similarity=0.580 Sum_probs=63.3
Q ss_pred eEEEEeeeeEEECCCCCCccHHHHHHHHHHhHhcCc---------------ccccceeeeCCCCeeeEEEEEEEeeccCC
Q 030455 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDK---------------EIEGGFVYPGEGASTHTVKFRLVVFRPFV 66 (177)
Q Consensus 2 F~~~~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k---------------~i~~g~I~~g~G~~~~~V~f~~~~f~p~~ 66 (177)
|++++++|+|+|||++||++++++|+++|+++|+|| ++++|+|.+|||+++|+|+|+|++||||+
T Consensus 1 F~~~~l~d~v~i~P~~fg~~l~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~~G~I~~gdG~~~~~V~F~aivfrPf~ 80 (80)
T cd04329 1 FFKIELEHNILLHPSYFGPNLKEYLEQKLLEEVEGTCTGDYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPFK 80 (80)
T ss_pred CEEEEEEEEEEECHHHhCccHHHHHHHHHHHHhCCcCcCceeEEEEEEEeeEecCcEEEcCCCCEEEEEEEEEEEEEccC
Confidence 789999999999999999999999999999999998 88999999999999999999999999985
No 11
>cd00655 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex.
Probab=99.84 E-value=9.5e-21 Score=130.62 Aligned_cols=65 Identities=29% Similarity=0.494 Sum_probs=63.2
Q ss_pred eEEEEeeeeEEECCCCCCccHHHHHHHHHHhHhcCc---------------ccccceeeeCCCCeeeEEEEEEEeeccCC
Q 030455 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDK---------------EIEGGFVYPGEGASTHTVKFRLVVFRPFV 66 (177)
Q Consensus 2 F~~~~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k---------------~i~~g~I~~g~G~~~~~V~f~~~~f~p~~ 66 (177)
|++++++|+|+|||++||++++++|.++|++||+|| ++++|+|.+|||+++|+|+|+|++||||+
T Consensus 1 f~l~~l~d~v~i~P~~f~~~~~~~i~~~L~~k~~gkv~~~~G~~v~v~di~~i~~G~I~~gdG~~~~~V~F~~ivFrPf~ 80 (80)
T cd00655 1 FQILEIADLVSVPPKYFGDDCKGVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPFS 80 (80)
T ss_pred CEEEEEEEEEEECHHHhCccHHHHHHHHHHHHhCCeEeCCccEEEEEEEeEEEcCCEEECCCCCEEEEEEEEEEEEEcCC
Confidence 789999999999999999999999999999999998 88999999999999999999999999985
No 12
>cd04331 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA.
Probab=99.82 E-value=3.8e-20 Score=127.57 Aligned_cols=64 Identities=31% Similarity=0.600 Sum_probs=62.4
Q ss_pred eEEEEeeeeEEECCCCCCccHHHHHHHHHHhHhcCc---------------ccccceeeeCCCCeeeEEEEEEEeeccC
Q 030455 2 FYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDK---------------EIEGGFVYPGEGASTHTVKFRLVVFRPF 65 (177)
Q Consensus 2 F~~~~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k---------------~i~~g~I~~g~G~~~~~V~f~~~~f~p~ 65 (177)
|++++++|+|+|||++||++++++|.++|+++|+|| ++++|+|.+|||+++|+|+|+|++|||.
T Consensus 1 f~~~~l~d~vri~P~~fg~~~~~~i~~~L~~~~egk~~~~~G~iv~v~di~~i~eG~I~~gdG~~~~~V~F~~ivFrP~ 79 (80)
T cd04331 1 YKLVELEDVVRVPPELFGEDLEEAVLEILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFKPE 79 (80)
T ss_pred CEEEEEEEeEEECHHHcCcCHHHHHHHHHHHHhcCcCcCCCCEEEEEEEEEEecCCEEEcCCCCEEEEEEEEEEEEecC
Confidence 789999999999999999999999999999999998 8899999999999999999999999995
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=99.55 E-value=3.2e-14 Score=101.43 Aligned_cols=93 Identities=19% Similarity=0.284 Sum_probs=79.3
Q ss_pred CEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCCCc
Q 030455 68 EIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPSIP 147 (177)
Q Consensus 68 Ev~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~~~ 147 (177)
|++.|+|++++++|+||+++..+++++.+++.++++.| ++.... |.+++.+..|++||.|+++|.+++..++
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~--~~~~~~-----~~~~~~~~~~~~Gd~v~vkI~~vd~~~~- 72 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISY--DPKNKR-----LIGEETKRVLKVGDVVRARIVAVSLKER- 72 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEe--chhhee-----ecccCcCCEECCCCEEEEEEEEEeHHHC-
Confidence 68999999999999999998789999999998888888 887776 8888888899999999999999986332
Q ss_pred ccccCCCCCCCCeEEEEEecCCCCccccC
Q 030455 148 IEQAEGSKPFAPMVINGSIDYDGLGPVSW 176 (177)
Q Consensus 148 ~~~~~~~~~~~~~~i~gs~~~~gLG~i~W 176 (177)
.+.. -.+..|+++++||++.|
T Consensus 73 --~~~~------~~i~ls~k~~~~g~~~~ 93 (99)
T cd04460 73 --RPRE------SKIGLTMRQPGLGKLEW 93 (99)
T ss_pred --cCCC------ceEEEEEecCCCCcHHH
Confidence 1000 27888999999999999
No 14
>PF03876 SHS2_Rpb7-N: SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397; InterPro: IPR005576 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable []. This entry represents the N-terminal, heterodimerisation domain of RPB7.; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2C35_F 3HKZ_E 2PMZ_T 2CKZ_D 2Y0S_E 2RF4_A 2JA7_G 1Y1V_G 2JA5_G 4A3D_G ....
Probab=99.44 E-value=3.1e-13 Score=90.46 Aligned_cols=55 Identities=42% Similarity=0.671 Sum_probs=50.8
Q ss_pred eeeEEECCCCCCccHHHHHHHHHHhHhcCc---------------ccccceeeeCCCCeeeEEEEEEEee
Q 030455 8 EHTLRLPPHLLRLPLNEAIKLELENVFLDK---------------EIEGGFVYPGEGASTHTVKFRLVVF 62 (177)
Q Consensus 8 ~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k---------------~i~~g~I~~g~G~~~~~V~f~~~~f 62 (177)
+|+|+|||++|+++++++|+++|.++|++| .+++|+|.+|+|+++|+|+|+|++|
T Consensus 1 e~~v~l~P~~l~~~~~~~i~~~L~~~~~~k~~~~~G~~i~v~~i~~~~~g~I~~~~g~~~~~V~f~~lvF 70 (70)
T PF03876_consen 1 EDTVRLPPSYLGPDLKDGIKEQLLDKYEGKYIPELGVVIAVTDIKEISEGKIIPGDGFVYFKVTFRALVF 70 (70)
T ss_dssp EEEEEE-GGGTTSTHHHHHHHHHHHHHTTEEETTTEEEEEEEEEEEESCEEE-TTTSSEEEEEEEEEEEE
T ss_pred CcEEEECHHHhCcCHHHHHHHHHHHHHhCcCcCCceEEEEEeeeeEecCcEEECCCCCEEEEEEEEEEEC
Confidence 689999999999899999999999999988 7899999999999999999999998
No 15
>cd04328 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, invo
Probab=99.30 E-value=1e-11 Score=87.03 Aligned_cols=64 Identities=28% Similarity=0.357 Sum_probs=57.0
Q ss_pred CeEEEEeeeeEEECCCCCCccHHHHHHHHHHhHhcCc----------------cccc--ceeeeCCCCeeeEEEEEEEee
Q 030455 1 MFYLSKIEHTLRLPPHLLRLPLNEAIKLELENVFLDK----------------EIEG--GFVYPGEGASTHTVKFRLVVF 62 (177)
Q Consensus 1 MF~~~~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k----------------~i~~--g~I~~g~G~~~~~V~f~~~~f 62 (177)
||.+.++++.|+|+|++|++.. ++|+++|+++|. | .+++ |+|.+++|.++++|+|++++|
T Consensus 8 ~f~~~~~~~~v~l~P~~~~~~~-~~i~~~l~~~l~-ky~~~l~Gv~l~~~di~~~~~~~~~i~~~~~~~~~~V~~~~lVF 85 (89)
T cd04328 8 CFETLTVSLYVSLAPKYLGNPL-TGIKAQLLNPLL-KYSPKLKGVVLAYSNIKLLEGELAKIVDDSPFIFVWISADFLVF 85 (89)
T ss_pred cEEEEEEEEEEEECchhhcCHh-HHHHHHHhhhHh-hhcccCCeEEEEecceEeccccceeeeCCCcEEEEEEEEEEEEE
Confidence 8999999999999999998654 599999999876 5 3335 999999999999999999999
Q ss_pred ccCC
Q 030455 63 RPFV 66 (177)
Q Consensus 63 ~p~~ 66 (177)
||++
T Consensus 86 rP~~ 89 (89)
T cd04328 86 RPKI 89 (89)
T ss_pred ecCC
Confidence 9985
No 16
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=99.20 E-value=2.2e-10 Score=78.19 Aligned_cols=71 Identities=24% Similarity=0.139 Sum_probs=62.2
Q ss_pred CCCEEEEEEEeeeCCeeEEEecc--cceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGF--FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~--~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
+|++++|+|++++++|+||+++. ++++++.+++.++.+.| |+.+.. +.++.....|++||.|+++|.+++.
T Consensus 1 ~g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~--d~~~~~-----~~~~~~~~~~~~gd~v~v~v~~vd~ 73 (83)
T cd04471 1 VGEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEF--DEENHA-----LVGERTGKVFRLGDKVKVRVVRVDL 73 (83)
T ss_pred CCCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEE--cccceE-----EEeccCCCEEcCCCEEEEEEEEecc
Confidence 48999999999999999999984 89999998887777778 887755 7777777899999999999999985
No 17
>PRK11642 exoribonuclease R; Provisional
Probab=99.20 E-value=3.2e-11 Score=113.51 Aligned_cols=84 Identities=18% Similarity=0.148 Sum_probs=75.9
Q ss_pred EEEEeeccCCCCEEEEEEEeeeCCeeEEEec--ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEE
Q 030455 57 FRLVVFRPFVGEIIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEI 134 (177)
Q Consensus 57 f~~~~f~p~~gEv~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~V 134 (177)
++|.+++.++|++++|+|++++++|+||+|. +++|+++.+++-+++|.| |+..+. +.+++++..|++||.|
T Consensus 634 ~~~~~m~~~iGe~f~G~Is~V~~fGifVeL~~~~vEGlV~vs~L~~d~y~~--d~~~~~-----L~g~~~~~~~~lGD~V 706 (813)
T PRK11642 634 LKCDFMLDQVGNVFKGVISSVTGFGFFVRLDDLFIDGLVHVSSLDNDYYRF--DQVGQR-----LIGESSGQTYRLGDRV 706 (813)
T ss_pred HHHhhhhccCCcEEEEEEEEeecCceEEEECCCCeeeeEEEeecCCcceEe--cchheE-----EecccCCcEECCCCEE
Confidence 4566788999999999999999999999995 499999999998888999 998888 8888889999999999
Q ss_pred EEEEEEEeCCCCc
Q 030455 135 KFRVLSVNYPSIP 147 (177)
Q Consensus 135 RvrV~~v~~~~~~ 147 (177)
+|+|.+++..++.
T Consensus 707 ~VkV~~vD~~~rk 719 (813)
T PRK11642 707 EVRVEAVNMDERK 719 (813)
T ss_pred EEEEEEeecCCCe
Confidence 9999999987653
No 18
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=99.01 E-value=7.7e-10 Score=102.27 Aligned_cols=83 Identities=14% Similarity=0.021 Sum_probs=74.9
Q ss_pred EEEEeeccCCCCEEEEEEEeeeCCeeEEEec--ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEE
Q 030455 57 FRLVVFRPFVGEIIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEI 134 (177)
Q Consensus 57 f~~~~f~p~~gEv~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~V 134 (177)
++|.+++.++|++++|+|++++++|+||+|. .++|+++.+++-+++|.| |+.... +.+++++..|++||+|
T Consensus 563 ~~~~yl~~~iG~~~~g~I~~v~~~GifV~L~~~~veGlV~~s~l~~d~y~~--d~~~~~-----l~g~~~~~~~~lGD~V 635 (654)
T TIGR00358 563 LKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHISTLHNDYYVF--DQEKMA-----LIGKGTGKVYRIGDRV 635 (654)
T ss_pred HHHHhhhhCCCcEEEEEEEeEEcCcEEEEecCCceEEEEEeEeCCCcceEE--eccccE-----EEeccCCcEECCCCEE
Confidence 4566788999999999999999999999995 589999999998888889 999888 8888888999999999
Q ss_pred EEEEEEEeCCCC
Q 030455 135 KFRVLSVNYPSI 146 (177)
Q Consensus 135 RvrV~~v~~~~~ 146 (177)
+|+|.+++..++
T Consensus 636 ~Vki~~vd~~~~ 647 (654)
T TIGR00358 636 TVKLTEVNMETR 647 (654)
T ss_pred EEEEEEEecccC
Confidence 999999997654
No 19
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=98.99 E-value=1.3e-09 Score=101.68 Aligned_cols=83 Identities=19% Similarity=0.076 Sum_probs=74.3
Q ss_pred EEEEeeccCCCCEEEEEEEeeeCCeeEEEec--ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEE
Q 030455 57 FRLVVFRPFVGEIIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEI 134 (177)
Q Consensus 57 f~~~~f~p~~gEv~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~V 134 (177)
++|.++++++|++++|+|++++++|+||+|. .++|+++.+++.++++.| |+.... +.+++.+..|++||+|
T Consensus 618 ~~~~yl~~~iG~~~~g~V~~v~~fGifV~L~~~~~eGlvhis~l~~d~~~~--d~~~~~-----l~g~~~~~~~~lGd~V 690 (709)
T TIGR02063 618 KKAEYMSEKIGEEFEGVISGVTSFGLFVELENNTIEGLVHISTLKDDYYVF--DEKGLA-----LVGERTGKVFRLGDRV 690 (709)
T ss_pred HHHHhhhccCCcEEEEEEEEEEeCCEEEEecCCceEEEEEeeecCCCcEEE--cccceE-----EEeccCCcEECCCCEE
Confidence 4566788999999999999999999999996 489999999998888889 998887 8888888899999999
Q ss_pred EEEEEEEeCCCC
Q 030455 135 KFRVLSVNYPSI 146 (177)
Q Consensus 135 RvrV~~v~~~~~ 146 (177)
+|+|.+++..++
T Consensus 691 ~Vkv~~vd~~~~ 702 (709)
T TIGR02063 691 KVRVVKADLDTG 702 (709)
T ss_pred EEEEEEEecccC
Confidence 999999987543
No 20
>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=98.95 E-value=5.9e-09 Score=69.74 Aligned_cols=65 Identities=20% Similarity=0.232 Sum_probs=50.9
Q ss_pred ccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEE
Q 030455 63 RPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 141 (177)
Q Consensus 63 ~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v 141 (177)
++..|++++|+|++++++|+||.++ .++++++.+++.++ + . .+....+++|+.|+++|.++
T Consensus 1 k~~~G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~---~--~-------------~~~~~~~~~G~~v~v~v~~v 62 (74)
T PF00575_consen 1 KLKEGDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDD---R--I-------------DDPSEVYKIGQTVRVKVIKV 62 (74)
T ss_dssp -SSTTSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSS---E--E-------------SSSHGTCETTCEEEEEEEEE
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCc---c--c-------------cccccccCCCCEEEEEEEEE
Confidence 5789999999999999999999998 88776666655432 2 1 22233889999999999999
Q ss_pred eCCC
Q 030455 142 NYPS 145 (177)
Q Consensus 142 ~~~~ 145 (177)
+...
T Consensus 63 d~~~ 66 (74)
T PF00575_consen 63 DKEK 66 (74)
T ss_dssp ETTT
T ss_pred ECCC
Confidence 9754
No 21
>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=98.88 E-value=8.6e-09 Score=71.17 Aligned_cols=84 Identities=15% Similarity=0.178 Sum_probs=65.3
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
|.|.+|++++|+|++++++|++|.++ .++++++.+++..+.. +... ++....+++||.|+++|.+
T Consensus 2 y~p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~----~~~~----------~~~~~~l~vGd~i~~~V~~ 67 (86)
T cd05789 2 YIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRT----DEDE----------LNMRSYLDEGDLIVAEVQS 67 (86)
T ss_pred CcCCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCC----ccch----------HHHHhhCCCCCEEEEEEEE
Confidence 57899999999999999999999996 7889988887653211 1100 2223478999999999999
Q ss_pred EeCCCCcccccCCCCCCCCeEEEEEecCCCCccc
Q 030455 141 VNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPV 174 (177)
Q Consensus 141 v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~i 174 (177)
++- . ..+..|+++++||.+
T Consensus 68 ~~~-------~--------~~i~LS~~~~~~g~~ 86 (86)
T cd05789 68 VDS-------D--------GSVSLHTRSLKYGKL 86 (86)
T ss_pred ECC-------C--------CCEEEEeCcccccCC
Confidence 852 1 278899999999975
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=98.73 E-value=1.4e-07 Score=63.19 Aligned_cols=73 Identities=14% Similarity=0.201 Sum_probs=56.1
Q ss_pred CCCEEEEEEEeeeCCeeEEEec--ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 66 VGEIIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
+|+++.|+|++++++|+||++. ..+++++.+++.+++ .. +....|++||.|+++|.+++.
T Consensus 2 ~g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~-~~-----------------~~~~~~~~Gd~v~v~i~~vd~ 63 (77)
T cd05708 2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNR-VA-----------------DASKLFRVGDKVRAKVLKIDA 63 (77)
T ss_pred CCCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCc-cC-----------------CHhHeecCCCEEEEEEEEEeC
Confidence 6999999999999999999996 578888887765431 11 123489999999999999985
Q ss_pred CCCcccccCCCCCCCCeEEEEEecCCC
Q 030455 144 PSIPIEQAEGSKPFAPMVINGSIDYDG 170 (177)
Q Consensus 144 ~~~~~~~~~~~~~~~~~~i~gs~~~~g 170 (177)
..+ ++..+++..+
T Consensus 64 ~~~--------------~i~ls~k~~~ 76 (77)
T cd05708 64 EKK--------------RISLGLKASY 76 (77)
T ss_pred CCC--------------EEEEEEEeec
Confidence 432 6777776654
No 23
>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=98.72 E-value=9e-08 Score=64.29 Aligned_cols=62 Identities=19% Similarity=0.301 Sum_probs=49.9
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEe-cc-cceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEE
Q 030455 64 PFVGEIIAAKLKESDANGLRLSL-GF-FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 141 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~l-g~-~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v 141 (177)
|..|++++|+|++++++|+|+++ |. .++++|.+++.++ .+ + +.+..+++||.|+++|.++
T Consensus 1 ~~~g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~--~~--~--------------~~~~~~~~Gd~v~vkv~~v 62 (73)
T cd05686 1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSC--RV--D--------------DPSEVVDVGEKVWVKVIGR 62 (73)
T ss_pred CcCCCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCC--cc--c--------------CHhhEECCCCEEEEEEEEE
Confidence 56899999999999999999999 43 6899888866442 23 2 2334799999999999998
Q ss_pred eC
Q 030455 142 NY 143 (177)
Q Consensus 142 ~~ 143 (177)
+.
T Consensus 63 d~ 64 (73)
T cd05686 63 EM 64 (73)
T ss_pred CC
Confidence 75
No 24
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=98.71 E-value=9.9e-08 Score=65.36 Aligned_cols=80 Identities=16% Similarity=0.147 Sum_probs=62.0
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
|.|.+|+++.|+|++++..|++|.++ .++++++.+++..+ + .. +....+++||.|+++|.+
T Consensus 2 y~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~---~--~~-------------~~~~~~~~GD~i~~~V~~ 63 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEK---D--KK-------------EIRKSLQPGDLILAKVIS 63 (82)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCc---c--hH-------------HHHhcCCCCCEEEEEEEE
Confidence 57999999999999999999999996 66666666555332 1 11 112268999999999999
Q ss_pred EeCCCCcccccCCCCCCCCeEEEEEecCCCCccc
Q 030455 141 VNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPV 174 (177)
Q Consensus 141 v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~i 174 (177)
++- . ..+..|++++.||.+
T Consensus 64 ~~~-------~--------~~i~LS~~~~~~Gvi 82 (82)
T cd04454 64 LGD-------D--------MNVLLTTADNELGVI 82 (82)
T ss_pred eCC-------C--------CCEEEEECCCCCccC
Confidence 863 1 279999999999975
No 25
>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=98.70 E-value=2.4e-07 Score=61.83 Aligned_cols=63 Identities=21% Similarity=0.249 Sum_probs=50.4
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
.+|+++.|+|++++++|+||+|+ .++++++.+++.++ | +.+. ...|++||.|+++|.+++.
T Consensus 2 ~~G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~---~--~~~~-------------~~~~~~Gd~v~~~V~~~d~ 63 (73)
T cd05706 2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDD---Y--SEAL-------------PYKFKKNDIVRACVLSVDV 63 (73)
T ss_pred CCCCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCc---c--cccc-------------ccccCCCCEEEEEEEEEeC
Confidence 47999999999999999999995 78898888877554 2 2111 2378999999999999986
Q ss_pred CC
Q 030455 144 PS 145 (177)
Q Consensus 144 ~~ 145 (177)
..
T Consensus 64 ~~ 65 (73)
T cd05706 64 PN 65 (73)
T ss_pred CC
Confidence 43
No 26
>PRK05054 exoribonuclease II; Provisional
Probab=98.66 E-value=6.3e-08 Score=89.53 Aligned_cols=84 Identities=14% Similarity=0.023 Sum_probs=64.9
Q ss_pred EEEEeeccCCCC--EEEEEEEeeeCCeeEEEec--ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCC
Q 030455 57 FRLVVFRPFVGE--IIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLD 132 (177)
Q Consensus 57 f~~~~f~p~~gE--v~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~ 132 (177)
++|.+++.++|+ .++|+|++++++|+||+|. .++++++.+++.++.+.|+++.+... .. ..+++.|++||
T Consensus 550 ~~~~y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~veglV~~~~l~~~~~~y~~~~~~~~-----~~-~~~~~~~~lGd 623 (644)
T PRK05054 550 LYARYLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAFIPASFLHAVRDELVCNQENGT-----VQ-IKGETVYKLGD 623 (644)
T ss_pred HHHHHHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEEEEccccCCCccceEEccccce-----EE-EeCCEEEcCCC
Confidence 455678899975 9999999999999999994 68899999888775444333655544 22 22447999999
Q ss_pred EEEEEEEEEeCCCC
Q 030455 133 EIKFRVLSVNYPSI 146 (177)
Q Consensus 133 ~VRvrV~~v~~~~~ 146 (177)
+|+|+|.+++..++
T Consensus 624 ~V~V~v~~vd~~~~ 637 (644)
T PRK05054 624 VIDVTLAEVRMETR 637 (644)
T ss_pred EEEEEEEEEccccC
Confidence 99999999997654
No 27
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=98.63 E-value=4e-08 Score=91.66 Aligned_cols=83 Identities=20% Similarity=0.150 Sum_probs=75.1
Q ss_pred EEEEeeccCCCCEEEEEEEeeeCCeeEEEec-c-cceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEE
Q 030455 57 FRLVVFRPFVGEIIAAKLKESDANGLRLSLG-F-FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEI 134 (177)
Q Consensus 57 f~~~~f~p~~gEv~~g~V~~v~~~Gifv~lg-~-~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~V 134 (177)
.+|.+++-++||+++|+|++++.+|+||.+. + +|++++++.+.+++|.| ++.... +.++.++..++.||.|
T Consensus 613 ~~~~~m~~~vg~~f~g~V~~v~~~g~~V~l~~~~ieglV~~s~L~~d~y~~--~~~~~~-----l~~~~~~~~~~lgd~v 685 (706)
T COG0557 613 LKAEYMKKRVGEEFDGVVTGVTSFGFFVELPELGLEGLVHISSLPDDYYHF--DERGQA-----LVGEKSGKVYRLGDEV 685 (706)
T ss_pred HHHHHHHHhcCCEEEEEEEEEEeccEEEEecccccccceEcccCCCceeee--ccccce-----eeccccccccccCCEE
Confidence 4566788999999999999999999999994 4 89999999999999999 998877 8899999999999999
Q ss_pred EEEEEEEeCCCC
Q 030455 135 KFRVLSVNYPSI 146 (177)
Q Consensus 135 RvrV~~v~~~~~ 146 (177)
+|||.+++..++
T Consensus 686 ~v~v~~v~~~~~ 697 (706)
T COG0557 686 KVKVTSVDLDER 697 (706)
T ss_pred EEEEEEEccccc
Confidence 999999987554
No 28
>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=98.59 E-value=6.6e-07 Score=59.93 Aligned_cols=64 Identities=20% Similarity=0.215 Sum_probs=50.0
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEec---ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 64 PFVGEIIAAKLKESDANGLRLSLG---FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~lg---~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
|.+|+++.|+|+++.++|+|+++. .++++++.+++.+++.. +-...|++||.|+++|.+
T Consensus 1 ~~~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~------------------~~~~~~~~Gd~v~vkv~~ 62 (76)
T cd04452 1 PEEGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIR------------------SIRKLVKVGRKEVVKVIR 62 (76)
T ss_pred CCCCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccC------------------CHHHeeCCCCEEEEEEEE
Confidence 568999999999999999999994 27888888766443211 113378999999999999
Q ss_pred EeCCC
Q 030455 141 VNYPS 145 (177)
Q Consensus 141 v~~~~ 145 (177)
++...
T Consensus 63 ~d~~~ 67 (76)
T cd04452 63 VDKEK 67 (76)
T ss_pred EECCC
Confidence 98643
No 29
>PRK08582 hypothetical protein; Provisional
Probab=98.58 E-value=5.1e-07 Score=68.33 Aligned_cols=64 Identities=19% Similarity=0.110 Sum_probs=51.7
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
|...+|++++|+|++++++|+||.|+ ..+++++.+++.+++. . + ....|++||.|+|+|.+
T Consensus 1 m~~kvG~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v-~--~---------------~~~~l~vGD~VkvkV~~ 62 (139)
T PRK08582 1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYV-K--D---------------INDHLKVGDEVEVKVLN 62 (139)
T ss_pred CCCcCCCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccc-c--c---------------cccccCCCCEEEEEEEE
Confidence 45678999999999999999999995 6889999887754421 1 1 12379999999999999
Q ss_pred EeC
Q 030455 141 VNY 143 (177)
Q Consensus 141 v~~ 143 (177)
++.
T Consensus 63 id~ 65 (139)
T PRK08582 63 VED 65 (139)
T ss_pred ECC
Confidence 985
No 30
>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=98.56 E-value=6.5e-07 Score=59.54 Aligned_cols=63 Identities=17% Similarity=0.102 Sum_probs=48.8
Q ss_pred CCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~ 144 (177)
+|+++.|+|++++++|+|++++ ..+++++.+++-. ++ .. .+.+..|++||.|+++|.+++..
T Consensus 3 ~g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~-------~~--~~--------~~~~~~~~~Gd~v~v~v~~id~~ 65 (72)
T cd05689 3 EGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDW-------TN--KN--------IHPSKVVSLGDEVEVMVLDIDEE 65 (72)
T ss_pred CCCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccC-------cc--cc--------cCcccEeCCCCEEEEEEEEeeCC
Confidence 6999999999999999999995 5888888776521 11 01 12335899999999999999864
Q ss_pred C
Q 030455 145 S 145 (177)
Q Consensus 145 ~ 145 (177)
+
T Consensus 66 ~ 66 (72)
T cd05689 66 R 66 (72)
T ss_pred c
Confidence 4
No 31
>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=98.55 E-value=4.4e-07 Score=62.27 Aligned_cols=64 Identities=11% Similarity=0.064 Sum_probs=50.4
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEe
Q 030455 64 PFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 142 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~ 142 (177)
...|+++.|+|++++++|+||+++ ..+++++.+++..++ + .+....|++||.|+++|.+++
T Consensus 12 ~~~G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~--~----------------~~~~~~~~~Gd~v~vkV~~id 73 (83)
T cd04461 12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEF--V----------------TDPSFGFKKGQSVTAKVTSVD 73 (83)
T ss_pred CCCCCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCccc--c----------------cCHHHhcCCCCEEEEEEEEEc
Confidence 679999999999999999999994 777777776553321 1 123348999999999999998
Q ss_pred CCC
Q 030455 143 YPS 145 (177)
Q Consensus 143 ~~~ 145 (177)
...
T Consensus 74 ~~~ 76 (83)
T cd04461 74 EEK 76 (83)
T ss_pred CCC
Confidence 643
No 32
>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=98.54 E-value=4.9e-07 Score=59.74 Aligned_cols=60 Identities=20% Similarity=0.149 Sum_probs=46.6
Q ss_pred CCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCC
Q 030455 67 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~ 144 (177)
|+++.|+|++++++|+||+++ .++++++.+++..+ ..+ +. ...+++||.|+++|.+++..
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~-~~~--~~---------------~~~~~~G~~i~v~v~~~d~~ 61 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEA-FIK--DP---------------EEHFRVGQVVKVKVLSCDPE 61 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChh-hcC--CH---------------HHcccCCCEEEEEEEEEcCC
Confidence 789999999999999999994 67777777655332 222 22 23789999999999999853
No 33
>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=98.51 E-value=7.2e-07 Score=58.96 Aligned_cols=61 Identities=20% Similarity=0.302 Sum_probs=47.7
Q ss_pred CCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 67 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
|++++|+|++++++|+||+++ .++++++.+++.+++ + ++....|++||.+++||.+++..+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~--~----------------~~~~~~~~~Gd~i~~~V~~id~~~ 62 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVR--L----------------KHPEKKFKPGLKVKCRVLSVEPER 62 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCcc--c----------------cCHHHcCCCCCEEEEEEEEEECCC
Confidence 789999999999999999994 688887776654331 1 122338999999999999998644
No 34
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=98.49 E-value=2.2e-07 Score=85.84 Aligned_cols=82 Identities=12% Similarity=-0.029 Sum_probs=64.6
Q ss_pred EEEEeeccCCCC--EEEEEEEeeeCCeeEEEec--ccceeEecCCCCC--CCcccccCCCCCeeeeEEEEeCCeeeEEcC
Q 030455 57 FRLVVFRPFVGE--IIAAKLKESDANGLRLSLG--FFEDIYVPSHLLP--SPSRSEPDPYGRYEVKWIWEFGDTKYVIDG 130 (177)
Q Consensus 57 f~~~~f~p~~gE--v~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~--~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~ 130 (177)
++|.+|+.++|+ .++|+|++++++|+||+|. .++++++.+++.+ +++.| |++... -.+.++ +.|++
T Consensus 546 ~~~~yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v~~~~l~~~~~~~~~--~~~~~~---~~l~g~---~~~~l 617 (639)
T TIGR02062 546 LYARFLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFIPAAFLHANREELVC--NQENGT---VQIKGE---TVYKI 617 (639)
T ss_pred HHHHHHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEEEhhhcCCCCcceEE--cccccE---EEEecc---EEEec
Confidence 344578888865 9999999999999999993 6889888888766 56667 876653 124433 49999
Q ss_pred CCEEEEEEEEEeCCCC
Q 030455 131 LDEIKFRVLSVNYPSI 146 (177)
Q Consensus 131 G~~VRvrV~~v~~~~~ 146 (177)
||+|+|+|.+|+..++
T Consensus 618 gd~v~V~v~~vd~~~~ 633 (639)
T TIGR02062 618 GDVIDVVLTEVRMETR 633 (639)
T ss_pred CCEEEEEEEEeccccC
Confidence 9999999999997654
No 35
>PRK05807 hypothetical protein; Provisional
Probab=98.48 E-value=1.1e-06 Score=66.29 Aligned_cols=63 Identities=14% Similarity=0.140 Sum_probs=50.4
Q ss_pred ccCCCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEe
Q 030455 63 RPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 142 (177)
Q Consensus 63 ~p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~ 142 (177)
+..+|++++|+|++++++|+||.|+..+++++.+++.+++ .. + -..++++||.|+|+|.+++
T Consensus 2 ~~~vG~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~-v~--~---------------~~~~~kvGd~V~VkV~~id 63 (136)
T PRK05807 2 TLKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTY-VK--D---------------IREHLKEQDKVKVKVISID 63 (136)
T ss_pred CccCCCEEEEEEEEEECCeEEEEECCEEEEEEhhhccccc-cc--C---------------ccccCCCCCEEEEEEEEEC
Confidence 4568999999999999999999997678899988775532 11 1 1126899999999999998
Q ss_pred C
Q 030455 143 Y 143 (177)
Q Consensus 143 ~ 143 (177)
.
T Consensus 64 ~ 64 (136)
T PRK05807 64 D 64 (136)
T ss_pred C
Confidence 6
No 36
>PRK07252 hypothetical protein; Provisional
Probab=98.48 E-value=1.4e-06 Score=64.44 Aligned_cols=64 Identities=11% Similarity=0.091 Sum_probs=50.5
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
.+|+++.|+|++++++|+||+++ .++++++.+++.++. + + +....|++||.|+++|.+++.
T Consensus 2 kvG~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~--~--~--------------~~~~~~~vGD~V~VkI~~iD~ 63 (120)
T PRK07252 2 KIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGF--I--D--------------NIHQLLKVGEEVLVQVVDFDE 63 (120)
T ss_pred CCCCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCcc--c--c--------------ChhhccCCCCEEEEEEEEEeC
Confidence 36999999999999999999994 688888887764431 1 1 112378999999999999997
Q ss_pred CCC
Q 030455 144 PSI 146 (177)
Q Consensus 144 ~~~ 146 (177)
..+
T Consensus 64 ~~~ 66 (120)
T PRK07252 64 YTG 66 (120)
T ss_pred CCC
Confidence 554
No 37
>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=98.47 E-value=1e-06 Score=57.89 Aligned_cols=63 Identities=14% Similarity=0.187 Sum_probs=48.5
Q ss_pred CCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 67 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
|+++.|+|++++++|+||+++ ..+++++.+++. + .. ..++....|++||.|+++|.+++...
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~-----~--~~----------~~~~~~~~~~~G~~v~v~v~~id~~~ 63 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDIS-----W--TQ----------RVRHPSEIYKKGQEVEAVVLNIDVER 63 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCC-----C--cc----------ccCChhhEECCCCEEEEEEEEEECCc
Confidence 789999999999999999995 678888877653 1 10 01223458999999999999998654
Q ss_pred C
Q 030455 146 I 146 (177)
Q Consensus 146 ~ 146 (177)
+
T Consensus 64 ~ 64 (69)
T cd05690 64 E 64 (69)
T ss_pred C
Confidence 3
No 38
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=98.46 E-value=1.4e-06 Score=58.27 Aligned_cols=61 Identities=15% Similarity=0.086 Sum_probs=47.1
Q ss_pred CCEEE-EEEEee-eCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 67 GEIIA-AKLKES-DANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 67 gEv~~-g~V~~v-~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
||+++ |+|+++ .++|+||++. .++++++.+++.++... + ....+++||.+++||.+++-
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~-------~-----------~~~~~~vG~~v~~kV~~id~ 62 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVP-------S-----------DTGPFKAGTTHKARIIGYSP 62 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhc-------C-----------cccccCCCCEEEEEEEEEeC
Confidence 79999 999999 6999999994 58888888876433111 1 12269999999999999885
Q ss_pred CC
Q 030455 144 PS 145 (177)
Q Consensus 144 ~~ 145 (177)
.+
T Consensus 63 ~~ 64 (71)
T cd05696 63 MD 64 (71)
T ss_pred CC
Confidence 43
No 39
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=98.46 E-value=8.7e-07 Score=72.55 Aligned_cols=85 Identities=20% Similarity=0.307 Sum_probs=65.8
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
+.|.+|+++.|+|++++++|.++.++ .++++++.++......+. |. .+....|++||.|++||.+
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~--d~------------~~~~~~~~~GDlV~akV~~ 124 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNV--EG------------TDLRKYLDIGDYIIAKVKD 124 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCcccc--ch------------hhhHhhCCCCCEEEEEEEE
Confidence 88999999999999999999999997 788888777654332111 21 2223478999999999999
Q ss_pred EeCCCCcccccCCCCCCCCeEEEEEecCCCCcccc
Q 030455 141 VNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPVS 175 (177)
Q Consensus 141 v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~i~ 175 (177)
++- . ..+..|+++++||.+.
T Consensus 125 i~~-------~--------~~~~LS~k~~~lG~L~ 144 (235)
T PRK04163 125 VDR-------T--------RDVVLTLKGKGLGKIE 144 (235)
T ss_pred ECC-------C--------CcEEEEEcCCCCCccC
Confidence 862 1 2488899999999874
No 40
>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=98.43 E-value=1.1e-06 Score=59.43 Aligned_cols=66 Identities=15% Similarity=0.110 Sum_probs=50.2
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
.+|+++.|+|++++++|+||+++ -++++++.+++..+... +. ++-...|++||.|+++|.+++.
T Consensus 2 k~G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~---~~------------~~~~~~~~~G~~v~~kVl~id~ 66 (74)
T cd05705 2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVS---DP------------SLYNKYLPEGKLLTAKVLSVNS 66 (74)
T ss_pred CCCCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCcccc---Ch------------hhHhcccCCCCEEEEEEEEEEC
Confidence 47999999999999999999996 67888887766443211 11 1112489999999999999986
Q ss_pred CC
Q 030455 144 PS 145 (177)
Q Consensus 144 ~~ 145 (177)
..
T Consensus 67 ~~ 68 (74)
T cd05705 67 EK 68 (74)
T ss_pred CC
Confidence 43
No 41
>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=98.43 E-value=2e-06 Score=56.94 Aligned_cols=61 Identities=23% Similarity=0.317 Sum_probs=48.2
Q ss_pred CCEEEEEEEeeeCCeeEEEe-cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 67 GEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~l-g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
|+++.|+|+++.++|+||++ +.++++++.+++.+++ + + +....|++||.|+++|.+++...
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~--~--~--------------~~~~~~~~Gd~v~~~v~~~d~~~ 62 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDR--V--E--------------DATERFKVGDEVEAKITNVDRKN 62 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCcc--c--c--------------CHHHccCCCCEEEEEEEEEeCCC
Confidence 78999999999999999999 4788888777665442 1 1 12337899999999999998643
No 42
>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=98.41 E-value=1.1e-06 Score=57.81 Aligned_cols=61 Identities=21% Similarity=0.185 Sum_probs=47.7
Q ss_pred CCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 67 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
|+++.|+|+++.++|+||+++ .++++++.+++.++ + .. +....|++||.|+++|.+++...
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~---~--~~-------------~~~~~~~~Gd~v~~~v~~~d~~~ 62 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDS---Y--LK-------------DWKKRFKVGQLVKGKIVSIDPDN 62 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCch---h--hc-------------CHhhccCCCCEEEEEEEEEeCCC
Confidence 789999999999999999995 68888888766433 1 11 12237899999999999998643
No 43
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=98.41 E-value=1.9e-06 Score=56.06 Aligned_cols=62 Identities=18% Similarity=0.231 Sum_probs=48.2
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
+|+++.|+|++++++|+||+++..+++++.+++.+ .+ . ...+..|++||.|+++|.+++..+
T Consensus 1 ~g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e~~~---~~--~-------------~~~~~~~~~Gd~v~v~i~~vd~~~ 62 (68)
T cd05688 1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSW---GR--V-------------KHPSEVVNVGDEVEVKVLKIDKER 62 (68)
T ss_pred CCCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCC---cc--c-------------cCHhHEECCCCEEEEEEEEEECCC
Confidence 48999999999999999999987888777765531 11 1 112347999999999999998643
No 44
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=98.40 E-value=3.2e-06 Score=54.75 Aligned_cols=61 Identities=30% Similarity=0.343 Sum_probs=47.6
Q ss_pred CCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~ 144 (177)
+|+++.|+|.+++++|+|++++ .++++++.+++.+++ . .+....|++||.|+++|.+++..
T Consensus 2 ~G~~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~-----~-------------~~~~~~~~~G~~v~~~V~~~~~~ 63 (72)
T smart00316 2 VGDVVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKR-----V-------------KDPEEVLKVGDEVKVKVLSVDEE 63 (72)
T ss_pred CCCEEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccc-----c-------------CCHHHeecCCCEEEEEEEEEeCC
Confidence 6999999999999999999997 777766665554321 1 12234799999999999999864
No 45
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=98.39 E-value=3.7e-06 Score=57.04 Aligned_cols=59 Identities=20% Similarity=0.198 Sum_probs=46.7
Q ss_pred CCEEEEEEEeeeCCeeEEEec----ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEe
Q 030455 67 GEIIAAKLKESDANGLRLSLG----FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 142 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg----~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~ 142 (177)
|++++|+|+++.++|+||+++ ..+++++.+++.++.. .++....|++||.|+++|.+++
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~-----------------~~~~~~~~~~Gd~v~v~v~~vd 63 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGR-----------------VANPSDVVKRGQKVKVKVISIQ 63 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCC-----------------cCChhheeCCCCEEEEEEEEEe
Confidence 789999999999999999997 4788888776543311 0223348999999999999998
No 46
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=98.39 E-value=9.7e-07 Score=79.61 Aligned_cols=63 Identities=21% Similarity=0.247 Sum_probs=52.2
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
+|++++|+|++++++|+||.||.++|++|++++...... + -..++++||+|.++|++++-..
T Consensus 192 ~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv~-------~-----------P~~vvkvGd~VkvkVi~~D~e~ 253 (541)
T COG0539 192 VGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVD-------H-----------PSEVVKVGDEVKVKVISLDEER 253 (541)
T ss_pred CCceEEEEEEEeecCcEEEEecCeeeEEehhhccccccC-------C-----------HHHhcccCCEEEEEEEEEccCC
Confidence 899999999999999999999889999999987543211 1 1238999999999999998655
Q ss_pred C
Q 030455 146 I 146 (177)
Q Consensus 146 ~ 146 (177)
.
T Consensus 254 ~ 254 (541)
T COG0539 254 G 254 (541)
T ss_pred C
Confidence 4
No 47
>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=98.37 E-value=2.5e-06 Score=55.43 Aligned_cols=59 Identities=22% Similarity=0.316 Sum_probs=46.0
Q ss_pred CCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 67 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
|+++.|+|++++++|+||+++ ..+++++.+++.++ +.. + ....+++||.|+++|.+++.
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~-~~~--~---------------~~~~~~~Gd~v~v~v~~~~~ 60 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHK-RVK--D---------------VKDVLKEGDKVKVKVLSIDA 60 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCc-ccC--C---------------HHHccCCCCEEEEEEEEECC
Confidence 789999999999999999996 77777777655432 111 1 12378999999999999874
No 48
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=98.36 E-value=4.4e-07 Score=66.77 Aligned_cols=64 Identities=19% Similarity=0.151 Sum_probs=51.9
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEe-cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~l-g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
+.+.+|+++.|+|++++++|+||+| +--.|++|+++..+. ||.|- ...+++||.|.|+|++
T Consensus 1 ~~~kvG~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~---fVkdI---------------~d~L~vG~eV~vKVl~ 62 (129)
T COG1098 1 MSMKVGSKLKGKITGITPYGAFVELEGGKTGLVHISEIADG---FVKDI---------------HDHLKVGQEVKVKVLD 62 (129)
T ss_pred CCccccceEEEEEEeeEecceEEEecCCCcceEEehHhhhh---hHHhH---------------HHHhcCCCEEEEEEEe
Confidence 3567999999999999999999999 345689999988765 42122 2278899999999999
Q ss_pred EeC
Q 030455 141 VNY 143 (177)
Q Consensus 141 v~~ 143 (177)
++-
T Consensus 63 ide 65 (129)
T COG1098 63 IDE 65 (129)
T ss_pred ecc
Confidence 986
No 49
>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=98.33 E-value=3.9e-06 Score=56.43 Aligned_cols=63 Identities=10% Similarity=0.010 Sum_probs=48.2
Q ss_pred CCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 67 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
|.++.|+|++++++|+||+|+ -++++++.+++..+ ... . ++-...|++||.|.++|.+++...
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~-~~~--~-------------~~~~~~~~vG~~v~~kV~~id~~~ 64 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDD-VSV--L-------------EHPEKKFPIGQALKAKVVGVDKEH 64 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCc-ccc--c-------------cCHHHhCCCCCEEEEEEEEEeCCC
Confidence 689999999999999999995 68888888776432 111 1 112237999999999999998644
No 50
>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=98.32 E-value=2.3e-06 Score=55.50 Aligned_cols=61 Identities=13% Similarity=0.175 Sum_probs=46.7
Q ss_pred CCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 67 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
|+++.|+|++++++|+||+++ ..+++++.+++.++. + . +....+++||.|+++|.+++..+
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~--~--~--------------~~~~~~~~Gd~v~v~i~~vd~~~ 62 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRF--V--S--------------HPSDVVSVGDIVEVKVISIDEER 62 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCcc--c--c--------------CHHHhcCCCCEEEEEEEEEECCC
Confidence 789999999999999999996 567777766553321 1 1 22347899999999999998644
No 51
>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=98.27 E-value=2.3e-06 Score=57.34 Aligned_cols=60 Identities=15% Similarity=0.009 Sum_probs=47.0
Q ss_pred CCCCEEEEEEEeeeC-CeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEe
Q 030455 65 FVGEIIAAKLKESDA-NGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 142 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~-~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~ 142 (177)
.+|+++.|+|+++.+ +|+|++++ ..++++|.+++.++ | ..+ . ...+++||.||++|.+++
T Consensus 2 ~~G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~---~--~~~--~-----------~~~~~~Gd~v~~kV~~~~ 63 (72)
T cd05704 2 EEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDS---Y--TEN--P-----------LEGFKPGKIVRCCILSKK 63 (72)
T ss_pred CCCCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCc---c--cCC--H-----------HHhCCCCCEEEEEEEEec
Confidence 379999999999986 89999995 67899998866543 2 211 1 127899999999999985
No 52
>PRK08059 general stress protein 13; Validated
Probab=98.26 E-value=7.5e-06 Score=60.58 Aligned_cols=65 Identities=22% Similarity=0.176 Sum_probs=50.8
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEe
Q 030455 64 PFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 142 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~ 142 (177)
..+|+++.|+|++++++|+||+++ ..+++++.+++.++ + . .+....|++||.|+++|.+++
T Consensus 5 ~k~G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~---~--~-------------~~~~~~~~vGD~I~vkI~~id 66 (123)
T PRK08059 5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHG---F--V-------------KDIHDFLSVGDEVKVKVLSVD 66 (123)
T ss_pred CCCCCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcc---c--c-------------cCHHHcCCCCCEEEEEEEEEE
Confidence 567999999999999999999996 67888887766433 2 1 112237899999999999998
Q ss_pred CCCC
Q 030455 143 YPSI 146 (177)
Q Consensus 143 ~~~~ 146 (177)
..++
T Consensus 67 ~~~~ 70 (123)
T PRK08059 67 EEKG 70 (123)
T ss_pred CCCC
Confidence 6544
No 53
>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=98.24 E-value=7e-06 Score=54.11 Aligned_cols=59 Identities=25% Similarity=0.345 Sum_probs=46.4
Q ss_pred CCEEEEEEEeeeCCeeEEEe-cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 67 GEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~l-g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
|++++|+|+++.++|++|+| +.++++++.+++.++ . .. ...|++|++|++||..++...
T Consensus 1 G~~V~g~V~~i~~~G~~v~l~~~v~g~v~~~~l~~~---~--~~---------------~~~~~~G~~i~~kVi~id~~~ 60 (66)
T cd05695 1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPE---K--SS---------------KSTYKEGQKVRARILYVDPST 60 (66)
T ss_pred CCEEEEEEEEEeCCcEEEEEcCCceEEEEHHHcCCc---c--Cc---------------ccCcCCCCEEEEEEEEEeCCC
Confidence 78999999999999999999 568888877765221 1 11 226999999999999998643
No 54
>KOG4134 consensus DNA-dependent RNA polymerase I [Transcription]
Probab=98.18 E-value=1.7e-05 Score=63.88 Aligned_cols=99 Identities=19% Similarity=0.298 Sum_probs=77.6
Q ss_pred EeeeeEEECCCCCCccHHHHHHHHHHhH---hcCc-------------ccccceeeeCCCCeeeEEEEEEEeeccCCCCE
Q 030455 6 KIEHTLRLPPHLLRLPLNEAIKLELENV---FLDK-------------EIEGGFVYPGEGASTHTVKFRLVVFRPFVGEI 69 (177)
Q Consensus 6 ~l~d~v~i~P~~~~~~~~~~i~~~L~~k---y~~k-------------~i~~g~I~~g~G~~~~~V~f~~~~f~p~~gEv 69 (177)
+...-|.+.|.++.++++..|++.|+.+ |..+ --..++|.+.+|..+..+.-..++|+|..|++
T Consensus 31 t~dlhlalaP~yl~npl~~~i~ehld~~vl~y~~~l~GivLgydnIKvLg~~aki~~D~pf~hlwi~adfyVf~Pk~Gd~ 110 (253)
T KOG4134|consen 31 TTDLHLALAPYYLANPLHALIEEHLDTKVLFYDSGLDGIVLGYDNIKVLGQTAKIRADDPFMHLWINADFYVFRPKAGDI 110 (253)
T ss_pred eeheeeeecchhhcchhHHHHHHHhhHHHhhhccCCCceEEeecceEeeccccceecCCCceEEEEeeeEEEECCCCCCe
Confidence 4566789999999888777888888885 4433 22568999999999999999999999999999
Q ss_pred EEEEEEeeeCCeeEEEe-cccceeEecCCCCCCCccc
Q 030455 70 IAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRS 105 (177)
Q Consensus 70 ~~g~V~~v~~~Gifv~l-g~~~~i~i~~~~~~~~~~y 105 (177)
++|+|-.|++..|=+-+ |.| +.-||....|..++|
T Consensus 111 LeG~Vn~vS~sHIglLIhg~F-NASIpk~nip~dw~f 146 (253)
T KOG4134|consen 111 LEGVVNHVSRSHIGLLIHGVF-NASIPKTNIPADWEF 146 (253)
T ss_pred eeeeeeecchhhhceeehhhh-hccCCCCCCccceee
Confidence 99999999999886655 555 345555555544433
No 55
>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=98.17 E-value=1.6e-05 Score=52.39 Aligned_cols=58 Identities=21% Similarity=0.253 Sum_probs=45.3
Q ss_pred CCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEe
Q 030455 67 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 142 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~ 142 (177)
|+++.|+|.++.++|++|+++ .++++++.+++.++ + .. +-...+++||.++++|.+++
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~---~--~~-------------~~~~~~~~Gd~i~~~i~~~~ 59 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDD---P--IE-------------NGEDEVKVGDEVEVYVLRVE 59 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCcc---c--cC-------------CHhHcCCCCCEEEEEEEEEE
Confidence 789999999999999999996 67777777665443 1 11 11226899999999999987
No 56
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=98.16 E-value=6.4e-06 Score=65.23 Aligned_cols=80 Identities=11% Similarity=-0.033 Sum_probs=58.6
Q ss_pred eeccCCCCEEEEEEEeeeCCeeEEEecc-----------cceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEc
Q 030455 61 VFRPFVGEIIAAKLKESDANGLRLSLGF-----------FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVID 129 (177)
Q Consensus 61 ~f~p~~gEv~~g~V~~v~~~Gifv~lg~-----------~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~ 129 (177)
...|.+|+++.|+|++++.+|++|+++. ++++++.++..++ + . ++-...|+
T Consensus 59 ~~~~~~GdiV~GkV~~i~~~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~---~--~-------------~~~~~~~~ 120 (189)
T PRK09521 59 PPLLKKGDIVYGRVVDVKEQRALVRIVSIEGSERELATSKLAYIHISQVSDG---Y--V-------------ESLTDAFK 120 (189)
T ss_pred CCCCCCCCEEEEEEEEEcCCeEEEEEEEecccccccCCCceeeEEhhHcChh---h--h-------------hhHHhccC
Confidence 3567899999999999999999999953 4455555443221 1 0 11133789
Q ss_pred CCCEEEEEEEEEeCCCCcccccCCCCCCCCeEEEEEecCCCCcccc
Q 030455 130 GLDEIKFRVLSVNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPVS 175 (177)
Q Consensus 130 ~G~~VRvrV~~v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~i~ 175 (177)
+||.|++||.+++ . .+..|++++.||.+.
T Consensus 121 ~GD~V~akV~~i~---~--------------~i~LS~k~~~lGvv~ 149 (189)
T PRK09521 121 IGDIVRAKVISYT---D--------------PLQLSTKGKDLGVIY 149 (189)
T ss_pred CCCEEEEEEEecC---C--------------cEEEEEecCCceEEE
Confidence 9999999999975 1 578888888888764
No 57
>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=98.13 E-value=1.1e-05 Score=52.52 Aligned_cols=59 Identities=20% Similarity=0.178 Sum_probs=45.6
Q ss_pred CCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 67 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
|+++.|+|+++.++|+|++++ ..+++++.+++.+++ + ......|++||.|+++|.+++.
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~--~----------------~~~~~~~~~Gd~v~v~v~~~d~ 60 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDER--V----------------EKVEDVLKVGDEVKVKVIEVDD 60 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCcc--c----------------cCHHHccCCCCEEEEEEEEECC
Confidence 689999999999999999996 567777776554331 1 1112379999999999999875
No 58
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=98.12 E-value=1e-05 Score=68.86 Aligned_cols=65 Identities=18% Similarity=0.090 Sum_probs=52.8
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEe---cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 64 PFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~l---g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
|.+|+++.|+|++++++|+||+| +-++|++|.+.+... +. ++-...+++|+.|.++|++
T Consensus 15 P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~-----------------ri-~~i~d~vkvGd~v~vkVl~ 76 (319)
T PTZ00248 15 PEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKR-----------------RI-RSINKLIRVGRHEVVVVLR 76 (319)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhccc-----------------cc-CCHHHhcCCCCEEEEEEEE
Confidence 67899999999999999999999 368999999865321 11 2334489999999999999
Q ss_pred EeCCCC
Q 030455 141 VNYPSI 146 (177)
Q Consensus 141 v~~~~~ 146 (177)
++...+
T Consensus 77 VD~ekg 82 (319)
T PTZ00248 77 VDKEKG 82 (319)
T ss_pred EeCCCC
Confidence 987554
No 59
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=98.11 E-value=1.9e-05 Score=67.35 Aligned_cols=64 Identities=16% Similarity=0.213 Sum_probs=51.5
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 64 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
..+|+++.|+|++++++|+||+++.++|++|.+++..+ + . .+....|++||.|+++|.+++.
T Consensus 194 ~k~G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~---~--~-------------~~~~~~~~vGd~VkvkVl~iD~ 255 (318)
T PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHE---H--I-------------ETPHSVFNVNDEMKVMIIDLDA 255 (318)
T ss_pred CCCCCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccc---c--c-------------cChhhccCCCCEEEEEEEEEeC
Confidence 55799999999999999999999888899888766443 1 1 1122479999999999999986
Q ss_pred CC
Q 030455 144 PS 145 (177)
Q Consensus 144 ~~ 145 (177)
..
T Consensus 256 e~ 257 (318)
T PRK07400 256 ER 257 (318)
T ss_pred CC
Confidence 44
No 60
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=98.08 E-value=2.6e-06 Score=79.42 Aligned_cols=116 Identities=16% Similarity=0.166 Sum_probs=75.7
Q ss_pred eeEEECCCCCCccH---HHHHHHHHHhHhcCc----ccccceeeeCCCCeeeEE--EEEEEeeccCCCCEEEEEEEeeeC
Q 030455 9 HTLRLPPHLLRLPL---NEAIKLELENVFLDK----EIEGGFVYPGEGASTHTV--KFRLVVFRPFVGEIIAAKLKESDA 79 (177)
Q Consensus 9 d~v~i~P~~~~~~~---~~~i~~~L~~ky~~k----~i~~g~I~~g~G~~~~~V--~f~~~~f~p~~gEv~~g~V~~v~~ 79 (177)
.++.|+|...+.=+ -.. .+.|.+++--+ +-+..+|...++..+-++ ..+.+...|.+|+++.|+|+++.+
T Consensus 553 ~~~~I~~~kI~~vIG~gGk~-Ik~I~~~tg~~I~i~ddG~V~i~~~~~~~~~~a~~~I~~~~~~~~~G~i~~G~V~~I~~ 631 (684)
T TIGR03591 553 ETIKINPDKIRDVIGPGGKV-IREITEETGAKIDIEDDGTVKIAASDGEAAEAAIKMIEGITAEPEVGKIYEGKVVRIMD 631 (684)
T ss_pred EEEecCHHHHHhhcCCCcHH-HHHHHHHHCCEEEEecCeEEEEEECcHHHHHHHHHHHHhhhcccccCcEEEEEEEEEeC
Confidence 35677776543210 111 23333343322 334444555555555544 444556679999999999999999
Q ss_pred CeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 80 NGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 80 ~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
+|+||++. ..++++|.+++.++ + . ++-...|++||.|+|+|.+++.
T Consensus 632 ~GafVei~~g~~GllHiSei~~~---~--v-------------~~~~~~~kvGD~V~VkVi~id~ 678 (684)
T TIGR03591 632 FGAFVEILPGKDGLVHISEIANE---R--V-------------EKVEDVLKEGDEVKVKVLEIDK 678 (684)
T ss_pred CEEEEEECCCcEEEEEHHHcCCC---c--c-------------cChhhccCCCCEEEEEEEEECC
Confidence 99999994 68899999876332 2 1 1223479999999999999985
No 61
>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=98.07 E-value=4.5e-05 Score=51.50 Aligned_cols=55 Identities=11% Similarity=0.037 Sum_probs=43.8
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec--ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEe
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG--FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 142 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg--~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~ 142 (177)
..|+++.|.|+++.++|+|+++| -++++++.+++ . + + ..+++|+.+.++|.+++
T Consensus 3 ~~G~~v~g~V~si~d~G~~v~~g~~gv~Gfl~~~~~-~----~--~-----------------~~~~~Gq~v~~~V~~vd 58 (74)
T cd05694 3 VEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDA-G----N--F-----------------SKLKVGQLLLCVVEKVK 58 (74)
T ss_pred CCCCEEEEEEEEEeCCEEEEEeCCCCcEEEEEHHHC-C----c--c-----------------cccCCCCEEEEEEEEEE
Confidence 46899999999999999999996 56676655432 1 1 1 37899999999999997
Q ss_pred C
Q 030455 143 Y 143 (177)
Q Consensus 143 ~ 143 (177)
-
T Consensus 59 ~ 59 (74)
T cd05694 59 D 59 (74)
T ss_pred C
Confidence 5
No 62
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=98.05 E-value=2e-05 Score=65.56 Aligned_cols=65 Identities=17% Similarity=0.154 Sum_probs=52.1
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEec---ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 64 PFVGEIIAAKLKESDANGLRLSLG---FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~lg---~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
|.+|+++.|+|+++.++|+||+|. .++++++.+++.++.... -...+++||.|+++|.+
T Consensus 6 P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~------------------i~~~~kvGd~V~vkVi~ 67 (262)
T PRK03987 6 PEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKN------------------IRDHVKEGQKVVCKVIR 67 (262)
T ss_pred CCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccC------------------HHHhCCCCCEEEEEEEE
Confidence 889999999999999999999994 478888888765432111 12378999999999999
Q ss_pred EeCCCC
Q 030455 141 VNYPSI 146 (177)
Q Consensus 141 v~~~~~ 146 (177)
++...+
T Consensus 68 VD~~k~ 73 (262)
T PRK03987 68 VDPRKG 73 (262)
T ss_pred EecccC
Confidence 987554
No 63
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=98.03 E-value=1.1e-05 Score=76.53 Aligned_cols=67 Identities=19% Similarity=0.188 Sum_probs=54.0
Q ss_pred EEeeccCCCCEEE-EEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEE
Q 030455 59 LVVFRPFVGEIIA-AKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKF 136 (177)
Q Consensus 59 ~~~f~p~~gEv~~-g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRv 136 (177)
-+++.|.+|++++ |+|+++.++|+||+|. ..+|++|.+++..+.+.+ ....|++||.|+|
T Consensus 746 ~l~~~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~------------------~~dv~kvGD~V~V 807 (891)
T PLN00207 746 SLTMVPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAK------------------PEDAFKVGDRIDV 807 (891)
T ss_pred HHhcCcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccC------------------HHHhcCCCCEEEE
Confidence 3456799999996 6999999999999994 689999999775432222 1237999999999
Q ss_pred EEEEEeC
Q 030455 137 RVLSVNY 143 (177)
Q Consensus 137 rV~~v~~ 143 (177)
+|.+++.
T Consensus 808 kVi~ID~ 814 (891)
T PLN00207 808 KLIEVND 814 (891)
T ss_pred EEEEECC
Confidence 9999985
No 64
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=97.96 E-value=4.1e-05 Score=50.73 Aligned_cols=61 Identities=18% Similarity=0.129 Sum_probs=46.7
Q ss_pred CCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 67 GEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
|+++.|+|+++.++|++|+++ .++++++.+++.+++ ... ++-...|++||.|+++|.+++-
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~-----~~~-----------~~~~~~~~~Gd~i~~kVl~~d~ 62 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEW-----PDG-----------KNPLSKFKIGQKIKARVIGGHD 62 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhcccc-----ccc-----------cChhHhCCCCCEEEEEEEEEeC
Confidence 789999999999999999995 788888877664431 111 1112368999999999999874
No 65
>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=97.92 E-value=4.6e-05 Score=53.16 Aligned_cols=67 Identities=18% Similarity=0.201 Sum_probs=49.6
Q ss_pred ccCCCCEEEEEEEeeeCC--eeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEE
Q 030455 63 RPFVGEIIAAKLKESDAN--GLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVL 139 (177)
Q Consensus 63 ~p~~gEv~~g~V~~v~~~--Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~ 139 (177)
++.+|+++.|+|+++.++ |+||+++ ..++++|.+++... .| +.. ..-...+++||.|.|+|.
T Consensus 4 ~~~~G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~--~~--~~v-----------~~~~~~~~~Gd~v~VqV~ 68 (88)
T cd04453 4 EPIVGNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPA--YF--KKH-----------KKIAKLLKEGQEILVQVV 68 (88)
T ss_pred cCCCCCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCch--hc--ccc-----------CCHHHcCCCCCEEEEEEE
Confidence 367999999999999996 9999996 57888888765321 11 111 112338999999999999
Q ss_pred EEeCC
Q 030455 140 SVNYP 144 (177)
Q Consensus 140 ~v~~~ 144 (177)
.....
T Consensus 69 ~~~~~ 73 (88)
T cd04453 69 KEPIG 73 (88)
T ss_pred EecCC
Confidence 96653
No 66
>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=97.90 E-value=3.3e-05 Score=55.16 Aligned_cols=72 Identities=14% Similarity=0.094 Sum_probs=51.0
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCccccc--------CCCCCeeeeEEEEeCCeeeEEcCCCEEE
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEP--------DPYGRYEVKWIWEFGDTKYVIDGLDEIK 135 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~--------d~~~~~~~~w~~~~~~~~~~~~~G~~VR 135 (177)
.+|+++.|+|++++++|+|++|+ .++++++.+++.+++..... +... ....+-...|++||.||
T Consensus 2 ~~G~vV~G~V~~v~~~gl~v~L~~g~~G~v~~seis~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~f~vGd~V~ 74 (100)
T cd05693 2 SEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEEEDDE-------EELPDLEDLFSVGQLVR 74 (100)
T ss_pred CCCCEEEEEEEEEcCCCEEEECCCCcEEEEEHHHhhHHHHHHHHHhhhhccccccc-------cccCCHHHhccCCCEEE
Confidence 47999999999999999999994 67888888776554211100 1111 11122345789999999
Q ss_pred EEEEEEeC
Q 030455 136 FRVLSVNY 143 (177)
Q Consensus 136 vrV~~v~~ 143 (177)
++|++++.
T Consensus 75 ~kVi~~d~ 82 (100)
T cd05693 75 CKVVSLDK 82 (100)
T ss_pred EEEEEccC
Confidence 99999985
No 67
>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=97.89 E-value=0.00011 Score=48.16 Aligned_cols=57 Identities=19% Similarity=0.270 Sum_probs=41.2
Q ss_pred CCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 67 GEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
|++++|+|+++.+.|++|+++-++++++.+++.+. + . ... .. .+|+.+.++|.+++-
T Consensus 1 G~iv~g~V~~v~~~G~~v~l~g~~gfip~s~~~~~---~--~--~~~----------~~---~vG~~i~~~i~~vd~ 57 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLR---P--V--EDL----------DE---YVGKELKFKIIEIDR 57 (67)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCc---c--c--CCh----------HH---hCCCEEEEEEEEEeC
Confidence 78999999999999999999767665555443222 1 1 111 11 389999999999985
No 68
>PHA02945 interferon resistance protein; Provisional
Probab=97.88 E-value=0.00011 Score=51.00 Aligned_cols=64 Identities=22% Similarity=0.244 Sum_probs=49.5
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEe---cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 64 PFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~l---g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
|-.||++.|+|.. ..+|+||.| +-.+++++.+.. +.... |+ +. +.++ .|++|.+||++
T Consensus 9 P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~sev----------eva~~-----wv-K~-rd~l-~GqkvV~KVir 69 (88)
T PHA02945 9 PNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQ----------MHMNR-----YF-KY-RDKL-VGKTVKVKVIR 69 (88)
T ss_pred CCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehh----------hhccc-----eE-ee-eeEe-cCCEEEEEEEE
Confidence 9999999999999 999999999 467777777632 11233 33 22 4466 99999999999
Q ss_pred EeCCCC
Q 030455 141 VNYPSI 146 (177)
Q Consensus 141 v~~~~~ 146 (177)
++...+
T Consensus 70 Vd~~kg 75 (88)
T PHA02945 70 VDYTKG 75 (88)
T ss_pred ECCCCC
Confidence 997665
No 69
>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=97.86 E-value=9e-05 Score=50.16 Aligned_cols=53 Identities=19% Similarity=0.202 Sum_probs=44.0
Q ss_pred ccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEE
Q 030455 63 RPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 141 (177)
Q Consensus 63 ~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v 141 (177)
....|+.++|+|++++++|+|+++. ..+++++.+++ . ..++.||.+++||.++
T Consensus 13 ~~~~G~~~~g~V~~i~~~G~fV~l~~~~~Glv~~se~-------------~-------------~~~~iGd~v~v~I~~i 66 (77)
T cd04473 13 DLEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL-------------L-------------RDYEVGDEVIVQVTDI 66 (77)
T ss_pred hCCCCCEEEEEEEeEecceEEEEECCCcEEEEEchhc-------------c-------------CcCCCCCEEEEEEEEE
Confidence 3678999999999999999999995 57777776542 0 1588999999999998
No 70
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.86 E-value=6.9e-05 Score=67.38 Aligned_cols=63 Identities=17% Similarity=0.141 Sum_probs=49.9
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
.|+++.|+|++++++|+||.||.++++++.+++... .. ++-...+++||.|+++|.+++...
T Consensus 208 ~G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~--~v----------------~~~~~~~kvGd~V~vkVl~iD~e~ 269 (486)
T PRK07899 208 KGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWK--HI----------------DHPSEVVEVGQEVTVEVLDVDMDR 269 (486)
T ss_pred CCCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCc--cc----------------CCHHHhcCCCCEEEEEEEEEECCC
Confidence 799999999999999999999888888877765321 11 122347899999999999998754
Q ss_pred C
Q 030455 146 I 146 (177)
Q Consensus 146 ~ 146 (177)
+
T Consensus 270 ~ 270 (486)
T PRK07899 270 E 270 (486)
T ss_pred C
Confidence 4
No 71
>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=97.82 E-value=9.3e-05 Score=52.07 Aligned_cols=82 Identities=17% Similarity=0.202 Sum_probs=58.5
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEe--------c-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCC
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSL--------G-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLD 132 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~l--------g-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~ 132 (177)
+.|.+|.++.|+|++++...+.+++ . ++.++++.++..+.+ . |+. +-...|++||
T Consensus 2 ~~P~~GDiVig~V~~v~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~--~--d~~------------~~~~~f~~GD 65 (92)
T cd05791 2 VLPKVGSIVIARVTRINPRFAKVDILCVGGRPLKESFRGVIRKEDIRATE--K--DKV------------EMYKCFRPGD 65 (92)
T ss_pred CCCCCCCEEEEEEEEEcCCEEEEEEEEecCeecCCCcccEEEHHHccccc--c--chH------------HHHhhcCCCC
Confidence 4699999999999999999999998 2 445555555433221 1 110 1124789999
Q ss_pred EEEEEEEEEeCCCCcccccCCCCCCCCeEEEEEecCCCCccc
Q 030455 133 EIKFRVLSVNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPV 174 (177)
Q Consensus 133 ~VRvrV~~v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~i 174 (177)
.||.||.+..- . .....|++++.||.+
T Consensus 66 iV~AkVis~~~------~---------~~~~Lst~~~~lGVv 92 (92)
T cd05791 66 IVRAKVISLGD------A---------SSYYLSTAENELGVV 92 (92)
T ss_pred EEEEEEEEcCC------C---------CCcEEEecCCCCccC
Confidence 99999999741 1 256789999999964
No 72
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=97.81 E-value=4.7e-05 Score=70.99 Aligned_cols=65 Identities=20% Similarity=0.222 Sum_probs=54.1
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
+.|++++|+|+++.+||+||.+| --|+++|.+.+.+. |++|+ +. ++++||.|.++|..++.
T Consensus 657 k~Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~---fv~~P--~~-------------vv~vGdiV~v~V~~vD~ 718 (780)
T COG2183 657 KPGMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDK---FVKDP--NE-------------VVKVGDIVKVKVIEVDT 718 (780)
T ss_pred cCCCEEEEEEEEeeeccceEEeccccceeeeHHHhhhh---hcCCh--HH-------------hcccCCEEEEEEEEEec
Confidence 58999999999999999999999 55788998887665 32255 22 78999999999999998
Q ss_pred CCCc
Q 030455 144 PSIP 147 (177)
Q Consensus 144 ~~~~ 147 (177)
...+
T Consensus 719 ~r~r 722 (780)
T COG2183 719 ARKR 722 (780)
T ss_pred ccCe
Confidence 7754
No 73
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=97.78 E-value=0.00013 Score=68.19 Aligned_cols=64 Identities=22% Similarity=0.196 Sum_probs=51.6
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
..+.+|+++.|+|+++.++|+||+++ ..++++|.+++.++ + . ++-...+++||.|+|+|.+
T Consensus 617 ~~~~vG~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~---~--v-------------~~~~~v~kvGD~V~VkV~~ 678 (693)
T PRK11824 617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADE---R--V-------------EKVEDVLKEGDEVKVKVLE 678 (693)
T ss_pred ccCcCCeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCc---c--c-------------cCccceeCCCCEEEEEEEE
Confidence 45889999999999999999999995 68899999876432 2 1 1122489999999999999
Q ss_pred EeC
Q 030455 141 VNY 143 (177)
Q Consensus 141 v~~ 143 (177)
++.
T Consensus 679 iD~ 681 (693)
T PRK11824 679 IDK 681 (693)
T ss_pred ECC
Confidence 974
No 74
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.77 E-value=0.00014 Score=65.39 Aligned_cols=64 Identities=17% Similarity=0.191 Sum_probs=51.1
Q ss_pred CCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~ 144 (177)
+|+++.|+|++++++|+||++. .++++++.+++.++. + ......|++||.|+++|.+++..
T Consensus 293 vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~--v----------------~~~~~~~kvGd~V~VkIi~ID~e 354 (486)
T PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERH--V----------------EVPEQVVQVGDEVFVKVIDIDLE 354 (486)
T ss_pred CCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCccc--c----------------cCccceeCCCCEEEEEEEEEECC
Confidence 6999999999999999999994 688999887764331 1 11224799999999999999976
Q ss_pred CCc
Q 030455 145 SIP 147 (177)
Q Consensus 145 ~~~ 147 (177)
+++
T Consensus 355 ~rr 357 (486)
T PRK07899 355 RRR 357 (486)
T ss_pred CCE
Confidence 653
No 75
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.72 E-value=0.00016 Score=69.11 Aligned_cols=67 Identities=18% Similarity=0.220 Sum_probs=52.7
Q ss_pred CCCCEEEEEEEeeeCCeeEEEe-cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~l-g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
.+|++++|+|++++++|+||+| +.++++++.+++.+++ .. + . .+....|++||.|+++|.+++.
T Consensus 751 ~vG~iV~GkV~~v~~~GvFVeL~~gVeGlI~~s~lsdd~-~~--~----~--------~~~~~~f~vGD~V~v~Vl~iD~ 815 (863)
T PRK12269 751 GVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENR-DG--D----P--------GEALRKYAVGDRVKAVIVDMNV 815 (863)
T ss_pred CCCCEEEEEEEEEecCeEEEEcCCCeEEEEEHHHcCCcc-cc--c----c--------hhhccccCCCCEEEEEEEEEEc
Confidence 3799999999999999999999 4789999888776542 21 1 1 1123479999999999999987
Q ss_pred CCC
Q 030455 144 PSI 146 (177)
Q Consensus 144 ~~~ 146 (177)
..+
T Consensus 816 ~~r 818 (863)
T PRK12269 816 KDR 818 (863)
T ss_pred CCC
Confidence 654
No 76
>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=97.72 E-value=0.00018 Score=47.38 Aligned_cols=55 Identities=29% Similarity=0.310 Sum_probs=42.7
Q ss_pred CCCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
..|++++|+|.++++.|+||.+|..+++++.+++.+. ..+++||.|++.|.+++-
T Consensus 2 ~~g~iV~G~V~~~~~~~~~vdig~~eg~lp~~e~~~~------------------------~~~~~Gd~v~v~v~~v~~ 56 (67)
T cd04455 2 REGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPG------------------------ESYRPGDRIKAYVLEVRK 56 (67)
T ss_pred CCCCEEEEEEEEEcCCCEEEEcCCeEEEeeHHHCCCC------------------------CcCCCCCEEEEEEEEEec
Confidence 5799999999999999999999877665544333211 145899999999999873
No 77
>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=97.71 E-value=9.4e-05 Score=69.00 Aligned_cols=66 Identities=18% Similarity=0.171 Sum_probs=51.4
Q ss_pred ccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEE
Q 030455 63 RPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 141 (177)
Q Consensus 63 ~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v 141 (177)
.|.+|++++|+|+++.++|+||+++ ..+|++|.+++.+- .+ . .. .++-...+++||.|+|+|.++
T Consensus 644 ~~~vG~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdl--s~--~--~r--------v~~~~dv~kvGd~V~VKVl~I 709 (719)
T TIGR02696 644 MPEVGERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKL--AG--G--KR--------VENVEDVLSVGQKIQVEIADI 709 (719)
T ss_pred cCCCCCEEEEEEEEEECceEEEEecCCceEEEEhhhcccc--cc--c--cC--------cCCHHHcCCCCCEEEEEEEEE
Confidence 5899999999999999999999994 68999999866321 00 0 00 022234899999999999999
Q ss_pred e
Q 030455 142 N 142 (177)
Q Consensus 142 ~ 142 (177)
+
T Consensus 710 D 710 (719)
T TIGR02696 710 D 710 (719)
T ss_pred C
Confidence 8
No 78
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.69 E-value=0.00018 Score=62.63 Aligned_cols=65 Identities=15% Similarity=0.204 Sum_probs=50.2
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 64 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
...|++++|+|++++++|+||.++.++++++.+++..+ + . ++-...+++||.|+++|.+++.
T Consensus 190 ~~~G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~---~--~-------------~~~~~~~~vGd~i~~~Vl~vd~ 251 (390)
T PRK06676 190 LKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHE---R--V-------------EKPSEVVSVGQEVEVKVLSIDW 251 (390)
T ss_pred CCCCCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCcc---c--c-------------CCHHHhcCCCCEEEEEEEEEeC
Confidence 46899999999999999999999888887776655421 2 1 1122368999999999999986
Q ss_pred CCC
Q 030455 144 PSI 146 (177)
Q Consensus 144 ~~~ 146 (177)
.+.
T Consensus 252 ~~~ 254 (390)
T PRK06676 252 ETE 254 (390)
T ss_pred CCC
Confidence 544
No 79
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.69 E-value=0.00018 Score=64.73 Aligned_cols=65 Identities=12% Similarity=0.103 Sum_probs=50.4
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
.+|+++.|+|++++++|+||+++ .+++++|.+++.. ... . .+-...+++||.|+++|.+++.
T Consensus 291 ~~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~--~~~--~-------------~~~~~~~~~Gd~v~vkVl~iD~ 353 (491)
T PRK13806 291 KAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSW--TRR--V-------------NKPEDVVAPGDAVAVKIKDIDP 353 (491)
T ss_pred CCCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCc--ccc--c-------------CCHHHcCCCCCEEEEEEEEEEc
Confidence 37999999999999999999995 6888888876531 111 0 1223479999999999999987
Q ss_pred CCC
Q 030455 144 PSI 146 (177)
Q Consensus 144 ~~~ 146 (177)
..+
T Consensus 354 e~~ 356 (491)
T PRK13806 354 AKR 356 (491)
T ss_pred cCC
Confidence 655
No 80
>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=97.67 E-value=0.0002 Score=45.29 Aligned_cols=57 Identities=23% Similarity=0.177 Sum_probs=42.1
Q ss_pred EEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCC
Q 030455 70 IAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 70 ~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~ 144 (177)
++|+|++++++|+|+.++ ..+++++.+++.++ + . .+....+++||.|+++|.+++..
T Consensus 1 v~g~V~~v~~~g~~v~l~~~~~g~~~~~~~~~~---~--~-------------~~~~~~~~~G~~v~~~v~~~d~~ 58 (65)
T cd00164 1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDK---F--V-------------KDPSEVFKVGDEVEVKVLEVDPE 58 (65)
T ss_pred CEEEEEEEEeeeEEEEecCCCEEEEEHHHCCCc---c--c-------------cCHhhEeCCCCEEEEEEEEEcCC
Confidence 479999999999999997 66666666554322 1 0 12234799999999999999753
No 81
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=97.66 E-value=0.0002 Score=64.48 Aligned_cols=63 Identities=13% Similarity=0.124 Sum_probs=50.3
Q ss_pred CCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~ 144 (177)
+|++++|+|++++++|+||++. -+++++|.+++.++ . . .. ....+++||.|+++|..++..
T Consensus 379 vG~~v~G~V~~i~~~G~FV~l~~gv~Gli~~se~s~~---~--~--~~-----------~~~~~~~Gd~v~~~V~~id~e 440 (491)
T PRK13806 379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRA---G--K--PA-----------TYEKLKPGDSVTLVVEEIDTA 440 (491)
T ss_pred CCCEEEEEEEEEecCceEEEcCCCcEEEEEHHHcCcc---c--c--cc-----------hhhcCCCCCEEEEEEEEEeCC
Confidence 7999999999999999999994 78899998876432 1 1 11 123679999999999999876
Q ss_pred CC
Q 030455 145 SI 146 (177)
Q Consensus 145 ~~ 146 (177)
.+
T Consensus 441 ~~ 442 (491)
T PRK13806 441 KR 442 (491)
T ss_pred CC
Confidence 54
No 82
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.58 E-value=0.00025 Score=64.62 Aligned_cols=65 Identities=18% Similarity=0.149 Sum_probs=51.1
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
.+|+++.|+|++++++|+||+++ .++++++.+++..+ + . .++....|++||.|+++|.+++.
T Consensus 372 ~~G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~---~--~------------~~~~~~~~~~Gd~v~v~Il~vd~ 434 (565)
T PRK06299 372 PVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWD---K--K------------GEEAVELYKKGDEVEAVVLKVDV 434 (565)
T ss_pred CCCCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCcc---c--c------------ccChHhhCCCCCEEEEEEEEEeC
Confidence 36999999999999999999997 88888888766432 2 1 12223478999999999999987
Q ss_pred CCC
Q 030455 144 PSI 146 (177)
Q Consensus 144 ~~~ 146 (177)
..+
T Consensus 435 ~~~ 437 (565)
T PRK06299 435 EKE 437 (565)
T ss_pred CCC
Confidence 554
No 83
>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=97.53 E-value=0.00041 Score=62.46 Aligned_cols=63 Identities=24% Similarity=0.265 Sum_probs=50.2
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
.+|+++.|+|++++++|+||+++ .++++++.+++.++ + .. +....|++||.|++||.+++.
T Consensus 445 ~~G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~---~--~~-------------~~~~~~~~Gd~v~~~V~~id~ 506 (516)
T TIGR00717 445 KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSEN---R--DE-------------DKTDEIKVGDEVEAKVVDIDK 506 (516)
T ss_pred CcceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCcc---c--cc-------------cccccCCCCCEEEEEEEEEeC
Confidence 37999999999999999999995 68888888877543 2 21 123379999999999999986
Q ss_pred CC
Q 030455 144 PS 145 (177)
Q Consensus 144 ~~ 145 (177)
.+
T Consensus 507 ~~ 508 (516)
T TIGR00717 507 KN 508 (516)
T ss_pred CC
Confidence 43
No 84
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=97.45 E-value=0.00039 Score=63.03 Aligned_cols=65 Identities=15% Similarity=0.135 Sum_probs=52.8
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
.+|..+.|+|+.++++|+||+++ .++|++|.+++... + .. . -..+++.||.|.|+|.+++.
T Consensus 276 ~~g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~---~--~~------------~-P~evv~~Gq~V~V~Vl~id~ 337 (541)
T COG0539 276 PVGDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWT---K--KN------------V-PSEVVKVGQEVEVKVLDIDP 337 (541)
T ss_pred CCCCEEEEEEEEeecCcEEEEecCCccceeechhhccc---c--cC------------C-HHHhcccCCEEEEEEEeeCc
Confidence 38999999999999999999995 88999999865322 1 11 1 23489999999999999998
Q ss_pred CCCc
Q 030455 144 PSIP 147 (177)
Q Consensus 144 ~~~~ 147 (177)
..++
T Consensus 338 e~rR 341 (541)
T COG0539 338 ERRR 341 (541)
T ss_pred hhce
Confidence 7765
No 85
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=97.43 E-value=0.00068 Score=57.92 Aligned_cols=64 Identities=13% Similarity=0.094 Sum_probs=47.0
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEecc-cceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEe
Q 030455 64 PFVGEIIAAKLKESDANGLRLSLGF-FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 142 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~lg~-~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~ 142 (177)
...|+++.|+|.++++.|++|.+|. .+++++.+++..+ | ..+. ...+++|+.|+|+|++++
T Consensus 29 ~~~G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~---~--~~~~-------------~~~~~~G~~v~~~Vi~~~ 90 (318)
T PRK07400 29 FKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSIN---R--VEGP-------------EEVLQPNETREFFILSDE 90 (318)
T ss_pred cCCCCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccc---c--ccCH-------------HHccCCCCEEEEEEEEEe
Confidence 4789999999999999999999985 5665555444322 2 2111 127899999999999987
Q ss_pred CCC
Q 030455 143 YPS 145 (177)
Q Consensus 143 ~~~ 145 (177)
-.+
T Consensus 91 ~~~ 93 (318)
T PRK07400 91 NED 93 (318)
T ss_pred CCC
Confidence 543
No 86
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.41 E-value=0.00098 Score=58.05 Aligned_cols=65 Identities=20% Similarity=0.165 Sum_probs=50.2
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
.+|+++.|+|++++++|+||++. .++++++.+++.++ . . .+....|++||.|+++|.+++.
T Consensus 276 ~~G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~---~--~-------------~~~~~~~~~Gd~v~v~V~~id~ 337 (390)
T PRK06676 276 PEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHK---H--I-------------ATPSEVLEEGQEVKVKVLEVNE 337 (390)
T ss_pred cCCcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCcc---c--c-------------CChhhccCCCCEEEEEEEEEEC
Confidence 37999999999999999999994 68888888765321 1 1 1122378999999999999987
Q ss_pred CCCc
Q 030455 144 PSIP 147 (177)
Q Consensus 144 ~~~~ 147 (177)
.++.
T Consensus 338 e~~~ 341 (390)
T PRK06676 338 EEKR 341 (390)
T ss_pred CCCE
Confidence 6543
No 87
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=97.39 E-value=0.00046 Score=61.87 Aligned_cols=61 Identities=23% Similarity=0.295 Sum_probs=49.0
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 141 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v 141 (177)
|++..|+++.|+|.++++.|++|.+|-.+++.+.+++.|. ..|++|+.||+.|..+
T Consensus 130 yk~~~GeIV~G~V~ri~~~giiVDLggvea~LP~sE~ip~------------------------E~~~~GdrIka~I~~V 185 (470)
T PRK09202 130 YKDRVGEIITGVVKRVERGNIIVDLGRAEAILPRKEQIPR------------------------ENFRPGDRVRAYVYEV 185 (470)
T ss_pred HHhhcCCEEEEEEEEEecCCEEEEECCeEEEecHHHcCCC------------------------ccCCCCCEEEEEEEEE
Confidence 5567899999999999999999999888776665554332 1567899999999999
Q ss_pred eCCCC
Q 030455 142 NYPSI 146 (177)
Q Consensus 142 ~~~~~ 146 (177)
+-..+
T Consensus 186 d~~~k 190 (470)
T PRK09202 186 RKEAR 190 (470)
T ss_pred ecCCC
Confidence 86543
No 88
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=97.38 E-value=0.00086 Score=64.16 Aligned_cols=63 Identities=11% Similarity=0.195 Sum_probs=47.7
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
+|++++|+|++++++|+||+++.+++++|.+++..+ + . .+-...+++|+.|++||++++-..
T Consensus 493 ~G~~V~G~Vk~i~~~G~fVdl~Gv~Gfvp~SeiS~~---~--v-------------~~~~~~~kvGq~v~vkVi~iD~e~ 554 (863)
T PRK12269 493 IEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWG---H--V-------------ARPREFVKKGQTIELKVIRLDQAE 554 (863)
T ss_pred CCCEEEEEEEEEeCCcEEEEECCEEEEEEchhcccc---c--c-------------CCHHHhccCCCEEEEEEEEEecCC
Confidence 689999999999999999999888888776655322 1 1 111225789999999999998654
Q ss_pred C
Q 030455 146 I 146 (177)
Q Consensus 146 ~ 146 (177)
+
T Consensus 555 ~ 555 (863)
T PRK12269 555 K 555 (863)
T ss_pred C
Confidence 4
No 89
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=97.38 E-value=0.00083 Score=61.26 Aligned_cols=65 Identities=17% Similarity=0.190 Sum_probs=49.8
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 64 PFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
...|++++|+|++++++|+||.+|.++++++.+++.. +.. .+-...+++||.|+++|.+++-
T Consensus 199 l~~G~iv~g~V~~v~~~G~~V~i~g~~glv~~se~s~-------~~~-----------~~~~~~~kvG~~v~v~V~~~d~ 260 (565)
T PRK06299 199 LEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISW-------KRV-----------NHPSEVVNVGDEVKVKVLKFDK 260 (565)
T ss_pred CCCCCEEEEEEEEEeCCeEEEEECCEEEEEEHHHhcc-------ccc-----------CCHhhcCCCCCEEEEEEEEEeC
Confidence 4589999999999999999999988888887765522 111 1112368999999999999986
Q ss_pred CCC
Q 030455 144 PSI 146 (177)
Q Consensus 144 ~~~ 146 (177)
+.+
T Consensus 261 ~~~ 263 (565)
T PRK06299 261 EKK 263 (565)
T ss_pred CCC
Confidence 543
No 90
>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=97.36 E-value=0.00085 Score=60.42 Aligned_cols=64 Identities=22% Similarity=0.215 Sum_probs=50.0
Q ss_pred CCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~ 144 (177)
+|+++.|+|++++++|+||+++ .++++++.+++..+ + .. ......+++|+.|.++|..++..
T Consensus 359 ~G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~---~--~~------------~~~~~~~~~G~~V~~~Vl~vd~~ 421 (516)
T TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWD---K--DG------------READHLYKKGDEIEAVVLAVDKE 421 (516)
T ss_pred CCCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCc---c--cC------------CCHhHccCCCCEEEEEEEEEeCc
Confidence 7999999999999999999997 78888877665321 1 11 11234799999999999999865
Q ss_pred CC
Q 030455 145 SI 146 (177)
Q Consensus 145 ~~ 146 (177)
++
T Consensus 422 ~~ 423 (516)
T TIGR00717 422 KK 423 (516)
T ss_pred CC
Confidence 54
No 91
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=97.32 E-value=0.0015 Score=53.46 Aligned_cols=85 Identities=19% Similarity=0.336 Sum_probs=64.4
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
|.|.+|+++.|.|.++...+..|.++ +...+.+.++.+.. .+ +.. .++.+.++++||.|-.||.+
T Consensus 60 YiP~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r--~~--~~~----------~~~~r~~l~vGD~v~AkV~~ 125 (239)
T COG1097 60 YIPEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRR--KF--ENA----------EKDLRPFLNVGDLVYAKVVD 125 (239)
T ss_pred ccCCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcc--cc--ccc----------ccccccccccCCEEEEEEEE
Confidence 88999999999999999999999997 67555555444222 12 211 23456699999999999999
Q ss_pred EeCCCCcccccCCCCCCCCeEEEEEecCCCCcccc
Q 030455 141 VNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPVS 175 (177)
Q Consensus 141 v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~i~ 175 (177)
++- . +.+..++++.|||++.
T Consensus 126 vd~-------~--------~~~~L~~k~~~~GkL~ 145 (239)
T COG1097 126 VDR-------D--------GEVELTLKDEGLGKLK 145 (239)
T ss_pred ccC-------C--------CceEEEeecCCCcccc
Confidence 863 1 4677788999999874
No 92
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.31 E-value=0.0012 Score=61.49 Aligned_cols=64 Identities=19% Similarity=0.158 Sum_probs=49.9
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
.+|+++.|+|++++++|+||+++ .++++++.+++.++ + . ++....|++||.|+++|.+++.
T Consensus 561 ~~G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~---~--~-------------~~~~~~~kvGd~V~vkV~~id~ 622 (647)
T PRK00087 561 PVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWK---R--I-------------DKPEDVLSEGEEVKAKILEVDP 622 (647)
T ss_pred cCCeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCcc---c--c-------------CCHhhcCCCCCEEEEEEEEEeC
Confidence 47999999999999999999994 68888888765432 1 1 1223378999999999999986
Q ss_pred CCC
Q 030455 144 PSI 146 (177)
Q Consensus 144 ~~~ 146 (177)
.++
T Consensus 623 e~~ 625 (647)
T PRK00087 623 EEK 625 (647)
T ss_pred CCC
Confidence 443
No 93
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=97.29 E-value=0.0024 Score=44.47 Aligned_cols=63 Identities=11% Similarity=0.075 Sum_probs=47.6
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
|.|.+|+.+-|+|++++..+.+|.++ +.+.+.+. ..| ...+ ++++..+++||-|-.||.+
T Consensus 2 Y~P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~-------~~f--~gat----------k~~rp~L~~GDlV~ArV~~ 62 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSY-------LAF--EGAT----------KRNRPNLNVGDLVYARVVK 62 (86)
T ss_pred CcCCCCCEEEEEEEEEcCCeEEEEcCCCcceEech-------HHc--cccc----------ccccccCCCCCEEEEEEEe
Confidence 67999999999999999999999996 44433322 223 2211 3456689999999999999
Q ss_pred EeC
Q 030455 141 VNY 143 (177)
Q Consensus 141 v~~ 143 (177)
++-
T Consensus 63 ~~~ 65 (86)
T cd05790 63 ANR 65 (86)
T ss_pred cCC
Confidence 864
No 94
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=97.23 E-value=0.0012 Score=61.34 Aligned_cols=64 Identities=17% Similarity=0.192 Sum_probs=49.9
Q ss_pred CCCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~ 144 (177)
.+|+++.|+|++++++|+||.++.++++++.+++... + . .+-...|++||.|+++|.+++..
T Consensus 476 ~~G~iV~g~V~~v~~~G~fV~l~gv~Gll~~sels~~---~--~-------------~~~~~~~~vGd~V~vkV~~id~~ 537 (647)
T PRK00087 476 EEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWG---R--V-------------EKPSDVLKVGDEIKVYILDIDKE 537 (647)
T ss_pred CCCCEEEEEEEEEeCCcEEEEECCEEEEEEHHHcCcc---c--c-------------CCHHHhcCCCCEEEEEEEEEECC
Confidence 3799999999999999999999888888777765321 1 1 11223789999999999999865
Q ss_pred CC
Q 030455 145 SI 146 (177)
Q Consensus 145 ~~ 146 (177)
++
T Consensus 538 ~~ 539 (647)
T PRK00087 538 NK 539 (647)
T ss_pred CC
Confidence 54
No 95
>PF03293 Pox_RNA_pol: Poxvirus DNA-directed RNA polymerase, 18 kD subunit; InterPro: IPR004973 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The Poxvirus DNA-directed RNA polymerase (2.7.7.6 from EC) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18 kDa subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0019083 viral transcription
Probab=97.02 E-value=0.063 Score=40.48 Aligned_cols=120 Identities=17% Similarity=0.247 Sum_probs=79.3
Q ss_pred EeeeeEEECCCCCCccHHHHHHHHHHhHhcCc----------------ccccceeeeCCCCeeeEEEEEEEeec-cCCCC
Q 030455 6 KIEHTLRLPPHLLRLPLNEAIKLELENVFLDK----------------EIEGGFVYPGEGASTHTVKFRLVVFR-PFVGE 68 (177)
Q Consensus 6 ~l~d~v~i~P~~~~~~~~~~i~~~L~~ky~~k----------------~i~~g~I~~g~G~~~~~V~f~~~~f~-p~~gE 68 (177)
.+--.|.++|++|+-|+.+.|++...++|.-| ...=|.|.. ..+..+|-..+- |+ -..|+
T Consensus 7 ~vYLpV~l~PhELtLd~~~Ni~~aV~~eYLhkE~~G~MakkIei~~d~~lPLGeivN--N~ivv~VPC~vt-ykyYk~GD 83 (160)
T PF03293_consen 7 NVYLPVTLQPHELTLDIRKNIKDAVYREYLHKESGGIMAKKIEICEDKELPLGEIVN--NHIVVKVPCNVT-YKYYKVGD 83 (160)
T ss_pred eeEEEEecCcceeeehHHHhHHHHHHHHHhhhcccCceeeeEEEEeccccchHhhcc--cEEEEEeeeEEE-EEEEeeCC
Confidence 34456889999999999999999999988755 222333332 223333322222 33 57899
Q ss_pred EEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEE
Q 030455 69 IIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSV 141 (177)
Q Consensus 69 v~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v 141 (177)
++.|+..=-++.-++|..| .+..+ .++ .....| ++...+ +. +++..|..|+.|.+.....
T Consensus 84 vV~GtLnIedESni~V~CgDLiCkl--~rd--sGtVSf--~dsKYC-----fi--rNg~vY~ngs~Vsv~LkEa 144 (160)
T PF03293_consen 84 VVRGTLNIEDESNITVQCGDLICKL--SRD--SGTVSF--NDSKYC-----FI--RNGVVYDNGSEVSVVLKEA 144 (160)
T ss_pred EEEEEEEecccCceEEEcCcEEEEe--ecc--CCeEEe--cCceEE-----EE--ECCEEecCCCEEEEEehhh
Confidence 9999999999999999997 33221 111 123446 655544 54 4566999999998877664
No 96
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=97.00 E-value=0.00062 Score=56.26 Aligned_cols=66 Identities=20% Similarity=0.225 Sum_probs=53.9
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEe---cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 64 PFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~l---g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
|-.||++-|+|.++.++|+||.| +-.++++|.+.... . |+ ++-+.+++.|+++-++|++
T Consensus 9 PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas------------~---wV---knIrd~vkegqkvV~kVlr 70 (269)
T COG1093 9 PEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVAS------------G---WV---KNIRDYVKEGQKVVAKVLR 70 (269)
T ss_pred CCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHH------------H---HH---HHHHHHhhcCCeEEEEEEE
Confidence 89999999999999999999999 46788888875432 2 32 4445689999999999999
Q ss_pred EeCCCCc
Q 030455 141 VNYPSIP 147 (177)
Q Consensus 141 v~~~~~~ 147 (177)
|+-..+.
T Consensus 71 Vd~~rg~ 77 (269)
T COG1093 71 VDPKRGH 77 (269)
T ss_pred EcCCCCe
Confidence 9976653
No 97
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=97.00 E-value=0.0021 Score=55.87 Aligned_cols=95 Identities=18% Similarity=0.260 Sum_probs=63.7
Q ss_pred EEECCCCCCccHHHHHHHHHHhHhcCcccccceeeeCCCCeeeEEEEEEEeeccCCCCEEEEEEEeeeCCeeEEEecccc
Q 030455 11 LRLPPHLLRLPLNEAIKLELENVFLDKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFE 90 (177)
Q Consensus 11 v~i~P~~~~~~~~~~i~~~L~~ky~~k~i~~g~I~~g~G~~~~~V~f~~~~f~p~~gEv~~g~V~~v~~~Gifv~lg~~~ 90 (177)
+.|.|..||+...+++++.|.++..... ...+ .--|++..|+++.|+|.+.++.|++|.+|-++
T Consensus 95 ~~I~~~~fgR~aaq~akqvI~Qkire~e--re~v--------------~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~vE 158 (362)
T PRK12327 95 IEVTPKDFGRIAAQTAKQVIMQRLREAE--REII--------------YNEFSEREGDIVTGVVQRRDNRFVYVNLGKIE 158 (362)
T ss_pred EecCcCCCChHHHHHHHHHHHHHHHHHH--HHHH--------------HHHHHHhcCCEEEEEEEEEeCCcEEEEeCCeE
Confidence 4566777777655555555555433220 0000 01267889999999999999999999998777
Q ss_pred eeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 91 DIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 91 ~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
++.+.+++.|. ..|++||.|++.|.+++...
T Consensus 159 a~LP~~E~ip~------------------------e~~~~Gd~Ika~V~~V~~~~ 189 (362)
T PRK12327 159 AVLPPAEQIPG------------------------ETYKHGDRIKVYVVKVEKTT 189 (362)
T ss_pred EEecHHHcCCC------------------------CCCCCCCEEEEEEEEEecCC
Confidence 65444443321 15788999999999998644
No 98
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=96.77 E-value=0.0044 Score=53.49 Aligned_cols=60 Identities=30% Similarity=0.351 Sum_probs=46.5
Q ss_pred eccCCCCEEEEEEEeeeCCe-eEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANG-LRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~G-ifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
|+...||++.|+|.++++.| ++|.+|-.+++.+.+++.|. + .|++||.|++.|.+
T Consensus 127 y~~k~GeiV~G~V~~v~~~g~v~VdiG~~ea~LP~~E~ip~--------------------E----~~~~Gd~ik~~V~~ 182 (341)
T TIGR01953 127 FSSKEGEIISGTVKRVNRRGNLYVELGKTEGILPKKEQIPG--------------------E----KFRIGDRIKAYVYE 182 (341)
T ss_pred HHhhcCCEEEEEEEEEecCCcEEEEECCeEEEecHHHcCCC--------------------c----CCCCCCEEEEEEEE
Confidence 55679999999999999988 69999977766555443321 0 37889999999999
Q ss_pred EeCCC
Q 030455 141 VNYPS 145 (177)
Q Consensus 141 v~~~~ 145 (177)
++-..
T Consensus 183 V~~~~ 187 (341)
T TIGR01953 183 VRKTA 187 (341)
T ss_pred EEcCC
Confidence 98543
No 99
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=96.34 E-value=0.0094 Score=55.26 Aligned_cols=63 Identities=21% Similarity=0.196 Sum_probs=50.5
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEe-cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~l-g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
=.+.+||++.|+|+.+..+|+||++ +.=++++|.+++... .. +.-..+.++||.|+|||..
T Consensus 615 ~e~evg~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~--rv----------------~kv~dvlk~Gd~v~Vkv~~ 676 (692)
T COG1185 615 REVEVGEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKE--RV----------------EKVEDVLKEGDEVKVKVIE 676 (692)
T ss_pred hhcccccEEEEEEEEEeecceEEEecCCcceeEEehhhhhh--hh----------------hcccceeecCceEEEEEee
Confidence 4478999999999999999999999 456789999876433 11 1223589999999999999
Q ss_pred Ee
Q 030455 141 VN 142 (177)
Q Consensus 141 v~ 142 (177)
++
T Consensus 677 iD 678 (692)
T COG1185 677 ID 678 (692)
T ss_pred ec
Confidence 87
No 100
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=95.73 E-value=0.032 Score=48.72 Aligned_cols=95 Identities=12% Similarity=0.075 Sum_probs=64.8
Q ss_pred EEECCCCCCccHHHHHHHHHHhHhcCcccccceeeeCCCCeeeEEEEEEEeeccCCCCEEEEEEEeeeCC-eeEEEeccc
Q 030455 11 LRLPPHLLRLPLNEAIKLELENVFLDKEIEGGFVYPGEGASTHTVKFRLVVFRPFVGEIIAAKLKESDAN-GLRLSLGFF 89 (177)
Q Consensus 11 v~i~P~~~~~~~~~~i~~~L~~ky~~k~i~~g~I~~g~G~~~~~V~f~~~~f~p~~gEv~~g~V~~v~~~-Gifv~lg~~ 89 (177)
+.+.|.+||+...+++++.|.++.... ..-.++ --|++.+||++.|+|..+... ++++.||-.
T Consensus 99 ~~i~~~~fgRiaaq~akq~i~Qkir~~--er~~i~--------------~ey~~~~Geiv~g~V~r~~~~~~i~vdlg~~ 162 (374)
T PRK12328 99 YELSLENMGRTAANTLFKELEYHIQRL--LEESIF--------------EKYKKKVGKIVFGTVVRVDNEENTFIEIDEI 162 (374)
T ss_pred EecChhhCCHHHHHHHHHHHHHHHHHH--HHHHHH--------------HHHHHhcCcEEEEEEEEEecCCCEEEEcCCe
Confidence 346788888877777776665554321 111111 137899999999999999974 599999877
Q ss_pred ceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCCC
Q 030455 90 EDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 90 ~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
+++....+++|. ..|++||.||+-|..|+-..
T Consensus 163 ea~LP~~eqip~------------------------E~~~~Gdrik~~i~~V~~~~ 194 (374)
T PRK12328 163 RAVLPMKNRIKG------------------------EKFKVGDVVKAVLKRVKIDK 194 (374)
T ss_pred EEEeCHHHcCCC------------------------CcCCCCCEEEEEEEEEecCC
Confidence 655444433322 15788999999999998644
No 101
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=95.30 E-value=0.13 Score=40.77 Aligned_cols=87 Identities=14% Similarity=0.078 Sum_probs=53.0
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEecccceeE--ecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSLGFFEDIY--VPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVL 139 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~--i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~ 139 (177)
..|..|.++-|.|+++....+-|++-.+++.- .+.. .....+. |+.... + .++-.-.|++||.||.||+
T Consensus 60 ~~~K~GdiV~grV~~v~~~~a~V~i~~ve~~~r~~~~~-~~~~ihv-s~~~~~------~-~~~~~d~f~~GDivrA~Vi 130 (188)
T COG1096 60 PLPKGGDIVYGRVTDVREQRALVRIVGVEGKERELATS-GAADIHV-SQVRDG------Y-VEKLSDAFRIGDIVRARVI 130 (188)
T ss_pred CCCCCCCEEEEEEeeccceEEEEEEEEEecccccCCCC-ceeeEEE-Eecccc------c-ccccccccccccEEEEEEE
Confidence 44778899999999999999999984443311 1110 0111111 111110 0 1233358999999999999
Q ss_pred EEeCCCCcccccCCCCCCCCeEEEEEecCCCCccc
Q 030455 140 SVNYPSIPIEQAEGSKPFAPMVINGSIDYDGLGPV 174 (177)
Q Consensus 140 ~v~~~~~~~~~~~~~~~~~~~~i~gs~~~~gLG~i 174 (177)
+.- ..+..|.+++-||.+
T Consensus 131 s~~-----------------~~~~Lst~~~dlGVI 148 (188)
T COG1096 131 STG-----------------DPIQLSTKGNDLGVI 148 (188)
T ss_pred ecC-----------------CCeEEEecCCcceEE
Confidence 964 135567777777754
No 102
>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=95.09 E-value=0.088 Score=36.30 Aligned_cols=24 Identities=21% Similarity=0.465 Sum_probs=18.5
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEec
Q 030455 64 PFVGEIIAAKLKESDANGLRLSLG 87 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~lg 87 (177)
|.+|.++.|+|+.+++.-+.+++=
T Consensus 2 P~vGdiV~~rVtrv~~~~a~v~Il 25 (82)
T PF10447_consen 2 PKVGDIVIARVTRVNPRQAKVEIL 25 (82)
T ss_dssp --TT-EEEEEEEEE-SSEEEEEEE
T ss_pred CCCCCEEEEEEEEEeccEEEEEEE
Confidence 889999999999999999998873
No 103
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=93.94 E-value=0.18 Score=45.00 Aligned_cols=59 Identities=14% Similarity=0.175 Sum_probs=44.9
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEe----cc--cceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSL----GF--FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIK 135 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~l----g~--~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VR 135 (177)
|++.+|+++.|+|..+.+.++++.+ |- .+++...++++|. -.|+.||.||
T Consensus 148 f~~~~GeIV~G~V~r~e~~~viv~l~~~~g~~~~EaiLP~~Eqip~------------------------E~y~~Gdrik 203 (449)
T PRK12329 148 FQDLEDTVLTARVLRFERQSVIMAVSSGFGQPEVEAELPKREQLPN------------------------DNYRANATFK 203 (449)
T ss_pred HHHhcCcEEEEEEEEEcCCCEEEEecccCCCcceEEEecHHHcCCC------------------------CcCCCCCEEE
Confidence 7899999999999999999999988 32 4444333333222 1578899999
Q ss_pred EEEEEEeCC
Q 030455 136 FRVLSVNYP 144 (177)
Q Consensus 136 vrV~~v~~~ 144 (177)
+-|..|+-.
T Consensus 204 a~i~~V~~~ 212 (449)
T PRK12329 204 VFLKEVSEG 212 (449)
T ss_pred EEEEEeecC
Confidence 999999764
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=92.47 E-value=0.34 Score=42.95 Aligned_cols=75 Identities=11% Similarity=0.065 Sum_probs=49.2
Q ss_pred ccCCCCEEEEEEEeeeCC--eeEEEecc-cceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEE
Q 030455 63 RPFVGEIIAAKLKESDAN--GLRLSLGF-FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVL 139 (177)
Q Consensus 63 ~p~~gEv~~g~V~~v~~~--Gifv~lg~-~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~ 139 (177)
.+.+|.++.|+|.++.+. |+||.+|. -+++.+.++..++.+.+ ...... - -...+-...++.||.|.|+|.
T Consensus 22 ~~~vGnIY~GrV~~i~p~l~aAFVdiG~~k~gfL~~~d~~~~~~~~--~~~~~~---~-~~~~~i~~~l~~G~~IlVQV~ 95 (414)
T TIGR00757 22 RQLKGNIYKGRVTRILPSLQAAFVDIGLEKNGFLHASDIGPNYECL--APAEAK---R-EAGPSISELLRPGQSVLVQVV 95 (414)
T ss_pred cCCCCCEEEEEEeeecCCCceEEEEcCCCceEEEEHHHcCchhhcc--cccccc---c-cccCCHHHhCcCCCEEEEEEe
Confidence 367999999999999999 99999984 45677777665543222 111100 0 000111235899999999999
Q ss_pred EEeC
Q 030455 140 SVNY 143 (177)
Q Consensus 140 ~v~~ 143 (177)
..-.
T Consensus 96 Ke~~ 99 (414)
T TIGR00757 96 KEPR 99 (414)
T ss_pred eCCc
Confidence 8443
No 105
>PF13509 S1_2: S1 domain; PDB: 3GO5_A.
Probab=92.14 E-value=0.17 Score=32.64 Aligned_cols=36 Identities=22% Similarity=0.387 Sum_probs=20.2
Q ss_pred CCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPS 101 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~ 101 (177)
+|++-..+|...+++|+|+..|--..++.|.+..+.
T Consensus 1 iG~~~~L~V~~~~~~g~fL~~~~~~~vlLp~~e~~~ 36 (61)
T PF13509_consen 1 IGQINTLKVVDKNEFGYFLDDGEGKEVLLPKSEVPE 36 (61)
T ss_dssp --------EEEE-SSEEEEEETT-EEEEEEGGG---
T ss_pred CCCCcceEEEEEeCCEEEEECCCCCEEEechHHcCC
Confidence 588889999999999999998876678888766554
No 106
>KOG3409 consensus Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis]
Probab=90.62 E-value=1.6 Score=34.30 Aligned_cols=64 Identities=14% Similarity=0.163 Sum_probs=39.6
Q ss_pred ccCCCCEEEEEEEeeeCCeeEEEeccc---------ceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCE
Q 030455 63 RPFVGEIIAAKLKESDANGLRLSLGFF---------EDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDE 133 (177)
Q Consensus 63 ~p~~gEv~~g~V~~v~~~Gifv~lg~~---------~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~ 133 (177)
-|+.|.++.++|+.++..=+-|.+=-+ .++++..+.-+. +.+.-. --..|++||.
T Consensus 65 LP~~G~IVtarV~~i~~rfAkv~I~~V~d~~lk~~FrglirkqdvR~t------Ekdrv~----------v~ksFrPgDi 128 (193)
T KOG3409|consen 65 LPFVGAIVTARVSRINLRFAKVDILSVGDKPLKKSFRGLIRKQDVRAT------EKDRVK----------VYKSFRPGDI 128 (193)
T ss_pred CCccCcEEEEEEEeeccceeeEEEEEEcCEEhhhhhcceeehhhcccc------ccchhh----------hhhccCCCcE
Confidence 399999999999999998666665222 223222221111 111100 0137889999
Q ss_pred EEEEEEEEe
Q 030455 134 IKFRVLSVN 142 (177)
Q Consensus 134 VRvrV~~v~ 142 (177)
|+.+|++..
T Consensus 129 VlAkVis~~ 137 (193)
T KOG3409|consen 129 VLAKVISLG 137 (193)
T ss_pred EEEEEeecC
Confidence 999999943
No 107
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=89.18 E-value=0.74 Score=31.88 Aligned_cols=65 Identities=15% Similarity=0.107 Sum_probs=45.3
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEe---cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRV 138 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~l---g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV 138 (177)
--|-+|++.. .|..+.+.|++|+| | +++++++.+ +. ...+. +.=+..+ +|-.+.++|
T Consensus 12 ~~P~v~dvv~-~Vv~i~d~~~YV~LleY~-iegmIl~~s------el--sr~ri---------rsi~kll-VGk~e~v~V 71 (86)
T PHA02858 12 VFPNINEVTK-GIVFVKDNIFYVKLIDYG-LEALIVNYV------NV--NADRA---------EKLKKKL-VGKTINVQV 71 (86)
T ss_pred ecCCCCeEEE-EEEEEeccEEEEEEecCc-cceEEecHH------HH--hHHHH---------Hhhhhhh-cCCeeEEEE
Confidence 3499999999 88899999999999 5 777766332 22 11110 1112244 899999999
Q ss_pred EEEeCCCC
Q 030455 139 LSVNYPSI 146 (177)
Q Consensus 139 ~~v~~~~~ 146 (177)
++++..++
T Consensus 72 iRVDk~KG 79 (86)
T PHA02858 72 IRTDKLKG 79 (86)
T ss_pred EEECCCCC
Confidence 99987654
No 108
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=88.39 E-value=0.81 Score=42.15 Aligned_cols=63 Identities=16% Similarity=0.146 Sum_probs=46.9
Q ss_pred CCCEEEEEEEeeeCCeeEEEecc-cceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCC
Q 030455 66 VGEIIAAKLKESDANGLRLSLGF-FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~lg~-~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~ 144 (177)
.|-++.|+|+++.+.|+||++-+ -.++.|.+++ | +. |+.+-+.. +++|+.|.++-.+.+..
T Consensus 668 ~g~vy~~tIt~~rd~G~~V~l~p~~~~Llh~sqL---------~---~e-----~iakpsd~-levGq~I~vk~ie~d~~ 729 (760)
T KOG1067|consen 668 FGGVYTATITEIRDTGVMVELYPMQQGLLHNSQL---------D---QE-----KIAKPSDL-LEVGQEIQVKYIERDPR 729 (760)
T ss_pred eeeEEEEEEeeecccceEEEecCCchhhccchhc---------c---cc-----cccChHHH-HhhcceeEEEEEeecCc
Confidence 46678999999999999999953 3567666655 2 22 33344555 99999999999998865
Q ss_pred CC
Q 030455 145 SI 146 (177)
Q Consensus 145 ~~ 146 (177)
.+
T Consensus 730 g~ 731 (760)
T KOG1067|consen 730 GG 731 (760)
T ss_pred cc
Confidence 54
No 109
>KOG1004 consensus Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis]
Probab=87.27 E-value=8 Score=31.40 Aligned_cols=94 Identities=14% Similarity=0.079 Sum_probs=66.3
Q ss_pred eeEEEEEEEeeccCCCCEEEEEEEeeeCCeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCC
Q 030455 52 THTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGL 131 (177)
Q Consensus 52 ~~~V~f~~~~f~p~~gEv~~g~V~~v~~~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G 131 (177)
.+.|..+-.-|-|.+|+.+.|+|++.+.....|.+|.-+-.-. .+..| ...+ ++++-.+++|
T Consensus 51 v~~vds~~kRYiP~~~D~VIGiV~~~~gd~ykVDigg~~~a~L------~~laF--e~At----------krNrPnl~vG 112 (230)
T KOG1004|consen 51 VYWVDSQQKRYIPVKGDHVIGIVTSKSGDIYKVDIGGSEPASL------SYLAF--EGAT----------KRNRPNLQVG 112 (230)
T ss_pred eEEEecccceecCCCCCEEEEEEEeccCceEEEecCCCCeeee------eeccc--cCcc----------ccCCCccccc
Confidence 5678888888999999999999999999999999985321111 13345 3222 4566689999
Q ss_pred CEEEEEEEEEeCCCCcccccCCCCCCCCeEEEEE-ecCCCCccc
Q 030455 132 DEIKFRVLSVNYPSIPIEQAEGSKPFAPMVINGS-IDYDGLGPV 174 (177)
Q Consensus 132 ~~VRvrV~~v~~~~~~~~~~~~~~~~~~~~i~gs-~~~~gLG~i 174 (177)
|-|-.||...+-.. .+ .+.++.+ =+..|.|++
T Consensus 113 dliyakv~~a~~~~----Ep-------el~Cids~graaGfG~L 145 (230)
T KOG1004|consen 113 DLIYAKVVDANKDM----EP-------ELTCIDSTGRAAGFGVL 145 (230)
T ss_pred cEEEEEEEecCCCc----Cc-------ceEEEcccCcccCcccc
Confidence 99999999876322 11 2566665 333577765
No 110
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=84.02 E-value=4.8 Score=40.89 Aligned_cols=85 Identities=15% Similarity=0.278 Sum_probs=51.9
Q ss_pred CCCCEEEEEEEeeeCCeeEEEe--cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEe
Q 030455 65 FVGEIIAAKLKESDANGLRLSL--GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 142 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~l--g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~ 142 (177)
-+|+.++|+|.++++.|+-|.+ |-+.+++.+.++.+-.-+| ......+..|.++ ||..++
T Consensus 508 ~iG~~V~~~I~~vt~~Gv~v~v~~~ni~g~lp~~hlsd~~~~~----------------p~~~f~v~~~~k~--RVl~~~ 569 (1710)
T KOG1070|consen 508 EIGQLVPGVIRKVTPQGVEVLVTFGNIKGVLPKEHLSDHPLQP----------------PLRDFKVGSGVKL--RVLSVN 569 (1710)
T ss_pred cccceeeeEEEEecCCcEEEEEecCceeeecChHhhhhccccc----------------ccceeeeccccEE--EEEEEE
Confidence 4899999999999999999988 4466666555554433222 2233344455555 666666
Q ss_pred CCCCc-----------c---cccCCCCCCCCeEEEEEec
Q 030455 143 YPSIP-----------I---EQAEGSKPFAPMVINGSID 167 (177)
Q Consensus 143 ~~~~~-----------~---~~~~~~~~~~~~~i~gs~~ 167 (177)
...++ . .........|.+...|++.
T Consensus 570 ~~~~~v~l~~K~slv~~~~plp~d~~~~~pg~~~~G~l~ 608 (1710)
T KOG1070|consen 570 RDRNRVALTLKKSLVNTQLPLPSDFEQAIPGKITKGTLC 608 (1710)
T ss_pred ccCCeeEEEechhhhcccCCCccchhhcCCCceEEEEEe
Confidence 54443 0 1111223467778888764
No 111
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=83.92 E-value=1.7 Score=43.93 Aligned_cols=63 Identities=13% Similarity=0.081 Sum_probs=46.5
Q ss_pred CCCEEEEEEEeeeCCeeEEEe-cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeCC
Q 030455 66 VGEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~l-g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~~ 144 (177)
.|++.-|.|..+.++|.||+. |.++|+-..+.+.++ +. .+....+.+|+.||++|.+++-.
T Consensus 599 pg~~~~G~l~~~~~~g~~V~F~g~lsGf~p~s~~sd~-~v-----------------~~~~ehf~vGqTv~~~i~nvd~e 660 (1710)
T KOG1070|consen 599 PGKITKGTLCAIKENGAFVTFTGGLSGFAPVSEMSDD-FV-----------------LSDSEHFPVGQTVRAKIVNVDDE 660 (1710)
T ss_pred CCceEEEEEeeeccCCeEEEecCccccccchhhhhhh-hh-----------------cChhhhcccccEEEEEEEecCch
Confidence 699999999999999999998 666665544444443 11 11223678999999999999854
Q ss_pred CC
Q 030455 145 SI 146 (177)
Q Consensus 145 ~~ 146 (177)
.+
T Consensus 661 k~ 662 (1710)
T KOG1070|consen 661 KR 662 (1710)
T ss_pred hc
Confidence 44
No 112
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=83.00 E-value=0.84 Score=41.13 Aligned_cols=73 Identities=16% Similarity=0.191 Sum_probs=52.5
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEe---cccceeEecCCCCCCCc---ccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEE
Q 030455 64 PFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHLLPSPS---RSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFR 137 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~l---g~~~~i~i~~~~~~~~~---~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvr 137 (177)
+-.+..|.+.|..++.-|+.|+| |- .+|||..++-+.- .+ +.++.. +. =+...+|++||.|.|+
T Consensus 559 ~~~~~~F~AEI~Di~R~G~RvrLleNGA--~~FIPa~lih~~reei~~--n~e~gt----v~--I~ge~~Yk~~D~i~V~ 628 (645)
T COG4776 559 AGTNTRFAAEIQDISRGGMRVRLLENGA--IAFIPAPLIHANREELVC--NQENGT----VQ--IKGETVYKVGDVIDVT 628 (645)
T ss_pred cccCchhhhhhhhhccCceEEEeccCCc--ceecchhhhccchhheEe--cCCCce----EE--EccEEEEeeccEEEEE
Confidence 44566788899999999999999 43 3788888776532 23 333333 12 2356799999999999
Q ss_pred EEEEeCCCC
Q 030455 138 VLSVNYPSI 146 (177)
Q Consensus 138 V~~v~~~~~ 146 (177)
+..|+-.++
T Consensus 629 l~eVr~etR 637 (645)
T COG4776 629 LAEVRMETR 637 (645)
T ss_pred eHHHHHhhh
Confidence 999886554
No 113
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=81.55 E-value=1.5 Score=40.52 Aligned_cols=58 Identities=16% Similarity=0.045 Sum_probs=42.5
Q ss_pred CCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 65 FVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 65 ~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
..|+.+.|+|+++.++|+|++|. -.-|+.+.+++..+ . .+.+|+.+-|++.+++-
T Consensus 121 e~g~~Y~g~v~~v~~~GvFv~Ln~~v~GL~~~~d~~~~-----------~-------------~~~vgdeiiV~v~~vr~ 176 (715)
T COG1107 121 EAGKYYKGIVSRVEKYGVFVELNSHVRGLIHRRDLGGD-----------P-------------DYAVGDEIIVQVSDVRP 176 (715)
T ss_pred ccceeeeccccchhhhcceeecChhhhccccccccCCC-----------C-------------CCCCCCeEEEEeeccCC
Confidence 47899999999999999999995 55577777765431 1 34566777777777766
Q ss_pred CCC
Q 030455 144 PSI 146 (177)
Q Consensus 144 ~~~ 146 (177)
+.+
T Consensus 177 ~~g 179 (715)
T COG1107 177 EKG 179 (715)
T ss_pred CCC
Confidence 543
No 114
>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=76.51 E-value=5 Score=26.93 Aligned_cols=57 Identities=19% Similarity=0.402 Sum_probs=39.0
Q ss_pred CCEEEEEEEeeeCCeeEEEecc--cceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEE-EEEEE
Q 030455 67 GEIIAAKLKESDANGLRLSLGF--FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEI-KFRVL 139 (177)
Q Consensus 67 gEv~~g~V~~v~~~Gifv~lg~--~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~V-RvrV~ 139 (177)
|.+++|+|..-++.++.|+++. +-+ ++|...+.| .+ ...... | ..+++||++ ++-|.
T Consensus 1 G~lV~~~V~EKt~D~l~v~l~~~~l~a-~l~~~HLsD--~~--~k~~~~---~--------~klrvG~~L~~~lvL 60 (72)
T cd05699 1 GKLVDARVLKKTLNGLEVAILPEEIRA-FLPTMHLSD--HV--SNCPLL---W--------HCLQEGDTIPNLMCL 60 (72)
T ss_pred CceEEEEEEEEcCCcEEEEecCCCcEE-EEEccccCC--ch--hhCHHH---H--------hhhhcCCCccceEEE
Confidence 6789999999999999999953 334 444444444 23 222222 2 278999999 88777
No 115
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=75.15 E-value=13 Score=26.63 Aligned_cols=59 Identities=14% Similarity=0.201 Sum_probs=40.7
Q ss_pred eccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 62 FRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 62 f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
+-+..|-++.|+|..+...-+|+..| =|. .+-+. |. .+...|..|++||+|+.+
T Consensus 19 lG~~~gk~V~G~I~hvv~ddLYIDfG~KFh-cVc~r---p~---------------------~~~~~y~~G~rV~lrLkd 73 (104)
T PF10246_consen 19 LGDPEGKIVIGKIFHVVDDDLYIDFGGKFH-CVCKR---PA---------------------VNGEKYVRGSRVRLRLKD 73 (104)
T ss_pred cCCccCCEEEEEEEEEecCceEEEeCCcee-EEEec---cc---------------------ccccccccCCEEEEEECC
Confidence 45779999999999999999999997 232 12111 10 011246779999999988
Q ss_pred EeCCC
Q 030455 141 VNYPS 145 (177)
Q Consensus 141 v~~~~ 145 (177)
.+...
T Consensus 74 lELs~ 78 (104)
T PF10246_consen 74 LELSA 78 (104)
T ss_pred Hhhhh
Confidence 76533
No 116
>PRK11712 ribonuclease G; Provisional
Probab=72.89 E-value=9.6 Score=34.67 Aligned_cols=76 Identities=13% Similarity=0.190 Sum_probs=47.8
Q ss_pred ccCCCCEEEEEEEeeeC--CeeEEEecc-cceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEE
Q 030455 63 RPFVGEIIAAKLKESDA--NGLRLSLGF-FEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVL 139 (177)
Q Consensus 63 ~p~~gEv~~g~V~~v~~--~Gifv~lg~-~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~ 139 (177)
+..+|.++-|+|.++.+ .++||.+|. -+++.+..+..|....+ .++.... .....-...++.||.|-|.|.
T Consensus 35 ~~~vGnIY~G~V~~v~pg~~AAFVdIG~~k~gFL~~~d~~~~~~~~-~~~~~~~-----~~~~~i~~~l~~Gq~iLVQV~ 108 (489)
T PRK11712 35 RGIVGNIYKGRVSRVLPGMQAAFVDIGLDKAAFLHASDIVPHTECV-AGEEQKQ-----FVVRDISELVRQGQDIMVQVV 108 (489)
T ss_pred ccccccEEEEEEeecCCCCceeEEeeCCCccEEEEhhhccchhhhc-ccccccc-----cccccHHHhccCCCEEEEEEE
Confidence 35699999999999999 599999983 34555556655542222 0111111 000111235899999999999
Q ss_pred EEeCC
Q 030455 140 SVNYP 144 (177)
Q Consensus 140 ~v~~~ 144 (177)
..-..
T Consensus 109 Ke~~~ 113 (489)
T PRK11712 109 KDPLG 113 (489)
T ss_pred eCCcC
Confidence 86543
No 117
>PRK10811 rne ribonuclease E; Reviewed
Probab=67.16 E-value=20 Score=35.35 Aligned_cols=72 Identities=8% Similarity=-0.044 Sum_probs=44.8
Q ss_pred cCCCCEEEEEEEeeeC--CeeEEEeccc-ceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 64 PFVGEIIAAKLKESDA--NGLRLSLGFF-EDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~--~Gifv~lg~~-~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
+.+|.++-|+|.++-+ .++||.||.= .++++..+..... | ...... -....-+..++.||.|-|.|..
T Consensus 36 ~~vGnIYkGkVenIvPGInAAFVDIG~gknGFL~L~Di~~~~--f--~~~~~~-----~~~~~i~~~Lk~GqeILVQV~K 106 (1068)
T PRK10811 36 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREY--F--PANYSA-----HGRPNIKDVLREGQEVIVQIDK 106 (1068)
T ss_pred cCccceEEEEEecccCCcceeEEEecCCcceEEEhhhccccc--c--cccccc-----ccccccccccCCCCEEEEEEee
Confidence 5689999999999999 4999999833 3444444442221 2 111000 0001123468899999999998
Q ss_pred EeCC
Q 030455 141 VNYP 144 (177)
Q Consensus 141 v~~~ 144 (177)
.-..
T Consensus 107 Ea~g 110 (1068)
T PRK10811 107 EERG 110 (1068)
T ss_pred cccC
Confidence 5543
No 118
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=64.85 E-value=39 Score=22.61 Aligned_cols=25 Identities=8% Similarity=0.094 Sum_probs=15.8
Q ss_pred EEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 119 WEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 119 ~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
+++......+++||.|++.=.-.++
T Consensus 36 fV~~~~~~~~~~Gd~V~vtG~v~ey 60 (78)
T cd04486 36 FVYTGSGADVAVGDLVRVTGTVTEY 60 (78)
T ss_pred EEecCCCCCCCCCCEEEEEEEEEee
Confidence 4443335678999999996443333
No 119
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=64.14 E-value=22 Score=30.05 Aligned_cols=52 Identities=12% Similarity=-0.050 Sum_probs=39.7
Q ss_pred CCCEEEEEEEeeeCCeeEEEe-cccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEeC
Q 030455 66 VGEIIAAKLKESDANGLRLSL-GFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~l-g~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~~ 143 (177)
.++.++|+|-...+.|.||-+ +..-+++|+++. | ...+.|+.+..||++++.
T Consensus 155 ~nq~v~~tVYr~~~~G~fv~~e~~~~GfIh~sEr------~--------------------~~prlG~~l~~rVi~~re 207 (287)
T COG2996 155 KNQEVDATVYRLLESGTFVITENGYLGFIHKSER------F--------------------AEPRLGERLTARVIGVRE 207 (287)
T ss_pred hcCeeeeEEEEEeccceEEEEcCCeEEEEcchhh------c--------------------ccccCCceEEEEEEEEcc
Confidence 589999999999999999887 333366666532 1 145689999999999987
No 120
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=55.60 E-value=11 Score=31.61 Aligned_cols=36 Identities=25% Similarity=0.325 Sum_probs=31.2
Q ss_pred cCCCCEEEEEEEeeeCCeeEEEe---cccceeEecCCCC
Q 030455 64 PFVGEIIAAKLKESDANGLRLSL---GFFEDIYVPSHLL 99 (177)
Q Consensus 64 p~~gEv~~g~V~~v~~~Gifv~l---g~~~~i~i~~~~~ 99 (177)
|.++|++-+.|.++...|++|.| +=++|++.-+.+.
T Consensus 14 Pev~e~VmvnV~sIaemGayv~LlEYnniEGmiLlsELS 52 (304)
T KOG2916|consen 14 PEVEEIVMVNVRSIAEMGAYVKLLEYNNIEGMILLSELS 52 (304)
T ss_pred CCcccEEEEEeeEehhccceEeeeecCCcccchhhhHHH
Confidence 99999999999999999999998 5677777766553
No 121
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=48.46 E-value=30 Score=22.69 Aligned_cols=55 Identities=11% Similarity=0.079 Sum_probs=29.4
Q ss_pred EEEEeeeC--CeeEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEEEe
Q 030455 72 AKLKESDA--NGLRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLSVN 142 (177)
Q Consensus 72 g~V~~v~~--~Gifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~v~ 142 (177)
|+|.+++. .-+-++-+++.++--|.--| .| .-... ..-.-++.||+|+|.+...+
T Consensus 1 G~V~~vd~~~~~iti~H~pIp~l~wpaMTM----~F--~v~~~----------~~l~~l~~Gd~V~F~~~~~~ 57 (70)
T PF11604_consen 1 GVVKSVDPEAGTITISHEPIPELGWPAMTM----DF--PVADP----------VDLAGLKPGDKVRFTFERTD 57 (70)
T ss_dssp EEEEEEETTTTEEEEEE--BCCCTB-SEEE----EE--E--TT----------SEESS-STT-EEEEEEEEET
T ss_pred CEEEEEecCCCEEEEecCccccCCCCCeEE----EE--EcCCh----------hhhhcCCCCCEEEEEEEECC
Confidence 78999994 45555557876544443222 23 21111 12237899999999998853
No 122
>PF03504 Chlam_OMP6: Chlamydia cysteine-rich outer membrane protein 6; InterPro: IPR003506 Three cysteine-rich proteins (also believed to be lipoproteins) make up the extracellular matrix of the Chlamydial outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. As these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism. The largest of these is the major outer membrane protein (MOMP), and constitutes around 60% of the total protein for the membrane []. OMP6 is the second largest, with a molecular mass of 58kDa, while the OMP3 protein is ~15kDa []. MOMP is believed to elicit the strongest immune response, and has recently been linked to heart disease through its sequence similarity to a murine heart-muscle specific alpha myosin []. The OMP6 family plays a structural role in the outer membrane during the EB stage of the Chlamydial cell, and different biovars show a small, yet highly significant, change at peptide charge level []. Members of this family include Chlamydia trachomatis, Chlamydia pneumoniae and Chlamydia psittaci.; GO: 0005201 extracellular matrix structural constituent
Probab=48.22 E-value=34 Score=23.70 Aligned_cols=39 Identities=21% Similarity=0.257 Sum_probs=22.3
Q ss_pred ecCCCCCCCcccc-cCCCCCe----eeeEEEEeCCeeeEEcCCCEEEEEE
Q 030455 94 VPSHLLPSPSRSE-PDPYGRY----EVKWIWEFGDTKYVIDGLDEIKFRV 138 (177)
Q Consensus 94 i~~~~~~~~~~y~-~d~~~~~----~~~w~~~~~~~~~~~~~G~~VRvrV 138 (177)
+..+.+|...+|| ||++.++ .++|-+- .+..|++..+.|
T Consensus 48 viTqqLPce~eFV~SdPettp~~D~kLVW~Ig------~l~~G~k~kItV 91 (95)
T PF03504_consen 48 VITQQLPCEVEFVRSDPETTPTPDGKLVWKIG------RLGQGEKCKITV 91 (95)
T ss_pred EEeecCCcceEEEecCCccccCCCCEEEEEec------cccCCceeEEEE
Confidence 3345667777777 5666542 2444432 556677766554
No 123
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=47.06 E-value=55 Score=23.84 Aligned_cols=55 Identities=13% Similarity=0.070 Sum_probs=34.9
Q ss_pred EEEEEEeeeCCe--eEEEecccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEEEEEE
Q 030455 70 IAAKLKESDANG--LRLSLGFFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKFRVLS 140 (177)
Q Consensus 70 ~~g~V~~v~~~G--ifv~lg~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRvrV~~ 140 (177)
.+|+|.+++... +.++-+++..+=-|.-- ..| .-.... .-..+++|+.|+|.+..
T Consensus 45 ~~G~V~~vd~~~~~iti~H~pIp~l~wPaMT----M~F--~v~~~~----------~l~~lk~G~~V~F~~~~ 101 (115)
T PRK09838 45 GTGVVKGIDLESKKITIHHEPIPAVNWPEMT----MRF--TITPQT----------KMSEIKTGDKVAFNFVQ 101 (115)
T ss_pred EEEEEEEEeCCCCEEEEeecccccCCCCCcc----ccc--cCCChh----------hhccCCCCCEEEEEEEE
Confidence 389999999877 77777888654233222 224 222211 11268999999999875
No 124
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=42.49 E-value=46 Score=20.74 Aligned_cols=30 Identities=23% Similarity=0.413 Sum_probs=20.7
Q ss_pred EEEEeec---cCCCCEEEEEEEeeeCCeeEEEe
Q 030455 57 FRLVVFR---PFVGEIIAAKLKESDANGLRLSL 86 (177)
Q Consensus 57 f~~~~f~---p~~gEv~~g~V~~v~~~Gifv~l 86 (177)
++.+.+. |.+||.+..+|++..++-++.++
T Consensus 28 ~~~V~v~~~~~~iG~~v~v~I~~~~~~~l~G~~ 60 (61)
T PF01938_consen 28 GKVVFVPGGLPLIGEFVKVRITKAKKNYLFGEL 60 (61)
T ss_dssp TEEEEETT--T--TEEEEEEEEEE-SSEEEEEE
T ss_pred CeEEEECCCCCCCCCEEEEEEEEeeCCcEEEEE
Confidence 4455544 66799999999999998887653
No 125
>KOG4078 consensus Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis]
Probab=41.91 E-value=37 Score=25.92 Aligned_cols=63 Identities=11% Similarity=0.196 Sum_probs=43.3
Q ss_pred EEEeeccCCCCEEEEEEEeeeCCeeEEEec-ccceeEecCCCCCCCcccccCCCCCeeeeEEEEeCCeeeEEcCCCEEEE
Q 030455 58 RLVVFRPFVGEIIAAKLKESDANGLRLSLG-FFEDIYVPSHLLPSPSRSEPDPYGRYEVKWIWEFGDTKYVIDGLDEIKF 136 (177)
Q Consensus 58 ~~~~f~p~~gEv~~g~V~~v~~~Gifv~lg-~~~~i~i~~~~~~~~~~y~~d~~~~~~~~w~~~~~~~~~~~~~G~~VRv 136 (177)
+++-+-|+.|.++.|+|-.+.+.-+|+..| -|.-+.- . -..++.-|+.|..||.
T Consensus 74 kl~qlg~a~gklV~GkIfhiV~~DlYIDFG~KFhcVC~-------------r------------P~~n~e~Y~~GaRVrl 128 (173)
T KOG4078|consen 74 KLMQLGDAKGKLVIGKIFHIVEEDLYIDFGGKFHCVCK-------------R------------PALNGEAYQKGARVRL 128 (173)
T ss_pred ccccccCcCCcEEEeeeeeeeccceEEecCCeEEEEEc-------------C------------cCcCHHHhhcCceEEE
Confidence 455577999999999999999998888876 2211110 0 1122336778899999
Q ss_pred EEEEEeCCC
Q 030455 137 RVLSVNYPS 145 (177)
Q Consensus 137 rV~~v~~~~ 145 (177)
|+++.+..+
T Consensus 129 Rl~DlELs~ 137 (173)
T KOG4078|consen 129 RLIDLELSE 137 (173)
T ss_pred EEcChhHhh
Confidence 998876544
No 126
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=39.90 E-value=94 Score=20.30 Aligned_cols=35 Identities=11% Similarity=0.102 Sum_probs=27.1
Q ss_pred eEEEEEEEeeccCCCCEEEEEEEeeeCCeeEEEec
Q 030455 53 HTVKFRLVVFRPFVGEIIAAKLKESDANGLRLSLG 87 (177)
Q Consensus 53 ~~V~f~~~~f~p~~gEv~~g~V~~v~~~Gifv~lg 87 (177)
+.+...+.......+..+.|.+.+++..|+.+.+.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~diS~~G~~~~~~ 42 (102)
T PF07238_consen 8 VPVNLPIRVILDPGGSSFQGTIVDISEGGCAFRSP 42 (102)
T ss_dssp EEEEEEEE-EEEETTEEEEEEEEEETTSEEEEEEC
T ss_pred EeccceEEEEEecCCcEEEEEEEEECccceEEEEC
Confidence 44555554566778899999999999999998873
No 127
>TIGR02866 CoxB cytochrome c oxidase, subunit II. Cytochrome c oxidase is the terminal electron acceptor of mitochondria (and one of several possible acceptors in prokaryotes) in the electron transport chain of aerobic respiration. The enzyme couples the oxidation of reduced cytochrome c with the reduction of molecular oxygen to water. This process results in the pumping of four protons across the membrane which are used in the proton gradient powered synthesis of ATP. The oxidase contains two heme a cofactors and three copper atoms as well as other bound ions.
Probab=33.05 E-value=80 Score=24.89 Aligned_cols=21 Identities=14% Similarity=0.216 Sum_probs=17.9
Q ss_pred eeeEEcCCCEEEEEEEEEeCC
Q 030455 124 TKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 124 ~~~~~~~G~~VRvrV~~v~~~ 144 (177)
+...+..|+.||+++.+.+..
T Consensus 117 ~~l~vp~g~~v~~~~ts~DV~ 137 (201)
T TIGR02866 117 NELVVPAGTPVRLQVTSKDVI 137 (201)
T ss_pred CEEEEEcCCEEEEEEEeCchh
Confidence 367899999999999997753
No 128
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=28.52 E-value=82 Score=26.64 Aligned_cols=38 Identities=34% Similarity=0.401 Sum_probs=33.1
Q ss_pred cCCCCEEEEEEEeee-CCeeEEEecccceeEecCCCCCC
Q 030455 64 PFVGEIIAAKLKESD-ANGLRLSLGFFEDIYVPSHLLPS 101 (177)
Q Consensus 64 p~~gEv~~g~V~~v~-~~Gifv~lg~~~~i~i~~~~~~~ 101 (177)
-.+|+---++|+.++ ..|+|+..|.-.++++|-+.+|.
T Consensus 71 ~tvg~~g~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~ 109 (287)
T COG2996 71 ATVGEYGWLKVVEVNKDLGAFLDWGLPKDLLVPLDELPT 109 (287)
T ss_pred EeecceeEEEEEEEcCCcceEEecCCCcceeeehhhccc
Confidence 358899999999999 88999999955789999888776
No 129
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=28.41 E-value=1.1e+02 Score=18.32 Aligned_cols=19 Identities=21% Similarity=0.123 Sum_probs=16.6
Q ss_pred CCCEEEEEEEeeeCCeeEE
Q 030455 66 VGEIIAAKLKESDANGLRL 84 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv 84 (177)
.++.++|++.++++.|..+
T Consensus 11 ~~~~~~G~~~gId~~G~L~ 29 (48)
T PF02237_consen 11 GDGEIEGIAEGIDDDGALL 29 (48)
T ss_dssp TSCEEEEEEEEEETTSEEE
T ss_pred CCeEEEEEEEEECCCCEEE
Confidence 6788999999999998764
No 130
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=27.34 E-value=3.6e+02 Score=23.59 Aligned_cols=57 Identities=19% Similarity=0.185 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhHhcCc--ccccceeee-CCCCeeeEEEEEEEeecc----------CCCCEEEEEEEeeeC
Q 030455 22 LNEAIKLELENVFLDK--EIEGGFVYP-GEGASTHTVKFRLVVFRP----------FVGEIIAAKLKESDA 79 (177)
Q Consensus 22 ~~~~i~~~L~~ky~~k--~i~~g~I~~-g~G~~~~~V~f~~~~f~p----------~~gEv~~g~V~~v~~ 79 (177)
+.++-++.+.++|..+ ++=.|.|.. ..|.+++.+.- +-.|.| ..|+.+++.|.++..
T Consensus 118 ire~ere~v~~ef~~k~GeiV~G~V~~~~~~~~~Vdlg~-vEa~LP~~E~ip~e~~~~Gd~Ika~V~~V~~ 187 (362)
T PRK12327 118 LREAEREIIYNEFSEREGDIVTGVVQRRDNRFVYVNLGK-IEAVLPPAEQIPGETYKHGDRIKVYVVKVEK 187 (362)
T ss_pred HHHHHHHHHHHHHHHhcCCEEEEEEEEEeCCcEEEEeCC-eEEEecHHHcCCCCCCCCCCEEEEEEEEEec
Confidence 3444455556667655 444444443 23455554432 333445 589999999999994
No 131
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=26.93 E-value=81 Score=21.33 Aligned_cols=20 Identities=10% Similarity=0.253 Sum_probs=15.1
Q ss_pred eeEEcCCCEEEEEEEEEeCC
Q 030455 125 KYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 125 ~~~~~~G~~VRvrV~~v~~~ 144 (177)
+-.|++||.|.+|+.-.+..
T Consensus 8 r~iYrPGetV~~~~~~~~~~ 27 (99)
T PF01835_consen 8 RPIYRPGETVHFRAIVRDLD 27 (99)
T ss_dssp SSEE-TTSEEEEEEEEEEEC
T ss_pred ccCcCCCCEEEEEEEEeccc
Confidence 44899999999999955543
No 132
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=25.27 E-value=1.6e+02 Score=19.49 Aligned_cols=14 Identities=36% Similarity=0.468 Sum_probs=12.0
Q ss_pred EEcCCCEEEEEEEE
Q 030455 127 VIDGLDEIKFRVLS 140 (177)
Q Consensus 127 ~~~~G~~VRvrV~~ 140 (177)
.|+.||.|+|++..
T Consensus 2 ~~~~Ge~v~~~~~~ 15 (83)
T PF14326_consen 2 VYRVGERVRFRVTS 15 (83)
T ss_pred cccCCCEEEEEEEe
Confidence 57889999999877
No 133
>PF00394 Cu-oxidase: Multicopper oxidase; InterPro: IPR001117 Copper is one of the most prevalent transition metals in living organisms and its biological function is intimately related to its redox properties. Since free copper is toxic, even at very low concentrations, its homeostasis in living organisms is tightly controlled by subtle molecular mechanisms. In eukaryotes, before being transported inside the cell via the high-affinity copper transporters of the CTR family, the copper (II) ion is reduced to copper (I). In blue copper proteins such as cupredoxin, the copper (I) ion form is stabilised by a constrained His2Cys coordination environment. Multicopper oxidases oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre; dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water []. There are three spectroscopically different copper centres found in multicopper oxidases: type 1 (or blue), type 2 (or normal) and type 3 (or coupled binuclear) [, ]. Multicopper oxidases consist of 2, 3 or 6 of these homologous domains, which also share homology to the cupredoxins azurin and plastocyanin. Structurally, these domains consist of a cupredoxin-like fold, a beta-sandwich consisting of 7 strands in 2 beta-sheets, arranged in a Greek-key beta-barrel []. Multicopper oxidases include: Ceruloplasmin (1.16.3.1 from EC) (ferroxidase), a 6-domain enzyme found in the serum of mammals and birds that oxidizes different inorganic and organic substances; exhibits internal sequence homology that appears to have evolved from the triplication of a Cu-binding domain similar to that of laccase and ascorbate oxidase. Laccase (1.10.3.2 from EC) (urishiol oxidase), a 3-domain enzyme found in fungi and plants, which oxidizes different phenols and diamines. CueO is a laccase found in Escherichia coli that is involved in copper-resistance []. Ascorbate oxidase (1.10.3.3 from EC), a 3-domain enzyme found in higher plants. Nitrite reductase (1.7.2.1 from EC), a 2-domain enzyme containing type-1 and type-2 copper centres [, ]. In addition to the above enzymes there are a number of other proteins that are similar to the multi-copper oxidases in terms of structure and sequence, some of which have lost the ability to bind copper. These include: copper resistance protein A (copA) from a plasmid in Pseudomonas syringae; domain A of (non-copper binding) blood coagulation factors V (Fa V) and VIII (Fa VIII) []; yeast FET3 required for ferrous iron uptake []; yeast hypothetical protein YFL041w; and the fission yeast homologue SpAC1F7.08. This entry represents multicopper oxidase type 1 (blue) domains. These domains are also present in proteins that have lost the ability to bind copper.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 1RZP_A 2AVF_D 1NIA_A 1KCB_A 2NRD_A 1NIB_A 2BW4_A 1RZQ_C 2BWD_A 2BWI_A ....
Probab=23.37 E-value=2.1e+02 Score=21.36 Aligned_cols=22 Identities=5% Similarity=0.170 Sum_probs=17.4
Q ss_pred eeeEEcCCCEEEEEEEEEeCCC
Q 030455 124 TKYVIDGLDEIKFRVLSVNYPS 145 (177)
Q Consensus 124 ~~~~~~~G~~VRvrV~~v~~~~ 145 (177)
....++.|+++|+|+++.....
T Consensus 60 ~~~~v~~g~~~rlRliNa~~~~ 81 (159)
T PF00394_consen 60 PVIKVKPGERYRLRLINAGAST 81 (159)
T ss_dssp GEEEEETTTEEEEEEEEESSS-
T ss_pred ceEEEcCCcEEEEEEEeccCCe
Confidence 3568999999999999876544
No 134
>PF11396 DUF2874: Protein of unknown function (DUF2874); InterPro: IPR021533 This bacterial family of proteins are probable periplasmic proteins with unknown function. There are between one and four copies of this domain per sequence. ; PDB: 3DUE_A 3U1W_B 3DB7_A 4DSD_A 3ELG_A.
Probab=22.69 E-value=98 Score=18.95 Aligned_cols=38 Identities=16% Similarity=0.172 Sum_probs=25.6
Q ss_pred cHHHHHHHHHHhHhcCcccccceeeeCCCCeeeEEEEE
Q 030455 21 PLNEAIKLELENVFLDKEIEGGFVYPGEGASTHTVKFR 58 (177)
Q Consensus 21 ~~~~~i~~~L~~ky~~k~i~~g~I~~g~G~~~~~V~f~ 58 (177)
++-++++..|.++|.|-.+.+-......+..+|.|+++
T Consensus 7 ~lP~~v~~~i~~~yp~~~i~~v~~~~~~~~~~Y~v~l~ 44 (61)
T PF11396_consen 7 ELPAAVKNAIKKNYPGAKIKEVEKETDPGGKYYEVELK 44 (61)
T ss_dssp GS-HHHHHHHHHHSTTSEEEEEEEEEETTEEEEEEEET
T ss_pred HCCHHHHHHHHHHCCCCeEEEEEEEEcCCCCEEEEEEE
Confidence 45678999999999987655544444333377888775
No 135
>COG1622 CyoA Heme/copper-type cytochrome/quinol oxidases, subunit 2 [Energy production and conversion]
Probab=21.69 E-value=1.7e+02 Score=24.20 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=23.2
Q ss_pred eeEEEEeCC------eeeEEcCCCEEEEEEEEEeC
Q 030455 115 VKWIWEFGD------TKYVIDGLDEIKFRVLSVNY 143 (177)
Q Consensus 115 ~~w~~~~~~------~~~~~~~G~~VRvrV~~v~~ 143 (177)
..|.+.|.+ +...+-.|..|+|++.+.+.
T Consensus 122 w~W~f~Yp~~~~~t~n~l~lPv~~~V~f~ltS~DV 156 (247)
T COG1622 122 WKWLFIYPDYGIATVNELVLPVGRPVRFKLTSADV 156 (247)
T ss_pred EEEEEEccCcCccccceEEEeCCCeEEEEEEechh
Confidence 346566665 78999999999999999874
No 136
>TIGR01433 CyoA cytochrome o ubiquinol oxidase subunit II. This enzyme catalyzes the oxidation of ubiquinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. Subunit II is responsible for binding and oxidation of the ubiquinone substrate. This sequence is closely related to QoxA, which oxidizes quinol in gram positive bacteria but which is in complex with subunits which utilize cytochromes a in the reduction of molecular oxygen. Slightly more distantly related is subunit II of cytochrome c oxidase which uses cyt. c as the oxidant.
Probab=21.10 E-value=1.6e+02 Score=23.84 Aligned_cols=21 Identities=14% Similarity=0.134 Sum_probs=18.5
Q ss_pred eeeEEcCCCEEEEEEEEEeCC
Q 030455 124 TKYVIDGLDEIKFRVLSVNYP 144 (177)
Q Consensus 124 ~~~~~~~G~~VRvrV~~v~~~ 144 (177)
+...+-.|..||+++.+.+..
T Consensus 139 nel~lP~g~pV~~~ltS~DVi 159 (226)
T TIGR01433 139 NEIAFPVNTPINFKITSNSVM 159 (226)
T ss_pred ceEEEECCCEEEEEEEECchh
Confidence 678999999999999998753
No 137
>COG0621 MiaB 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]
Probab=21.06 E-value=3.2e+02 Score=24.65 Aligned_cols=21 Identities=29% Similarity=0.496 Sum_probs=18.6
Q ss_pred CCCEEEEEEEeeeCCeeEEEe
Q 030455 66 VGEIIAAKLKESDANGLRLSL 86 (177)
Q Consensus 66 ~gEv~~g~V~~v~~~Gifv~l 86 (177)
+|+.++.+|++...+.++.++
T Consensus 415 ~G~~v~VkIt~~~~~~L~g~~ 435 (437)
T COG0621 415 IGEFVEVKITEADEYSLIGEV 435 (437)
T ss_pred CCCEEEEEEEecCCCceEEEe
Confidence 799999999999999887654
No 138
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=20.32 E-value=3.7e+02 Score=23.75 Aligned_cols=53 Identities=19% Similarity=0.268 Sum_probs=32.5
Q ss_pred HHHHHhHhcCc--ccccceeeeCC--CCeeeEEEEEEEeeccC----------CCCEEEEEEEeeeCC
Q 030455 27 KLELENVFLDK--EIEGGFVYPGE--GASTHTVKFRLVVFRPF----------VGEIIAAKLKESDAN 80 (177)
Q Consensus 27 ~~~L~~ky~~k--~i~~g~I~~g~--G~~~~~V~f~~~~f~p~----------~gEv~~g~V~~v~~~ 80 (177)
++.+.+.|.++ ++-.|.|..-+ |.++..+. ++..+.|. .|+.+.+.|.+|...
T Consensus 127 r~~i~~ey~~~~Geiv~g~V~r~~~~~~i~vdlg-~~ea~LP~~eqip~E~~~~Gdrik~~i~~V~~~ 193 (374)
T PRK12328 127 EESIFEKYKKKVGKIVFGTVVRVDNEENTFIEID-EIRAVLPMKNRIKGEKFKVGDVVKAVLKRVKID 193 (374)
T ss_pred HHHHHHHHHHhcCcEEEEEEEEEecCCCEEEEcC-CeEEEeCHHHcCCCCcCCCCCEEEEEEEEEecC
Confidence 44455567766 56666665433 34554443 34444443 799999999999774
Done!