Query 007798
Match_columns 589
No_of_seqs 335 out of 1603
Neff 6.3
Searched_HMMs 46136
Date Thu Mar 28 15:29:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007798.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007798hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00358 3_prime_RNase VacB a 100.0 4.5E-94 9.7E-99 815.6 50.1 459 121-587 122-654 (654)
2 TIGR02063 RNase_R ribonuclease 100.0 8.5E-93 1.8E-97 813.4 49.2 458 121-587 174-709 (709)
3 PRK11642 exoribonuclease R; Pr 100.0 2E-92 4.4E-97 812.4 48.4 461 120-588 187-726 (813)
4 PRK05054 exoribonuclease II; P 100.0 2.4E-91 5.1E-96 790.4 49.4 455 120-587 123-644 (644)
5 TIGR02062 RNase_B exoribonucle 100.0 4.4E-91 9.6E-96 786.9 50.7 451 121-585 121-638 (639)
6 COG0557 VacB Exoribonuclease R 100.0 2.8E-90 6.1E-95 790.9 47.6 401 182-588 245-705 (706)
7 PF00773 RNB: RNB domain CAUTI 100.0 4.2E-75 9.1E-80 610.9 30.3 292 185-480 1-324 (325)
8 COG4776 Rnb Exoribonuclease II 100.0 5.1E-73 1.1E-77 588.5 25.1 447 126-582 97-639 (645)
9 KOG2102 Exosomal 3'-5' exoribo 100.0 2.3E-67 4.9E-72 609.6 34.6 470 113-588 371-927 (941)
10 cd05697 S1_Rrp5_repeat_hs5 S1_ 96.7 0.0048 1E-07 50.1 6.7 59 527-585 1-68 (69)
11 cd05706 S1_Rrp5_repeat_sc10 S1 96.6 0.011 2.4E-07 48.3 8.1 60 527-586 4-72 (73)
12 cd05685 S1_Tex S1_Tex: The C-t 96.6 0.0054 1.2E-07 48.8 5.7 59 527-585 1-68 (68)
13 cd05690 S1_RPS1_repeat_ec5 S1_ 96.5 0.0058 1.3E-07 49.2 5.7 58 527-584 1-68 (69)
14 cd05689 S1_RPS1_repeat_ec4 S1_ 96.5 0.011 2.3E-07 48.3 7.1 58 527-584 4-71 (72)
15 cd04472 S1_PNPase S1_PNPase: P 96.5 0.0078 1.7E-07 48.0 6.1 58 527-585 1-67 (68)
16 cd05698 S1_Rrp5_repeat_hs6_sc5 96.4 0.0089 1.9E-07 48.4 6.3 60 527-586 1-69 (70)
17 cd05688 S1_RPS1_repeat_ec3 S1_ 96.4 0.0079 1.7E-07 47.9 5.9 59 527-585 2-68 (68)
18 cd05707 S1_Rrp5_repeat_sc11 S1 96.4 0.0073 1.6E-07 48.8 5.7 59 527-585 1-68 (68)
19 cd04471 S1_RNase_R S1_RNase_R: 96.4 0.022 4.7E-07 47.5 8.4 60 527-586 2-82 (83)
20 PRK07252 hypothetical protein; 96.4 0.014 3E-07 53.3 7.7 61 527-587 4-73 (120)
21 cd04461 S1_Rrp5_repeat_hs8_sc7 96.3 0.013 2.8E-07 49.4 7.0 59 527-585 15-82 (83)
22 PF00575 S1: S1 RNA binding do 96.3 0.016 3.5E-07 47.4 7.3 60 527-586 5-73 (74)
23 cd05686 S1_pNO40 S1_pNO40: pNO 96.3 0.013 2.9E-07 48.3 6.7 59 527-586 4-72 (73)
24 cd05708 S1_Rrp5_repeat_sc12 S1 96.2 0.015 3.3E-07 47.6 6.7 61 527-587 3-73 (77)
25 PRK08582 hypothetical protein; 96.1 0.025 5.5E-07 52.9 8.2 60 527-587 6-74 (139)
26 cd04452 S1_IF2_alpha S1_IF2_al 96.0 0.025 5.4E-07 46.4 6.8 60 527-586 4-74 (76)
27 PRK05807 hypothetical protein; 96.0 0.028 6E-07 52.4 7.8 59 527-586 6-72 (136)
28 cd05692 S1_RPS1_repeat_hs4 S1_ 95.9 0.022 4.8E-07 45.2 6.2 59 527-586 1-68 (69)
29 cd05691 S1_RPS1_repeat_ec6 S1_ 95.9 0.031 6.7E-07 45.3 7.0 61 527-587 1-70 (73)
30 cd05696 S1_Rrp5_repeat_hs4 S1_ 95.7 0.039 8.4E-07 45.3 6.9 59 527-585 1-70 (71)
31 cd05684 S1_DHX8_helicase S1_DH 95.5 0.049 1.1E-06 45.4 6.9 59 527-587 1-72 (79)
32 PRK08059 general stress protei 95.4 0.056 1.2E-06 49.4 7.3 61 527-587 8-77 (123)
33 cd05703 S1_Rrp5_repeat_hs12_sc 95.1 0.072 1.6E-06 44.0 6.7 60 527-586 1-71 (73)
34 smart00316 S1 Ribosomal protei 95.0 0.069 1.5E-06 42.2 5.9 58 527-586 3-71 (72)
35 cd05687 S1_RPS1_repeat_ec1_hs1 94.7 0.12 2.7E-06 41.7 6.8 60 527-586 1-69 (70)
36 COG1098 VacB Predicted RNA bin 94.5 0.038 8.3E-07 50.3 3.7 59 527-586 6-73 (129)
37 cd05705 S1_Rrp5_repeat_hs14 S1 94.5 0.12 2.6E-06 42.9 6.4 58 527-584 4-73 (74)
38 cd04473 S1_RecJ_like S1_RecJ_l 94.1 0.31 6.8E-06 40.5 8.1 58 527-587 17-77 (77)
39 PLN00207 polyribonucleotide nu 93.5 0.22 4.8E-06 59.2 8.4 65 521-587 749-823 (891)
40 cd05695 S1_Rrp5_repeat_hs3 S1_ 93.0 0.34 7.4E-06 39.1 6.3 56 527-584 1-65 (66)
41 cd00164 S1_like S1_like: Ribos 92.7 0.23 4.9E-06 38.4 4.8 25 560-584 40-64 (65)
42 PHA02945 interferon resistance 92.6 0.8 1.7E-05 39.4 8.2 57 527-586 12-81 (88)
43 COG0539 RpsA Ribosomal protein 92.4 0.43 9.4E-06 53.9 8.2 66 521-586 187-260 (541)
44 PRK07899 rpsA 30S ribosomal pr 92.3 0.42 9.1E-06 53.7 8.0 68 520-587 287-363 (486)
45 cd05704 S1_Rrp5_repeat_hs13 S1 92.1 0.42 9.1E-06 39.3 6.0 58 527-586 4-71 (72)
46 PTZ00248 eukaryotic translatio 91.9 0.32 7E-06 51.6 6.2 68 518-586 7-88 (319)
47 PRK11824 polynucleotide phosph 91.6 0.9 1.9E-05 53.3 10.1 62 524-587 620-690 (693)
48 cd04460 S1_RpoE S1_RpoE: RpoE, 91.6 0.91 2E-05 39.5 7.9 59 528-586 1-83 (99)
49 PRK03987 translation initiatio 91.0 0.54 1.2E-05 48.7 6.6 59 527-586 9-79 (262)
50 PRK07400 30S ribosomal protein 90.6 0.71 1.5E-05 49.1 7.3 61 527-587 197-265 (318)
51 PRK07899 rpsA 30S ribosomal pr 90.0 1.4 3E-05 49.6 9.4 60 527-586 209-276 (486)
52 PRK13806 rpsA 30S ribosomal pr 89.0 1 2.2E-05 50.8 7.3 61 527-587 293-363 (491)
53 TIGR03591 polynuc_phos polyrib 88.4 1.1 2.5E-05 52.4 7.5 57 527-584 619-684 (684)
54 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 88.3 1.3 2.7E-05 37.4 5.8 60 527-587 7-79 (86)
55 PRK06676 rpsA 30S ribosomal pr 88.1 1.8 4E-05 47.0 8.5 62 524-586 191-260 (390)
56 cd05694 S1_Rrp5_repeat_hs2_sc2 88.1 3.2 6.9E-05 34.4 8.0 59 527-586 5-68 (74)
57 TIGR00448 rpoE DNA-directed RN 88.0 1.5 3.3E-05 42.5 7.0 67 519-586 75-165 (179)
58 cd04465 S1_RPS1_repeat_ec2_hs2 87.8 5.3 0.00012 31.8 9.0 57 527-586 1-66 (67)
59 TIGR00717 rpsA ribosomal prote 87.1 1.7 3.7E-05 49.0 7.7 60 527-586 447-515 (516)
60 cd04454 S1_Rrp4_like S1_Rrp4_l 86.7 2.1 4.5E-05 35.8 6.2 61 527-588 7-76 (82)
61 PRK06676 rpsA 30S ribosomal pr 85.8 2.1 4.6E-05 46.5 7.4 61 527-587 278-347 (390)
62 COG0539 RpsA Ribosomal protein 85.7 1.6 3.4E-05 49.5 6.3 60 527-586 278-346 (541)
63 PRK00087 4-hydroxy-3-methylbut 85.6 1.9 4E-05 50.4 7.1 61 527-587 563-632 (647)
64 PRK06299 rpsA 30S ribosomal pr 85.3 2.3 5.1E-05 48.5 7.7 60 527-586 374-443 (565)
65 PRK12269 bifunctional cytidyla 85.1 3.1 6.8E-05 50.0 8.8 68 520-587 746-825 (863)
66 TIGR02696 pppGpp_PNP guanosine 84.9 1.4 3.1E-05 51.5 5.7 58 527-585 648-718 (719)
67 PRK12442 translation initiatio 84.9 5.2 0.00011 34.5 7.7 58 528-586 7-71 (87)
68 PRK13806 rpsA 30S ribosomal pr 83.5 4.2 9E-05 45.9 8.6 60 527-586 203-275 (491)
69 PRK09202 nusA transcription el 81.4 22 0.00047 40.0 13.0 67 516-586 125-198 (470)
70 cd04453 S1_RNase_E S1_RNase_E: 81.3 4.1 8.9E-05 35.0 5.8 59 527-585 8-80 (88)
71 cd05702 S1_Rrp5_repeat_hs11_sc 81.2 4.4 9.5E-05 32.8 5.7 54 527-580 1-65 (70)
72 PRK12269 bifunctional cytidyla 79.6 9.6 0.00021 45.9 10.1 60 527-586 494-561 (863)
73 PRK07400 30S ribosomal protein 79.5 8.4 0.00018 41.0 8.7 59 527-585 32-99 (318)
74 TIGR00008 infA translation ini 78.7 12 0.00027 30.8 7.5 55 529-584 6-67 (68)
75 PRK00087 4-hydroxy-3-methylbut 77.5 12 0.00026 43.7 9.9 58 527-586 303-371 (647)
76 TIGR01953 NusA transcription t 77.0 42 0.00091 36.2 13.1 61 523-586 129-196 (341)
77 cd05693 S1_Rrp5_repeat_hs1_sc1 76.5 4.3 9.3E-05 35.7 4.6 27 560-586 65-94 (100)
78 TIGR00717 rpsA ribosomal prote 75.8 7.8 0.00017 43.7 7.6 60 527-586 360-429 (516)
79 PRK06299 rpsA 30S ribosomal pr 75.6 9.7 0.00021 43.6 8.4 60 527-586 202-269 (565)
80 cd04455 S1_NusA S1_NusA: N-uti 75.1 15 0.00032 29.5 7.1 56 527-585 4-66 (67)
81 PHA02858 EIF2a-like PKR inhibi 74.7 11 0.00023 32.4 6.2 58 527-587 17-86 (86)
82 COG2183 Tex Transcriptional ac 74.3 4.5 9.7E-05 47.5 5.2 61 527-587 659-728 (780)
83 PRK12327 nusA transcription el 71.4 68 0.0015 34.9 13.1 65 517-585 126-197 (362)
84 COG1185 Pnp Polyribonucleotide 69.4 9 0.0002 44.4 6.1 59 527-586 620-687 (692)
85 COG1093 SUI2 Translation initi 67.5 16 0.00036 37.6 6.9 59 527-586 12-82 (269)
86 PRK08563 DNA-directed RNA poly 67.3 23 0.00051 34.4 7.8 58 522-580 78-154 (187)
87 COG0361 InfA Translation initi 58.6 29 0.00062 29.2 5.6 57 528-585 7-70 (75)
88 COG3269 Predicted RNA-binding 58.1 47 0.001 27.8 6.7 47 527-578 16-62 (73)
89 PRK12328 nusA transcription el 55.7 1.7E+02 0.0038 32.0 12.5 62 521-585 134-203 (374)
90 PRK09521 exosome complex RNA-b 48.2 41 0.00088 32.9 5.9 57 527-587 65-141 (189)
91 PF01938 TRAM: TRAM domain; I 48.1 70 0.0015 25.0 6.2 50 527-578 5-54 (61)
92 COG2996 Predicted RNA-bindinin 34.3 1.3E+02 0.0028 31.5 7.0 57 527-586 156-215 (287)
93 PF05800 GvpO: Gas vesicle syn 34.2 87 0.0019 27.9 5.0 24 205-228 39-62 (100)
94 PRK12329 nusA transcription el 33.7 6.4E+02 0.014 28.4 12.7 68 505-578 136-212 (449)
95 PF03544 TonB_C: Gram-negative 32.4 77 0.0017 25.5 4.3 24 275-298 15-38 (79)
96 PF13103 TonB_2: TonB C termin 31.9 69 0.0015 26.5 4.0 24 274-297 24-47 (85)
97 PRK00276 infA translation init 28.4 2.6E+02 0.0055 23.0 6.7 56 528-584 7-69 (72)
98 PRK04163 exosome complex RNA-b 28.2 1.5E+02 0.0032 30.1 6.4 59 527-586 64-135 (235)
99 PRK11570 peptidyl-prolyl cis-t 27.7 6.2E+02 0.013 25.2 11.9 51 475-525 42-92 (206)
100 TIGR01352 tonB_Cterm TonB fami 26.9 1E+02 0.0022 24.4 4.1 21 277-297 11-31 (74)
101 COG1095 RPB7 DNA-directed RNA 24.8 1.5E+02 0.0033 29.1 5.5 22 559-580 133-154 (183)
102 CHL00010 infA translation init 24.7 3.9E+02 0.0084 22.4 7.3 56 529-585 8-70 (78)
103 PF06345 Drf_DAD: DRF Autoregu 24.2 75 0.0016 18.3 1.8 12 71-82 1-12 (15)
104 COG1107 Archaea-specific RecJ- 24.0 80 0.0017 36.4 3.7 61 527-588 123-187 (715)
105 PF01176 eIF-1a: Translation i 21.9 3.9E+02 0.0084 21.4 6.5 54 529-583 4-63 (65)
106 PRK04012 translation initiatio 20.8 4.7E+02 0.01 23.2 7.3 57 528-585 21-83 (100)
No 1
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=100.00 E-value=4.5e-94 Score=815.57 Aligned_cols=459 Identities=25% Similarity=0.326 Sum_probs=384.4
Q ss_pred cCCeeeEEeccCCCCCccc--eEEccCCCccccC----CCceEeecCCCCCCCHHHHHHHHHH---hc-ccccCCCCCCC
Q 007798 121 DSDRVLLAVAQRPDGKKNW--MVYDQNGASCSIK----PQQVTFVVPGVEKFDHKDISNFLQK---AE-DNLLNRKDLTH 190 (589)
Q Consensus 121 ~~~rv~~~i~~~p~~~~~~--~~~~~~g~~~~l~----p~~~~~~l~~~~~~~~~~~~~~~~~---~~-~~~~~R~Dl~~ 190 (589)
.|++|++.|..||.....+ .++...|...... .--..|.++. .|+++.++++..- +. .....|+|||+
T Consensus 122 ~g~~V~v~i~~~p~~~~~~~g~i~~~lG~~~d~~~~~~~il~~~~i~~--~f~~~v~~~a~~~~~~~~~~~~~~R~Dlr~ 199 (654)
T TIGR00358 122 EGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPF--EFPDGVEQQAAKLQFDVDEQAKKYREDLTD 199 (654)
T ss_pred CCCEEEEEEccCCCCCCCceEEEEEEEcCCCCcccHHHHHHHHcCcCC--CCCHHHHHHHHhccccCChhHhhCcccccc
Confidence 4667777888888766544 2344444322210 0013466665 3777666544321 11 23467999999
Q ss_pred CeeEEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHHhcCceeecCCCccCCCChhhhhccCcCC
Q 007798 191 LKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLR 270 (589)
Q Consensus 191 l~~fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~~RgtSvYLP~~~ipMLP~~Ls~~~~SL~ 270 (589)
+++|||||++|+|+||||||+++++|+|+|||||||||+||++||+||+||++||||+|||++++||||+.||+++|||+
T Consensus 200 ~~~~TID~~~a~D~DDAisie~~~~g~~~l~VHIADVs~~V~~~s~LD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL~ 279 (654)
T TIGR00358 200 LAFVTIDGADAKDLDDAVYVKKLPDGGWKLYVAIADVSYYVAENSPLDKEAKHRGFSVYLPGFVIPMLPEELSNGLCSLN 279 (654)
T ss_pred CcEEEECCCCCCcccceEEEEEeCCCcEEEEEEEechhheeCCCCHHHHHHHHhCcCccCCCCeecCCCHHHhcCccccC
Confidence 99999999999999999999999899999999999999999999999999999999999999999999999999999999
Q ss_pred CCCeeeEEEEEEEECCCCeEeEEEEEEEEEecccccCHHHHHHHHhcCCC-------ChHHHHHHHHHHHHHHHHHHhCC
Q 007798 271 QGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLE-------EEAELKILSEAAALRLQWRLQQG 343 (589)
Q Consensus 271 ~g~~r~AlS~~~~ld~~G~I~~~~~~~s~I~s~~~LtY~~v~~~l~~~~~-------~~~~L~~L~~la~~l~~~R~~~G 343 (589)
||++|+|+||.+++|++|+|.+++|++|+|+|.++|||++|+++|+++.. ..++|..|+++|+.|+++|.++|
T Consensus 280 p~~~R~a~s~~~~id~~G~i~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~lr~~R~~~G 359 (654)
T TIGR00358 280 PNEDRLVLVCEMTISAQGRITDNEFYPATIESKARLTYDKVNDWLENDDELQPEYETLVEQLKALHQLSQALGEWRHKRG 359 (654)
T ss_pred CCCcceEEEEEEEECCCCCEeEEEEEEEEEEECcEEcHHHHHHHHcCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHCC
Confidence 99999999999999999999999999999999999999999999987531 23579999999999999999999
Q ss_pred CcccCCcceEEEecCCCCCCCeEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhcCCCcccccCCCCCCChh-hhh---
Q 007798 344 AIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVS-AFA--- 419 (589)
Q Consensus 344 ai~~~~pe~~i~l~~~~d~~~~v~i~~~~~~~~a~~LVeE~MIlAN~~~A~~l~~~~ip~lyR~q~~p~~~~~-~l~--- 419 (589)
+++|+.||.+|.+++ + +.++.+...+ +++||.|||||||+||++||+|+.++++|++||+|+.|+..+. ++.
T Consensus 360 ai~~~~~e~~~~~d~--~-g~~~~i~~~~-~~~a~~lIeE~MilAN~~vA~~~~~~~~p~iyR~h~~p~~~~~~~l~~~~ 435 (654)
T TIGR00358 360 LIDFEHPETKFIVDE--E-GRVIDIVAEV-RRIAEKIIEEAMIVANICAARFLHNHKVPGIYRVHPGPSKKKLQSLLEFL 435 (654)
T ss_pred CcccCCCceeEEECC--C-CCeeEEEecc-CcHHHHHHHHHHHHHHHHHHHHHHHcCCCeEEecCCCCCHHHHHHHHHHH
Confidence 999999999999986 2 3457887777 8999999999999999999999999999999999999976543 111
Q ss_pred -----cCCC---C---c-----------------chHHHHHHhhhcCccccCCCCCccccCCCCcccccccccchhhHHH
Q 007798 420 -----HLPE---G---P-----------------VRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLA 471 (589)
Q Consensus 420 -----~l~~---~---~-----------------~~~~~l~r~m~~a~ys~~~p~~HfgLgl~~YthfTSPIRRY~DLiv 471 (589)
.++. + + +....++|+|++|.|++ +|.+|||||++.|||||||||||+||+|
T Consensus 436 ~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~llr~m~~A~y~~-~~~~HfgL~~~~YthfTSPIRRY~DLiv 514 (654)
T TIGR00358 436 AELGLTLPGGNAENVTTLDGACWLREVKDRPEYEILVTRLLRSLSQAEYSP-EPLGHFGLGLEHYAHFTSPIRRYPDLTN 514 (654)
T ss_pred HHcCCCccCCCcCCCChHHHHHHHHHhhCCCHHHHHHHHHHHhhcccccCC-CCCCccccccccccccCCccccchHHHH
Confidence 1111 0 0 12346789999999999 9999999999999999999999999999
Q ss_pred HHHHHHHHcCCCC----CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcEEEEEEEEEeeC-------
Q 007798 472 HYQVKACLRGESP----PFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKD------- 540 (589)
Q Consensus 472 HrqL~a~L~g~~~----~~~~~~L~~i~~~~~~~~r~a~~aer~~~~~~~~~~L~~~~~g~~~~a~V~~~~~~------- 540 (589)
||||+++|.|+.. +++.++|..++.+||.+++.++++||++.+||.++||+++. |++|+|+|+++...
T Consensus 515 Hr~L~a~l~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~i-G~~~~g~I~~v~~~GifV~L~ 593 (654)
T TIGR00358 515 HRLIKAVLAKEQTDTERYQPQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKV-GTEFSGEISSVTRFGMFVRLD 593 (654)
T ss_pred HHHHHHHHcCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhCC-CcEEEEEEEeEEcCcEEEEec
Confidence 9999999987632 25677899999999999999999999999999999999999 79999999995332
Q ss_pred ---eeEEEEeeccceeE----------EE-EeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 541 ---RTAALLLVEVGLQA----------AA-WVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 541 ---~~~~V~l~~lg~~~----------~~-~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
.+|+|++++++-+. .. +.+..|++||+|+|+|.+||+.+++|+|+.+
T Consensus 594 ~~~veGlV~~s~l~~d~y~~d~~~~~l~g~~~~~~~~lGD~V~Vki~~vd~~~~~I~f~l~ 654 (654)
T TIGR00358 594 DNGIDGLIHISTLHNDYYVFDQEKMALIGKGTGKVYRIGDRVTVKLTEVNMETRSIIFELV 654 (654)
T ss_pred CCceEEEEEeEeCCCcceEEeccccEEEeccCCcEECCCCEEEEEEEEEecccCeEEEEEC
Confidence 35667777664332 11 2235699999999999999999999999853
No 2
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=100.00 E-value=8.5e-93 Score=813.43 Aligned_cols=458 Identities=25% Similarity=0.350 Sum_probs=380.8
Q ss_pred cCCeeeEEeccCCCCCccc--eEEccCCCccccCCC----ceEeecCCCCCCCHHHHHHHHHHhc-----ccccCCCCCC
Q 007798 121 DSDRVLLAVAQRPDGKKNW--MVYDQNGASCSIKPQ----QVTFVVPGVEKFDHKDISNFLQKAE-----DNLLNRKDLT 189 (589)
Q Consensus 121 ~~~rv~~~i~~~p~~~~~~--~~~~~~g~~~~l~p~----~~~~~l~~~~~~~~~~~~~~~~~~~-----~~~~~R~Dl~ 189 (589)
.|++|++.|..||.....+ .++...|........ -..|+++. .|+++.+++. +++. .....|+|||
T Consensus 174 ~g~~v~v~i~~~p~~~~~~~g~i~~~lg~~~d~~~~~~~il~~~~i~~--~f~~~v~~~a-~~~~~~~~~~~~~~R~Dl~ 250 (709)
T TIGR02063 174 EGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPY--EFPEEVLDEA-AKIPEEVPEEEIKGRKDLR 250 (709)
T ss_pred CCCEEEEEEccCCCCCCCceEEEEEEeCCCCcccchHHHHHHHcCcCC--CCCHHHHHHH-HhCCCCCChhHhhcccccc
Confidence 3455566677776554433 233333332221100 02355554 3666555443 2222 2246799999
Q ss_pred CCeeEEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHHhcCceeecCCCccCCCChhhhhccCcC
Q 007798 190 HLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSL 269 (589)
Q Consensus 190 ~l~~fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~~RgtSvYLP~~~ipMLP~~Ls~~~~SL 269 (589)
++++|||||++|+|+||||||++.++|+|+|||||||||+||++||+||+||++||||+|||++++||||+.||+++|||
T Consensus 251 ~~~~~tID~~~a~D~DDAisie~~~~g~~~l~VhIADVs~~V~~~s~lD~eA~~R~tSvYlp~~~ipMLP~~Ls~~~cSL 330 (709)
T TIGR02063 251 DLPFVTIDGEDAKDFDDAVYVEKLKDGNYKLGVAIADVSHYVREGSALDKEALKRGTSVYLPDRVIPMLPERLSNGICSL 330 (709)
T ss_pred cCcEEEECCCCCcccccEEEEEEcCCCCEEEEEEEechhhEeCCCChHHHHHHHhCeeEeCCCCcccCCChHHccCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeeeEEEEEEEECCCCeEeEEEEEEEEEecccccCHHHHHHHHhcCCC-------ChHHHHHHHHHHHHHHHHHHhC
Q 007798 270 RQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLE-------EEAELKILSEAAALRLQWRLQQ 342 (589)
Q Consensus 270 ~~g~~r~AlS~~~~ld~~G~I~~~~~~~s~I~s~~~LtY~~v~~~l~~~~~-------~~~~L~~L~~la~~l~~~R~~~ 342 (589)
+||++|+|+||.|+||++|+|.+++|++|+|+|+++|||++|+++|+++.. ..++|..|+++|+.|+++|.++
T Consensus 331 ~p~~~r~a~s~~~~id~~G~i~~~~~~~svI~s~~~ltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~l~~~R~~~ 410 (709)
T TIGR02063 331 NPNEDRLTLSCEMEIDKKGRVKKYEFYEAVINSHARLTYNQVNDIIEGKDALDKKEPPLKEMLKNLFELYKILRKKRKKR 410 (709)
T ss_pred CCCCceEEEEEEEEECCCCCEEEeEEEEEEEEeCeEEcHHHHHHHHcCCccccchhhHHHHHHHHHHHHHHHHHHHHHhC
Confidence 999999999999999999999999999999999999999999999987532 2367999999999999999999
Q ss_pred CCcccCCcceEEEecCCCCCCCeEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhcCCCcccccCCCCCCChh-hhh--
Q 007798 343 GAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVS-AFA-- 419 (589)
Q Consensus 343 Gai~~~~pe~~i~l~~~~d~~~~v~i~~~~~~~~a~~LVeE~MIlAN~~~A~~l~~~~ip~lyR~q~~p~~~~~-~l~-- 419 (589)
|+++|+.||.+|.+++ + +.++.+...+ +++||.|||||||+||++||+|+.++++|++||+|+.|+..+. ++.
T Consensus 411 G~i~~~~~e~~~~~d~--~-g~~~~i~~~~-~~~a~~lIeE~MllAN~~vA~~l~~~~~p~iyR~h~~P~~~~~~~l~~~ 486 (709)
T TIGR02063 411 GAIDFDSKEAKIILDE--N-GKPIDIVPRE-RGDAHKLIEEFMIAANETVAEHLEKAKLPFIYRVHERPSEEKLQNLREF 486 (709)
T ss_pred CCcccCCccceeEECC--C-CCeEEEEecc-chHHHHHHHHHHHHHHHHHHHHHHhCCCCeEEecCCCCCHHHHHHHHHH
Confidence 9999999999999987 2 3457888887 8999999999999999999999999999999999999986553 221
Q ss_pred ------cCCC-----C------------------cchHHHHHHhhhcCccccCCCCCccccCCCCcccccccccchhhHH
Q 007798 420 ------HLPE-----G------------------PVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLL 470 (589)
Q Consensus 420 ------~l~~-----~------------------~~~~~~l~r~m~~a~ys~~~p~~HfgLgl~~YthfTSPIRRY~DLi 470 (589)
.++. . .+.+..++|+|++|.|++ +|.+|||||++.|||||||||||+||+
T Consensus 487 ~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~~llr~m~~A~y~~-~~~~HfgL~~~~YthfTSPIRRY~DLi 565 (709)
T TIGR02063 487 LKTLGITLKGGTSDKPQPKDFQKLLEKVKGRPEEELINTVLLRSMQQAKYSP-ENIGHFGLALEYYTHFTSPIRRYPDLI 565 (709)
T ss_pred HHHcCCCccCCCCCCCCHHHHHHHHHHhhCCcHHHHHHHHHHHHhcCcccCC-CCCCccccccccccccCCccccchHHH
Confidence 1111 0 112346789999999999 999999999999999999999999999
Q ss_pred HHHHHHHHHcCCCC-------CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcEEEEEEEEEee----
Q 007798 471 AHYQVKACLRGESP-------PFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIK---- 539 (589)
Q Consensus 471 vHrqL~a~L~g~~~-------~~~~~~L~~i~~~~~~~~r~a~~aer~~~~~~~~~~L~~~~~g~~~~a~V~~~~~---- 539 (589)
|||||+++|.++.. +++.++|..++.+||.+++.++++||++.++|.++||++++ |++|+|.|+++..
T Consensus 566 vHr~L~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~er~a~~aer~~~~~~~~~yl~~~i-G~~~~g~V~~v~~fGif 644 (709)
T TIGR02063 566 VHRLIKKALFGGENTTTEKEREYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKI-GEEFEGVISGVTSFGLF 644 (709)
T ss_pred HHHHHHHHHcCCCCCCccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccC-CcEEEEEEEEEEeCCEE
Confidence 99999999987631 45567799999999999999999999999999999999999 7999999999522
Q ss_pred ------CeeEEEEeeccceeEE----------E-EeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 540 ------DRTAALLLVEVGLQAA----------A-WVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 540 ------~~~~~V~l~~lg~~~~----------~-~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
..+|+|++++++-+.. . +.+..|++||+|+|+|.+||+.+++|+|+.+
T Consensus 645 V~L~~~~~eGlvhis~l~~d~~~~d~~~~~l~g~~~~~~~~lGd~V~Vkv~~vd~~~~~I~~~l~ 709 (709)
T TIGR02063 645 VELENNTIEGLVHISTLKDDYYVFDEKGLALVGERTGKVFRLGDRVKVRVVKADLDTGKIDFELV 709 (709)
T ss_pred EEecCCceEEEEEeeecCCCcEEEcccceEEEeccCCcEECCCCEEEEEEEEEecccCeEEEEEC
Confidence 1478888888753221 1 2235699999999999999999999999853
No 3
>PRK11642 exoribonuclease R; Provisional
Probab=100.00 E-value=2e-92 Score=812.45 Aligned_cols=461 Identities=21% Similarity=0.289 Sum_probs=385.4
Q ss_pred ecCCeeeEEeccCCCCCccc--eEEccCCCccccC----CCceEeecCCCCCCCHHHHHHHHHH---hc-ccccCCCCCC
Q 007798 120 KDSDRVLLAVAQRPDGKKNW--MVYDQNGASCSIK----PQQVTFVVPGVEKFDHKDISNFLQK---AE-DNLLNRKDLT 189 (589)
Q Consensus 120 ~~~~rv~~~i~~~p~~~~~~--~~~~~~g~~~~l~----p~~~~~~l~~~~~~~~~~~~~~~~~---~~-~~~~~R~Dl~ 189 (589)
+.|++|++.|..+|.....+ .++...|....-. .--..|+++. .|++..++++..- +. ....+|+|||
T Consensus 187 ~~gd~V~v~I~~~p~~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~ip~--~Fp~~v~~ea~~~~~~~~~~~~~~R~DLr 264 (813)
T PRK11642 187 RMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPY--IWPQAVEQQVAGLKEEVPEEAKAGRVDLR 264 (813)
T ss_pred CCCCEEEEEEecCCCcCCCCCEEEEEEecCCCCcchHHHHHHHHcCCCC--CCCHHHHHHHHhccccCChhHhccccccc
Confidence 34667788888888776544 3444444332200 0012466765 3877766654331 21 2346799999
Q ss_pred CCeeEEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHHhcCceeecCCCccCCCChhhhhccCcC
Q 007798 190 HLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSL 269 (589)
Q Consensus 190 ~l~~fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~~RgtSvYLP~~~ipMLP~~Ls~~~~SL 269 (589)
++++|||||++|+|+|||||++++++|+|+|||||||||+||++||+||+||++||||||||++++||||+.||+++|||
T Consensus 265 ~l~~vTID~~~akD~DDAvsie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYlpd~viPMLP~~Lsn~lcSL 344 (813)
T PRK11642 265 DLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIADVSYYVRPPTPLDREARNRGTSVYFPSQVVPMLPEVLSNGLCSL 344 (813)
T ss_pred cCcEEEECCCCCCcccceEEEEEeCCCcEEEEEEecchhheeCCCCHHHHHHHHhCCeEeCCCceeeCCCHHHhcCcccc
Confidence 99999999999999999999999988899999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeeeEEEEEEEECCCCeEeEEEEEEEEEecccccCHHHHHHHHhcCCC-------ChHHHHHHHHHHHHHHHHHHhC
Q 007798 270 RQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLE-------EEAELKILSEAAALRLQWRLQQ 342 (589)
Q Consensus 270 ~~g~~r~AlS~~~~ld~~G~I~~~~~~~s~I~s~~~LtY~~v~~~l~~~~~-------~~~~L~~L~~la~~l~~~R~~~ 342 (589)
+||++|+|+||.|+||++|+|.+++|++|+|+|.++|||++|+++|+++.. ..+.|..|+++|+.|+++|.++
T Consensus 345 ~p~~dRla~s~~~~id~~G~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~~~~~L~~l~~la~~Lr~~R~~~ 424 (813)
T PRK11642 345 NPQVDRLCMVCEMTISSKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKAREER 424 (813)
T ss_pred CCCCceeEEEEEEEECCCCCCcCCEEEEEEEEECceECHHHHHHHHcCCcccchhhhHHHHHHHHHHHHHHHHHHHHHHC
Confidence 999999999999999999999999999999999999999999999987532 1357889999999999999999
Q ss_pred CCcccCCcceEEEecCCCCCCCeEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhcCCCcccccCCCCCCChh-hhh--
Q 007798 343 GAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVS-AFA-- 419 (589)
Q Consensus 343 Gai~~~~pe~~i~l~~~~d~~~~v~i~~~~~~~~a~~LVeE~MIlAN~~~A~~l~~~~ip~lyR~q~~p~~~~~-~l~-- 419 (589)
|+++|+.||++|.+++. +..+.+...+ +.+||.|||||||+||++||+|+.++++|++||+|+.|+..+. +|.
T Consensus 425 Gai~~d~~E~~i~ld~~---g~~~~i~~~~-~~~a~~lIEE~MllAN~~vA~~l~~~~~p~lyR~H~~P~~ekl~~l~~~ 500 (813)
T PRK11642 425 GGISFESEEAKFIFNAE---RRIERIEQTQ-RNDAHKLIEECMILANISAARFVEKAKEPALFRIHDKPSTEAITSFRSV 500 (813)
T ss_pred CCcccCCCceEEEECCC---CCEeeEEecc-cccHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEeCCCCCHHHHHHHHHH
Confidence 99999999999999872 3457787777 8999999999999999999999999999999999999986653 211
Q ss_pred --c----CCC---------------------CcchHHHHHHhhhcCccccCCCCCccccCCCCcccccccccchhhHHHH
Q 007798 420 --H----LPE---------------------GPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAH 472 (589)
Q Consensus 420 --~----l~~---------------------~~~~~~~l~r~m~~a~ys~~~p~~HfgLgl~~YthfTSPIRRY~DLivH 472 (589)
. ++. ..+.+.+++|+|++|.|++ +|.+|||||++.|||||||||||+||+||
T Consensus 501 l~~lG~~l~~~~~~~~~~~~~ll~~~~~~~~~~~l~~~llRsm~~A~Y~~-~~~gHfGLa~~~YtHFTSPIRRY~DLivH 579 (813)
T PRK11642 501 LAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLLRSMKQAIYDP-ENRGHFGLALQSYAHFTSPIRRYPDLSLH 579 (813)
T ss_pred HHHcCCcccCCCCCCHHHHHHHHHHHhCCcHHHHHHHHHHHhccccccCC-CCCCccccccccccccCchhhhhHHHHHH
Confidence 1 110 1122457799999999999 99999999999999999999999999999
Q ss_pred HHHHHHHcCCCC-----------CCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcEEEEEEEEEeeC-
Q 007798 473 YQVKACLRGESP-----------PFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKD- 540 (589)
Q Consensus 473 rqL~a~L~g~~~-----------~~~~~~L~~i~~~~~~~~r~a~~aer~~~~~~~~~~L~~~~~g~~~~a~V~~~~~~- 540 (589)
|+|+++|.++.. ++..++|..++.+||.+++++.++||++++|+.++||++++ |++|+|+|+++...
T Consensus 580 R~Lk~~L~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~s~~er~A~~aeR~~~~~~~~~~m~~~i-Ge~f~G~Is~V~~fG 658 (813)
T PRK11642 580 RAIKYLLAKEQGHKGNTTETGGYHYSMEEMLQLGQHCSMTERRADEATRDVADWLKCDFMLDQV-GNVFKGVISSVTGFG 658 (813)
T ss_pred HHHHHHHhCCCCcccccccccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccC-CcEEEEEEEEeecCc
Confidence 999999986421 12235689999999999999999999999999999999998 79999999995322
Q ss_pred ---------eeEEEEeeccceeEE----------E-EeCccCCCCCEEEEEEEeeeCCCCeEEEEEec
Q 007798 541 ---------RTAALLLVEVGLQAA----------A-WVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVV 588 (589)
Q Consensus 541 ---------~~~~V~l~~lg~~~~----------~-~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v~ 588 (589)
.+|+|++++|+-++. . +.+..|++||+|+|+|.+||+.+++|+|+.+.
T Consensus 659 ifVeL~~~~vEGlV~vs~L~~d~y~~d~~~~~L~g~~~~~~~~lGD~V~VkV~~vD~~~rkI~f~l~~ 726 (813)
T PRK11642 659 FFVRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLIGESSGQTYRLGDRVEVRVEAVNMDERKIDFSLIS 726 (813)
T ss_pred eEEEECCCCeeeeEEEeecCCcceEecchheEEecccCCcEECCCCEEEEEEEEeecCCCeEEEEEec
Confidence 467788887753311 1 22456999999999999999999999999763
No 4
>PRK05054 exoribonuclease II; Provisional
Probab=100.00 E-value=2.4e-91 Score=790.36 Aligned_cols=455 Identities=22% Similarity=0.303 Sum_probs=375.4
Q ss_pred ecCCeeeEEeccCCCCC-ccc--eEEccCCCccccCC----CceEeecCCCCCCCHHHHHHHHHHhcccccCCCCCCCCe
Q 007798 120 KDSDRVLLAVAQRPDGK-KNW--MVYDQNGASCSIKP----QQVTFVVPGVEKFDHKDISNFLQKAEDNLLNRKDLTHLK 192 (589)
Q Consensus 120 ~~~~rv~~~i~~~p~~~-~~~--~~~~~~g~~~~l~p----~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~R~Dl~~l~ 192 (589)
+.+++|.+.|..+|... +++ .++...|....-.- --..|+++.. |++..++. ++.+....|+|||+++
T Consensus 123 ~~gd~V~v~i~~~p~~~~~~~~g~i~~~lG~~~d~~~d~~~il~~~~l~~~--f~~~~~~~---~~~~~~~~R~Dlr~~~ 197 (644)
T PRK05054 123 KEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHFAPWWVTLARHNLERE--APAGGVAW---EMLDEGLEREDLTALD 197 (644)
T ss_pred CCCCEEEEEEecCCCCCCCCceEEEEEEECCCCCCccHHHHHHHHcCCCCC--CCchhhhc---cCChhccCcccccCCc
Confidence 35667778888888742 222 34444443322100 0124566653 65554321 2221113799999999
Q ss_pred eEEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHHhcCceeecCCCccCCCChhhhhccCcCCCC
Q 007798 193 VYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQG 272 (589)
Q Consensus 193 ~fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~~RgtSvYLP~~~ipMLP~~Ls~~~~SL~~g 272 (589)
+|||||++|+|+|||||++++++|+|+|||||||||+||+|||+||+||++||||+|||++++||||+.||+++|||+||
T Consensus 198 ~~TID~~~akD~DDAisve~~~~g~~~l~VHIADVs~yV~~gS~LD~eA~~RgtSvYlp~~vipMLP~~Ls~~~cSL~p~ 277 (644)
T PRK05054 198 FVTIDSASTEDMDDALYVEKLPDGGLQLTVAIADPTAYIAEGSKLDKAARQRAFTNYLPGFNIPMLPRELSDDLCSLRPN 277 (644)
T ss_pred EEEECCCCCCcccceEEEEEeCCCCEEEEEEEcchhhEeCCCCHHHHHHHHhCceEeCCCCcccCCChHHhcCccccCCC
Confidence 99999999999999999999989999999999999999999999999999999999999999999999999999999999
Q ss_pred CeeeEEEEEEEECCCCeEeE-EEEEEEEEecccccCHHHHHHHHhcCCC-------ChHHHHHHHHHHHHHHHHHHhCCC
Q 007798 273 EVCNAVTVSVVLHSDGSIAE-YSVDNSIIKPTYMLTYESATELLHLNLE-------EEAELKILSEAAALRLQWRLQQGA 344 (589)
Q Consensus 273 ~~r~AlS~~~~ld~~G~I~~-~~~~~s~I~s~~~LtY~~v~~~l~~~~~-------~~~~L~~L~~la~~l~~~R~~~Ga 344 (589)
++|+|+||.|+||++|+|++ ++|++|+|+|.++|||++|+++|+++.+ ..+.|..|+++++.++++|.++|+
T Consensus 278 ~~R~als~~~~id~~G~i~~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~~~i~~~l~~L~~l~~~l~~~R~~~G~ 357 (644)
T PRK05054 278 ERRPALACRVTIDADGTIEDDIRFFAAWIESKAKLAYDNVSDWLENGGDWQPESEAIAEQIRLLHQFCLARSEWRKQHAL 357 (644)
T ss_pred CCceEEEEEEEEeCCCCcccccEEEEEEEEcCCeecHHHHHHHHhCCCccccchhHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 99999999999999999998 8999999999999999999999987532 135688999999999999999999
Q ss_pred cccCCcceEEEecCCCCCCCeEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhcCCCcccccCCCCCCChh-hhh----
Q 007798 345 IDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVS-AFA---- 419 (589)
Q Consensus 345 i~~~~pe~~i~l~~~~d~~~~v~i~~~~~~~~a~~LVeE~MIlAN~~~A~~l~~~~ip~lyR~q~~p~~~~~-~l~---- 419 (589)
++++.||++|.+++ + +....+...+ +++||+|||||||+||++||+|+.++++|++||+|+.|+..+. ++.
T Consensus 358 i~~d~~e~~i~ld~--~-g~~~~i~~~~-~~~a~~lIeE~MllAN~~vA~~l~~~~~p~iyRvH~~P~~~~l~~l~~~~~ 433 (644)
T PRK05054 358 VFKDRPDYRFELGE--K-GEVLDIVAEP-RRIANRIVEESMIAANICAARVLRDKLGFGIYNVHSGFDPANAEQAVALLK 433 (644)
T ss_pred ccccCCceEEEECC--C-CCEEEEEEec-CcHHHHHHHHHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHH
Confidence 99999999999987 2 3456888888 8999999999999999999999999999999999999976543 111
Q ss_pred c----CCCC---cc-----------------hHHHHHHhhhcCccccCCCCCccccCCCCcccccccccchhhHHHHHHH
Q 007798 420 H----LPEG---PV-----------------RSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQV 475 (589)
Q Consensus 420 ~----l~~~---~~-----------------~~~~l~r~m~~a~ys~~~p~~HfgLgl~~YthfTSPIRRY~DLivHrqL 475 (589)
. ++.. .. ....++|+|++|.|++ +|.+|||||++.|||||||||||+||+|||||
T Consensus 434 ~~g~~~~~~~~~~l~~~~~~~~~l~~~~~~~l~~~llr~~~~a~ys~-~~~gHfgL~~~~YthfTSPIRRY~DLivHR~L 512 (644)
T PRK05054 434 EHGLHFDAEELLTLEGFCKLRRELDAQPTGYLDSRIRRFQSFAEIST-EPGPHFGLGLEAYATWTSPIRKYGDMINHRLL 512 (644)
T ss_pred HCCCCcCCCcccChHHHHHHHHHHhcchHHHHHHHHHHHHhceecCC-CCcCccccccccccccCChhhhhHHHHHHHHH
Confidence 1 1100 00 0134689999999999 99999999999999999999999999999999
Q ss_pred HHHHcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CcEEEEEEEEEeeC----------eeEE
Q 007798 476 KACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPK-ERQYRALILRFIKD----------RTAA 544 (589)
Q Consensus 476 ~a~L~g~~~~~~~~~L~~i~~~~~~~~r~a~~aer~~~~~~~~~~L~~~~~-g~~~~a~V~~~~~~----------~~~~ 544 (589)
+++|.|++.+ ..++.++.++|.+++.++++||+++++|.++||+++++ |++|+|+|+++... .+|+
T Consensus 513 ~a~l~~~~~~---~~~~~~~~~~s~~er~a~~aer~~~~~~~~~y~~~~~G~~~~f~g~I~~v~~~G~fV~l~~~~vegl 589 (644)
T PRK05054 513 KAVIKGETAE---RPQDEITVQLAERRRLNRMAERDVGDWLYARYLKDKAGTDTRFAAEIIDISRGGMRVRLLENGAVAF 589 (644)
T ss_pred HHHHcCCCCC---ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEEEEEeeecCcEEEEEeCCceEEE
Confidence 9999987543 34788999999999999999999999999999999984 35999999995332 4677
Q ss_pred EEeeccce---eEE--------E-EeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 545 LLLVEVGL---QAA--------A-WVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 545 V~l~~lg~---~~~--------~-~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|++++|+- ++. . +.++.|++||+|+|+|.+||+.+++|+|+.|
T Consensus 590 V~~~~l~~~~~~y~~~~~~~~~~~~~~~~~~lGd~V~V~v~~vd~~~~~i~~~~~ 644 (644)
T PRK05054 590 IPASFLHAVRDELVCNQENGTVQIKGETVYKLGDVIDVTLAEVRMETRSIIARPV 644 (644)
T ss_pred EEccccCCCccceEEccccceEEEeCCEEEcCCCEEEEEEEEEccccCeEEEEEC
Confidence 88776632 221 1 1135699999999999999999999999875
No 5
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=100.00 E-value=4.4e-91 Score=786.91 Aligned_cols=451 Identities=23% Similarity=0.317 Sum_probs=375.9
Q ss_pred cCCeeeEEeccCCCCCc-cc--eEEccCCCccccCC----CceEeecCCCCCCCHHHHHHHHHHhcccccCCCCCCCCee
Q 007798 121 DSDRVLLAVAQRPDGKK-NW--MVYDQNGASCSIKP----QQVTFVVPGVEKFDHKDISNFLQKAEDNLLNRKDLTHLKV 193 (589)
Q Consensus 121 ~~~rv~~~i~~~p~~~~-~~--~~~~~~g~~~~l~p----~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~R~Dl~~l~~ 193 (589)
.++.|++.|..+|.... .+ .++...|....-.. --..|.++.. |+++.+++... . ..+|+|||++++
T Consensus 121 ~gd~V~v~I~~~p~~~~~~~~~~I~~vLG~~~d~~~d~~~il~~~~l~~~--f~~~v~~ea~~---~-~~~R~DLr~~~~ 194 (639)
T TIGR02062 121 EGDWAVAELRRHPLKGDRSFYAELTQYITFADDHLAPWWVTLARHNLERE--EPDGVADEMLL---D-GLVREDLTALDF 194 (639)
T ss_pred CCCEEEEEEeccCCCCCCCceEEEEEEeCCCCCCccHHHHHHHHcCcCCC--CCHHHHHhhhh---c-cccCcccccCCE
Confidence 57788889999997542 22 34444443332100 0124667764 77776665432 2 257999999999
Q ss_pred EEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHHhcCceeecCCCccCCCChhhhhccCcCCCCC
Q 007798 194 YAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAMEGMSLRQGE 273 (589)
Q Consensus 194 fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~~RgtSvYLP~~~ipMLP~~Ls~~~~SL~~g~ 273 (589)
|||||++|+|+|||||++++++|+|+|||||||||+||+|||+||+||++||||+|||++++||||+.||+++|||+||+
T Consensus 195 ~TID~~~akD~DDAisie~~~~g~~~L~VHIADVs~yV~~gS~LD~eA~~RgtSvYLp~~vipMLP~~Ls~~~cSL~p~e 274 (639)
T TIGR02062 195 VTIDSESTKDMDDALFAEALPNGKLQLIVAIADPTAYIAEGSKLDKAAKIRGFTNYLPGFNIPMLPRELSDDLCSLRANE 274 (639)
T ss_pred EEECCCCCCcccceEEEEEeCCCcEEEEEEEcCccccCCCCCHHHHHHHHhCCcEeCCCceecCCCHHHhcCccccCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEEEEEEEECCCCeEeE-EEEEEEEEecccccCHHHHHHHHhcCCC-------ChHHHHHHHHHHHHHHHHHHhCCCc
Q 007798 274 VCNAVTVSVVLHSDGSIAE-YSVDNSIIKPTYMLTYESATELLHLNLE-------EEAELKILSEAAALRLQWRLQQGAI 345 (589)
Q Consensus 274 ~r~AlS~~~~ld~~G~I~~-~~~~~s~I~s~~~LtY~~v~~~l~~~~~-------~~~~L~~L~~la~~l~~~R~~~Gai 345 (589)
+|+|+||.|+||++|+|.+ ++|++|+|+|.++|||++|+++|+++.. ..+.|..|.++|+.|+++|.++|++
T Consensus 275 ~R~als~~~~ld~~G~i~~~~~~~~svIrs~~rltY~~v~~~l~~~~~~~~~~~~i~~~L~~L~~la~~l~~~R~~~G~i 354 (639)
T TIGR02062 275 VRPVLACRITISKDGNIEDKIEFFAATIKSKAKLVYDQVSDWLENTSDWQPESEEIAQQVRLLHQFCQARIEWRHTHALV 354 (639)
T ss_pred CeeEEEEEEEEcCCCcEeecCEEEEEEEEeCcEEeHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHhCCcc
Confidence 9999999999999999999 7999999999999999999999987532 1246889999999999999999999
Q ss_pred ccCCcceEEEecCCCCCCCeEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhcCCCcccccCCCCCCChh-hhh-----
Q 007798 346 DTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVS-AFA----- 419 (589)
Q Consensus 346 ~~~~pe~~i~l~~~~d~~~~v~i~~~~~~~~a~~LVeE~MIlAN~~~A~~l~~~~ip~lyR~q~~p~~~~~-~l~----- 419 (589)
+++.||+++.+++. +.+..+...+ +++||+|||||||+||++||+|+.++++|++||+|+.|+..+. ++.
T Consensus 355 ~ld~pE~~~~ld~~---g~~~~i~~~~-~~~a~~lIeE~MllAN~~vA~~l~~~~~p~iyR~H~~P~~~~l~~l~~~~~~ 430 (639)
T TIGR02062 355 FKDRPDYRFILSEK---GEVLDIVAEP-RRIANRIVEEAMIIANICAARFLRDKLGFGIYNTHAGFDPANAENVVALLKT 430 (639)
T ss_pred cccCCceEEEECCC---CCEEEEEEec-CCHHHHHHHHHHHHHHHHHHHHHHHhCCCeEEecCCCCCHHHHHHHHHHHHH
Confidence 99999999999872 3456787777 8999999999999999999999999999999999999986543 221
Q ss_pred ---cCCCC--------------------cchHHHHHHhhhcCccccCCCCCccccCCCCcccccccccchhhHHHHHHHH
Q 007798 420 ---HLPEG--------------------PVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVK 476 (589)
Q Consensus 420 ---~l~~~--------------------~~~~~~l~r~m~~a~ys~~~p~~HfgLgl~~YthfTSPIRRY~DLivHrqL~ 476 (589)
.++.. ......++|+|++|.|++ +|.+|||||++.|||||||||||+||+|||||+
T Consensus 431 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~r~~~~a~ys~-~~~~HfgL~~~~YthfTSPIRRY~DLivHR~L~ 509 (639)
T TIGR02062 431 NGLHVDAEELATLDGFCKLRRELDAQETGYLDSRIRRYQSFAEIST-EPGPHFGLGLEAYATWTSPIRKYGDMINHRLLK 509 (639)
T ss_pred cCCCCCcccccCHHHHHHHHHHhhcchHHHHHHHHHHHhhhcccCC-CCcCcchhccccccccCChhhhhHHHHHHHHHH
Confidence 11110 011335789999999999 999999999999999999999999999999999
Q ss_pred HHHcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CcEEEEEEEEEeeC----------eeEEE
Q 007798 477 ACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPK-ERQYRALILRFIKD----------RTAAL 545 (589)
Q Consensus 477 a~L~g~~~~~~~~~L~~i~~~~~~~~r~a~~aer~~~~~~~~~~L~~~~~-g~~~~a~V~~~~~~----------~~~~V 545 (589)
++|.|++.+. .++.++.+++.+++.++++||++++||.++||+++++ |++|+|+|+++... .+|+|
T Consensus 510 ~~l~~~~~~~---~~~~~~~~~s~~er~a~~aeR~~~~~~~~~yl~~~~g~~~~f~g~I~~v~~~g~~v~l~~~~~~g~v 586 (639)
T TIGR02062 510 AVIKGETATR---PQEDITVQLAERRRLNRIAERDVADWLYARFLADKAAKNTRFAAEIVDISRGGMRVRLLENGAIAFI 586 (639)
T ss_pred HHHcCCCCCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEEEEEeeeCCcEEEEEecCceEEEE
Confidence 9999875443 4678899999999999999999999999999999983 35999999986442 35566
Q ss_pred Eeeccce--e-E-------EEEe-C-ccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 546 LLVEVGL--Q-A-------AAWV-S-VGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 546 ~l~~lg~--~-~-------~~~~-~-~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
++.+|.- + + .... + +.|++||+|+|+|.+||..+++|+|+
T Consensus 587 ~~~~l~~~~~~~~~~~~~~~~~l~g~~~~~lgd~v~V~v~~vd~~~~~i~~~ 638 (639)
T TIGR02062 587 PAAFLHANREELVCNQENGTVQIKGETVYKIGDVIDVVLTEVRMETRSIIAR 638 (639)
T ss_pred EhhhcCCCCcceEEcccccEEEEeccEEEecCCEEEEEEEEeccccCcEeee
Confidence 6555521 1 1 0121 2 36999999999999999999999996
No 6
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=100.00 E-value=2.8e-90 Score=790.94 Aligned_cols=401 Identities=30% Similarity=0.429 Sum_probs=358.9
Q ss_pred ccCCCCCCCCeeEEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHHhcCceeecCCCccCCCChh
Q 007798 182 LLNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEK 261 (589)
Q Consensus 182 ~~~R~Dl~~l~~fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~~RgtSvYLP~~~ipMLP~~ 261 (589)
..+|.|||++++|||||++|+|+|||||+++++||+|+|||||||||+||+|||+||+||++||||||||+++|||||+.
T Consensus 245 ~~~R~Dlr~l~~~TID~~~akD~DDAv~~~~l~~g~~~LgVhIADVs~yV~p~s~LD~EA~~RgtSVYlp~~vipMLPe~ 324 (706)
T COG0557 245 LKGRVDLRDLPIFTIDPEDAKDLDDAVSVEKLRNGGYRLGVHIADVSHYVQPGSALDKEARKRGTSVYLPDRVIPMLPEA 324 (706)
T ss_pred hcCccccccCCEEEECCCCCccccceEEEEEeCCCcEEEEEEEecceeecCCCChhhHHHHHcCCeEEcCCcccCCCchh
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccCcCCCCCeeeEEEEEEEECCCCeEeEEEEEEEEEecccccCHHHHHHHHhcCC-----CChHHHHHHHHHHHHHH
Q 007798 262 LAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNL-----EEEAELKILSEAAALRL 336 (589)
Q Consensus 262 Ls~~~~SL~~g~~r~AlS~~~~ld~~G~I~~~~~~~s~I~s~~~LtY~~v~~~l~~~~-----~~~~~L~~L~~la~~l~ 336 (589)
||+++|||+||++|+|+||.|++|++|+|.+++|++|+|+|.++|||++|+++|+++. +..+.|..+..+++.++
T Consensus 325 Ls~~lcSL~p~~dRla~s~~m~ld~~g~v~~~~~~~svI~s~~rltY~~v~~~l~~~~~~~~~~l~~~l~~~~~l~~~l~ 404 (706)
T COG0557 325 LSNGLCSLNPGVDRLALSCEMTLDSEGRVKKYEIYPSVIKSAARLTYEEVQAILDGKEDDKYAPLLDSLLELLELAKILK 404 (706)
T ss_pred hcCCccccCCCCceEEEEEEEEECCCCCEEEEEEEEEEEeccccCCHHHHHHHHhcCcchhcccchHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999852 23477888888999999
Q ss_pred HHHHhCCCcccCCcceEEEecCCCCCCCeEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhcCCCcccccCCCCCCChh
Q 007798 337 QWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDVS 416 (589)
Q Consensus 337 ~~R~~~Gai~~~~pe~~i~l~~~~d~~~~v~i~~~~~~~~a~~LVeE~MIlAN~~~A~~l~~~~ip~lyR~q~~p~~~~~ 416 (589)
++|.++|+++|+.+|.++.+++. +.++.|...+ +++++.||||||++||+++|+++.++++|.+||+|+.|+..+.
T Consensus 405 ~~R~~rg~i~~~~~E~ki~~d~~---~~~~~i~~~~-r~~a~~lIee~Ml~AN~~vA~~l~~~~~~~~~R~h~~P~~ek~ 480 (706)
T COG0557 405 KKRLSRGAIDFDTPEAKIVLDEE---GRPVEIEIRE-RLDAEKLIEEFMLLANETVAEHLEKHKIPLLYRTHERPSTEKL 480 (706)
T ss_pred HHHHhCCCcccCCcceeEEECCC---CCeeeEEEec-ccHHHHHHHHHHHHHHHHHHHHHHHcCCCcceeCCCCCCHHHH
Confidence 99999999999999999999872 3468888888 8899999999999999999999999999999999999976543
Q ss_pred ----hhh-cC----C----------------C---C---cchHHHHHHhhhcCccccCCCCCccccCCCCcccccccccc
Q 007798 417 ----AFA-HL----P----------------E---G---PVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRR 465 (589)
Q Consensus 417 ----~l~-~l----~----------------~---~---~~~~~~l~r~m~~a~ys~~~p~~HfgLgl~~YthfTSPIRR 465 (589)
++. .+ + . . .+.+..++|+|++|.|++ .|.+|||||++.||||||||||
T Consensus 481 ~~l~~~l~~lg~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~lRsm~~a~Ys~-~~~~HfgL~~~~YtHFTSPIRR 559 (706)
T COG0557 481 QSLREFLQNLGLVLPLGGSKPQPQDYQILLETVKGRPLEAVLQTLLLRSMKQAEYSP-DNVGHFGLALDYYTHFTSPIRR 559 (706)
T ss_pred HHHHHHHHHcCceecCCCCcCCHHHHHHHHhhccCChHHHHHHHHHHHhhhcCeecC-CCCCceeccccchhccCCchhh
Confidence 111 00 0 0 0 133457889999999999 9999999999999999999999
Q ss_pred hhhHHHHHHHHHHHcCCCCCCCh---hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcEEEEEEEEEeeC--
Q 007798 466 YMDLLAHYQVKACLRGESPPFSA---GQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKD-- 540 (589)
Q Consensus 466 Y~DLivHrqL~a~L~g~~~~~~~---~~L~~i~~~~~~~~r~a~~aer~~~~~~~~~~L~~~~~g~~~~a~V~~~~~~-- 540 (589)
|+||+|||||+++|.++..+.+. ++|..++.+++.+++++.+++|++.+||.++||++++ |++|+|+|+++...
T Consensus 560 Y~DLivHR~L~~~l~~~~~~~~~~~~~~l~~i~~~~s~~er~a~~aer~~~~~~~~~~m~~~v-g~~f~g~V~~v~~~g~ 638 (706)
T COG0557 560 YPDLIVHRQLKALLSGEPIPEKKTSEEELDELAAHISSAERRAQEAERDVIDLLKAEYMKKRV-GEEFDGVVTGVTSFGF 638 (706)
T ss_pred chHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHhc-CCEEEEEEEEEEeccE
Confidence 99999999999999987665553 6899999999999999999999999999999999999 69999999996544
Q ss_pred --------eeEEEEeeccceeEE-----------EEeCccCCCCCEEEEEEEeeeCCCCeEEEEEec
Q 007798 541 --------RTAALLLVEVGLQAA-----------AWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVV 588 (589)
Q Consensus 541 --------~~~~V~l~~lg~~~~-----------~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v~ 588 (589)
-+|+|+++.|..++. .+.+..+++||.|+|++.+||...++|+|+.+.
T Consensus 639 ~V~l~~~~ieglV~~s~L~~d~y~~~~~~~~l~~~~~~~~~~lgd~v~v~v~~v~~~~~~i~~~~v~ 705 (706)
T COG0557 639 FVELPELGLEGLVHISSLPDDYYHFDERGQALVGEKSGKVYRLGDEVKVKVTSVDLDERKIDFELVE 705 (706)
T ss_pred EEEecccccccceEcccCCCceeeeccccceeeccccccccccCCEEEEEEEEEcccccceEEEecC
Confidence 256666666653221 233457999999999999999999999999875
No 7
>PF00773 RNB: RNB domain CAUTION: The Prosite pattern does not correspond to this Pfam.; InterPro: IPR001900 This entry represents the catalytic domain of ribonuclease II []. It includes characterised and related sequences to exoribonuclease II (RNase II) and ribonuclease R, a bacterial 3' --> 5' exoribonuclease homologous to RNase II [,,].; GO: 0003723 RNA binding, 0004540 ribonuclease activity; PDB: 2R7D_A 2R7F_A 2ID0_D 2IX1_A 2IX0_A 2VNU_D 2WP8_J.
Probab=100.00 E-value=4.2e-75 Score=610.88 Aligned_cols=292 Identities=39% Similarity=0.573 Sum_probs=239.6
Q ss_pred CCCCCCCeeEEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHHhcCceeecCCCccCCCChhhhh
Q 007798 185 RKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFLPTATYPMFPEKLAM 264 (589)
Q Consensus 185 R~Dl~~l~~fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~~RgtSvYLP~~~ipMLP~~Ls~ 264 (589)
|+|||++++||||+++|+|+||||||++.++|+|+|||||||||+||++||+||++|++||+|+|||++++||||+.|++
T Consensus 1 R~Dl~~~~~~tID~~~~~d~DDAisie~~~~~~~~v~VHIaDvt~~i~~~s~ld~~A~~r~~s~Ylp~~~~pMlP~~l~~ 80 (325)
T PF00773_consen 1 RKDLRDLPVFTIDPPGAKDIDDAISIEKLPDGKYEVGVHIADVTSFIPPDSPLDREARKRGTSVYLPEKVVPMLPPELSE 80 (325)
T ss_dssp SEECTTSEEEEEESTTSS---EEEEEEEETTTEEEEEEEEE-GGGTS-TTSHHHHHHHHH-B-EEETTEEE-SS-HHHHC
T ss_pred CccCCCCCEEEEcCCCCCCCCCeEEEEECCCCcEEEEEEcCCHHHhhccChHHHHHHHhcCccEECCCCccccCChhHhc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCcCCCCCeeeEEEEEEEECCCCeEeEEEEEEEEEecccccCHHHHHHHHhcCCCC------hHHHHHHHHHHHHHHHH
Q 007798 265 EGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLEE------EAELKILSEAAALRLQW 338 (589)
Q Consensus 265 ~~~SL~~g~~r~AlS~~~~ld~~G~I~~~~~~~s~I~s~~~LtY~~v~~~l~~~~~~------~~~L~~L~~la~~l~~~ 338 (589)
++|||.||++|+|||+.+++|++|+|.+++|++++|+|.++|||++|+++|++.... .++|..|+++|+.++++
T Consensus 81 ~~~SL~~~~~r~a~S~~~~l~~~G~i~~~~i~~s~I~~~~~lty~~v~~~l~~~~~~~~~~~~~~~L~~l~~la~~l~~~ 160 (325)
T PF00773_consen 81 DLCSLNPGKDRLAFSVIFTLDEDGEILDYEIYPSIIRSVARLTYEEVDEILEGKSQEEPESPIEEDLKLLYELAKALRKK 160 (325)
T ss_dssp TTSSTTBTSEEEEEEEEEEE-TTS-EEEEEEEEEEEEBSEEEEHHHHHHHHHTTTS--HCSHCHHHHHHHHHHHHHHHHH
T ss_pred ccccCCCCCCceEEEEEEEEeeCCeEeeeEEEEEEEecccccCHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999999985432 67999999999999999
Q ss_pred HHhCCCccc-CCcceEEEecCCCCCCCeEEEEEec--CCChHHHHHHHHHHHHHHHHHHHhhhcCCCcccccCCCCCCCh
Q 007798 339 RLQQGAIDT-ATLETRIKVANPEDPEPIINLYVED--QADPAMRLVSEMMILCGEAIATYGSFNNLALPYRGQPQSNIDV 415 (589)
Q Consensus 339 R~~~Gai~~-~~pe~~i~l~~~~d~~~~v~i~~~~--~~~~a~~LVeE~MIlAN~~~A~~l~~~~ip~lyR~q~~p~~~~ 415 (589)
|..+|++.+ +.|+..+.+++. +....+.... ...+++.||+||||+||++||+|+.++++|++||+|+.|+...
T Consensus 161 R~~~Ga~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~a~~lV~E~MilAN~~vA~~~~~~~ip~iyR~~~~p~~~~ 237 (325)
T PF00773_consen 161 RLSRGAIELFNSPELKFSLDED---GPPKEINRESSDESSPAHSLVEELMILANRAVAQFLSENGIPAIYRVQPEPDPER 237 (325)
T ss_dssp HHHTTS-----SHCEEEEEETT---TTEEEEEEE------HHHHHHHHHHHHHHHHHHHHHHHCTTTSEEEEB-SSSCCC
T ss_pred hhhccCccccCCCceEEEEecC---CCcceEEEEeccCCchHHHHHHHHHHHHHHHHHHHHHHcCCCceeeeCCCCCHHH
Confidence 999999999 789999999762 2334444332 3789999999999999999999999999999999999998774
Q ss_pred h-hh---hcC----------------CC---CcchHHHHHHhhhcCccccCCCCCccccCCCCcccccccccchhhHHHH
Q 007798 416 S-AF---AHL----------------PE---GPVRSSAIVKIMRAAAIDFRKPVRHGVLGLPGYVQFTSPIRRYMDLLAH 472 (589)
Q Consensus 416 ~-~l---~~l----------------~~---~~~~~~~l~r~m~~a~ys~~~p~~HfgLgl~~YthfTSPIRRY~DLivH 472 (589)
. ++ ..+ .. .......++++|++|.|++ +|.+|||||++.|||||||||||+||+||
T Consensus 238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~a~y~~-~p~~H~~L~l~~Yt~~TSPlRRY~Dl~~h 316 (325)
T PF00773_consen 238 LEELLKLLKLDLDETKSLTLQNLLQAENPPNSLALRYLLLKTLPPAEYST-EPSGHFGLGLPAYTHFTSPLRRYADLVVH 316 (325)
T ss_dssp HHHHHHHHT---STCHHHCHHCHHCCCCTTSSHHHHHHHHCCC--EEEES-SGC-BTTTTBSS-B--S-TTTBHHHHHHH
T ss_pred HHHHHHHhcCCCCCcchhhHHHHHHhcCChHHHHHHHHHHHhhccccccc-CCCcceeeeccccccccChhhhhHHHHHH
Confidence 2 21 110 11 1234567889999999999 99999999999999999999999999999
Q ss_pred HHHHHHHc
Q 007798 473 YQVKACLR 480 (589)
Q Consensus 473 rqL~a~L~ 480 (589)
|||+++|.
T Consensus 317 rql~~~L~ 324 (325)
T PF00773_consen 317 RQLKAALR 324 (325)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHhh
Confidence 99999986
No 8
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=100.00 E-value=5.1e-73 Score=588.51 Aligned_cols=447 Identities=24% Similarity=0.325 Sum_probs=369.3
Q ss_pred eEEeccCCCCCccceEEccCCCccccCCCc------eEeecCCCCCCCHHHHHHHHHHhcccc-----------------
Q 007798 126 LLAVAQRPDGKKNWMVYDQNGASCSIKPQQ------VTFVVPGVEKFDHKDISNFLQKAEDNL----------------- 182 (589)
Q Consensus 126 ~~~i~~~p~~~~~~~~~~~~g~~~~l~p~~------~~~~l~~~~~~~~~~~~~~~~~~~~~~----------------- 182 (589)
+..++++|.-+....+-...|..+.+..++ ..|.+.|+. +...++.+++...++.+
T Consensus 97 L~i~pDhP~lk~~i~~~~~k~l~~~fQeGDW~VA~lk~HpLkgDr-~F~a~lt~~It~~dD~l~PWWVTLArh~l~r~~p 175 (645)
T COG4776 97 LQIVPDHPLLKDAIPCRAAKGLNEEFQEGDWAVAELKRHPLKGDR-SFYAELTQKITFADDHLAPWWVTLARHNLEREAP 175 (645)
T ss_pred eEEcCCChhhhhhcccccccchhhhhhcCceehhhhhcCCCCCch-hHHHHHHHHhhccCCcccceeeehhhccCCccCC
Confidence 556778887666655555555555554443 357788886 55888888876644322
Q ss_pred ------------cCCCCCCCCeeEEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHHhcCceeec
Q 007798 183 ------------LNRKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAMKRGTSVFL 250 (589)
Q Consensus 183 ------------~~R~Dl~~l~~fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~~RgtSvYL 250 (589)
..|+|||.++++|||+++|+|+|||++++++++|.|.+-|+|||||.||.+||.||++|++|+.|.||
T Consensus 176 ~g~~d~~m~d~~l~RedLTaL~FvTID~~sT~DmDDALy~~~~~~~~~~L~vAIADPTAyI~~~s~ld~~A~~R~FTnYL 255 (645)
T COG4776 176 AGIVDTEMLDEGLVREDLTALDFVTIDSESTEDMDDALYAEPLPDGDWQLIVAIADPTAYIAEGSKLDKEAKIRAFTNYL 255 (645)
T ss_pred CcccchhhhhhhhhhccccccceEEecCccccccchhhhccccCCCcEEEEEEecCCccccCCcchhhHHHHHHHHhhcC
Confidence 37999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCccCCCChhhhhccCcCCCCCeeeEEEEEEEECCCCeEe-EEEEEEEEEecccccCHHHHHHHHhcCCC-------Ch
Q 007798 251 PTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIA-EYSVDNSIIKPTYMLTYESATELLHLNLE-------EE 322 (589)
Q Consensus 251 P~~~ipMLP~~Ls~~~~SL~~g~~r~AlS~~~~ld~~G~I~-~~~~~~s~I~s~~~LtY~~v~~~l~~~~~-------~~ 322 (589)
||..|||||++||+++|||.|++.|||+.|+++++.+|+|. +.+|..++|+|+++|.|+.|.++|++... ..
T Consensus 256 PGfNIPMLPreLsd~lCSL~~ne~RPaL~C~it~~~~G~I~~~i~F~aA~i~SkakL~YdhVSDwlE~~~~WqPe~~~iA 335 (645)
T COG4776 256 PGFNIPMLPRELSDDLCSLRANEVRPALACRITIDKDGNITDKIRFFAATIESKAKLVYDHVSDWLENTGDWQPESEAIA 335 (645)
T ss_pred CCCCCCCCChhhhhhhhhccccccCceEEEEEEEecCCccccchhhHHHhhhhhhhhhhhhHHHHHhcCCCCCCCCHHHH
Confidence 99999999999999999999999999999999999999996 68999999999999999999999997432 24
Q ss_pred HHHHHHHHHHHHHHHHHHhCCCcccCCcceEEEecCCCCCCCeEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhcCCC
Q 007798 323 AELKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFNNLA 402 (589)
Q Consensus 323 ~~L~~L~~la~~l~~~R~~~Gai~~~~pe~~i~l~~~~d~~~~v~i~~~~~~~~a~~LVeE~MIlAN~~~A~~l~~~~ip 402 (589)
.++..|+.+++++.+||..+..+.-+.|+|+|.+.+. +..+.|.... +..|++||||.||+||.|+|++|.++---
T Consensus 336 qqi~~L~~~~~aR~~WRk~hal~FkdrpdYrF~l~e~---g~V~~I~ae~-RRiAnriVEE~MI~ANIcAa~~L~~~~gf 411 (645)
T COG4776 336 QQIRLLHQFCQARIEWRKTHALVFKDRPDYRFILGEK---GEVLDIVAEP-RRIANRIVEESMIAANICAARVLREKLGF 411 (645)
T ss_pred HHHHHHHHHHHHHHHHHhhceeeccCCCceEEEecCC---CceEeeehhH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 6899999999999999998888888899999999873 3356777766 88999999999999999999999998767
Q ss_pred cccccCCCCCCChh-----------------hhhcCC------------CCcchHHHHHHhhhcCccccCCCCCccccCC
Q 007798 403 LPYRGQPQSNIDVS-----------------AFAHLP------------EGPVRSSAIVKIMRAAAIDFRKPVRHGVLGL 453 (589)
Q Consensus 403 ~lyR~q~~p~~~~~-----------------~l~~l~------------~~~~~~~~l~r~m~~a~ys~~~p~~HfgLgl 453 (589)
++|-+|..-+.... ++.+++ ........++|+++-|++++ .|.||||||+
T Consensus 412 GI~N~HsGFd~~~~e~a~~~l~~~~~~~~~e~l~Tl~Gfc~lRr~l~~~~t~yld~RiRrfqsfae~~t-~p~PHFglGl 490 (645)
T COG4776 412 GIYNVHSGFDPANAEAAAALLKTNGLNVDAEELLTLEGFCKLRRELDAQPTGYLDSRIRRFQSFAEIST-EPGPHFGLGL 490 (645)
T ss_pred ceeeccccCCHHHHHHHHHHHHhcCcCCCHHHHhhhHHHHHHHHHhhccccchHHHHHHHHHhHHhhcc-CcCccccccc
Confidence 88999986543221 122221 01122357899999999999 9999999999
Q ss_pred CCcccccccccchhhHHHHHHHHHHHcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CcEEEE
Q 007798 454 PGYVQFTSPIRRYMDLLAHYQVKACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQPK-ERQYRA 532 (589)
Q Consensus 454 ~~YthfTSPIRRY~DLivHrqL~a~L~g~~~~~~~~~L~~i~~~~~~~~r~a~~aer~~~~~~~~~~L~~~~~-g~~~~a 532 (589)
+.|+.||||||+|+|+||||.||++|.|+...-+.+ .+...+.++.|..+.+||+.-+|..++||+.+.. ..+|.|
T Consensus 491 ~~YATWTSPIRKY~DMiNHRLlKavi~~~~~~kPqe---di~v~lae~Rr~nrmaERdv~DWLY~r~L~~k~~~~~~F~A 567 (645)
T COG4776 491 EAYATWTSPIRKYGDMINHRLLKAVIKGETAEKPQE---DITVQLAERRRLNRMAERDVADWLYARFLADKAGTNTRFAA 567 (645)
T ss_pred hheeeccchhhhhhhHHHHHHHHHHHcCCCcCCCch---HHHHHHHHHHHhhhhhhhhhHHHHHHHHhccccccCchhhh
Confidence 999999999999999999999999999986433333 4556788999999999999999999999999874 368999
Q ss_pred EEEEEeeCeeEEEEeeccceeE---------------------EE--EeCccCCCCCEEEEEEEeeeCCCCeE
Q 007798 533 LILRFIKDRTAALLLVEVGLQA---------------------AA--WVSVGAQIGDEVEVKVEEAHPRDDII 582 (589)
Q Consensus 533 ~V~~~~~~~~~~V~l~~lg~~~---------------------~~--~~~~~~~lGd~V~V~I~~vD~~~~~i 582 (589)
.|.++.+.+.. |++-+-|... .+ .....|++||.|+|++.+|....+.|
T Consensus 568 EI~Di~R~G~R-vrLleNGA~~FIPa~lih~~reei~~n~e~gtv~I~ge~~Yk~~D~i~V~l~eVr~etRsi 639 (645)
T COG4776 568 EIQDISRGGMR-VRLLENGAIAFIPAPLIHANREELVCNQENGTVQIKGETVYKVGDVIDVTLAEVRMETRSI 639 (645)
T ss_pred hhhhhccCceE-EEeccCCcceecchhhhccchhheEecCCCceEEEccEEEEeeccEEEEEeHHHHHhhhhh
Confidence 99987766543 3433333221 11 11245999999999999999887765
No 9
>KOG2102 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-67 Score=609.61 Aligned_cols=470 Identities=26% Similarity=0.350 Sum_probs=373.0
Q ss_pred CcEEEEEecCCeeeE-EeccCCCCCc----cceEEccCCCccccCCCceEeecCCCCCCCHHHHHHHHHH----------
Q 007798 113 GLLLEFKKDSDRVLL-AVAQRPDGKK----NWMVYDQNGASCSIKPQQVTFVVPGVEKFDHKDISNFLQK---------- 177 (589)
Q Consensus 113 g~l~~~~~~~~rv~~-~i~~~p~~~~----~~~~~~~~g~~~~l~p~~~~~~l~~~~~~~~~~~~~~~~~---------- 177 (589)
.+.+||.+.|+||+. .|+.+-.... ...+-...|..++.+|.+..+...|..+-...+....+-+
T Consensus 371 ~~~~~~~p~DkRvP~i~i~t~~~~~~~~~~~~~~~I~~W~~ts~~p~g~~v~~lG~i~~~~~e~~aLL~en~v~~~~f~~ 450 (941)
T KOG2102|consen 371 ALIVLFIPSDKRVPLIRILTDDQAQDLIDKRIVAAIDRWPRTSLYPFGHLVRELGTIGDTETETEALLLENGVPHKPFSQ 450 (941)
T ss_pred cceeeeccccCCCCeeeccccccccchhceeEEEEecccccCCcccCceehhhccCcCCccchhhhhhhcCCCcccccCH
Confidence 344999999999866 4444411111 2345567899999999998887777654545544433322
Q ss_pred -h----cc---------cccC-CCCCCCCeeEEEeCCCCCCccceeEEEEecCCeEEEEEEEcCCccccCCCCHHHHHHH
Q 007798 178 -A----ED---------NLLN-RKDLTHLKVYAIDVDEADELDDALSAMRLQDGRIKVYIHVADPTKYIEPGSLSDKDAM 242 (589)
Q Consensus 178 -~----~~---------~~~~-R~Dl~~l~~fTID~~~a~DiDDAiSie~~~dG~~~l~VHIADvs~~V~~gS~LD~eA~ 242 (589)
+ .. .... |.|||++.+|+|||.++.|||||+|+..++||+|+|||||||||+||+|||+||+||+
T Consensus 451 ~~~~~lp~~~~~~~~~~~~~~~R~Dlr~~~i~~IDp~~~~dlDdAL~~~~l~nG~~evGVHIADVt~fV~pgs~lD~eA~ 530 (941)
T KOG2102|consen 451 ALLDCLPRSHPWPITEEELQKLRKDLRDLLIFSIDPPGATDLDDALHVRNLPNGNLEVGVHIADVTHFVKPGSALDREAA 530 (941)
T ss_pred HHHhcCCccCCCCcChHHhhhhhhhhhhceEEeecCCCccchhhhhheeecCCCcEEEEEEeccchhhcCCCCccCHHHH
Confidence 1 11 1134 9999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCceeecCCCccCCCChhhhhccCcCCCCCeeeEEEEEEEECCCCeEeEEEEEEEEEecccccCHHHHHHHHhcCCC--
Q 007798 243 KRGTSVFLPTATYPMFPEKLAMEGMSLRQGEVCNAVTVSVVLHSDGSIAEYSVDNSIIKPTYMLTYESATELLHLNLE-- 320 (589)
Q Consensus 243 ~RgtSvYLP~~~ipMLP~~Ls~~~~SL~~g~~r~AlS~~~~ld~~G~I~~~~~~~s~I~s~~~LtY~~v~~~l~~~~~-- 320 (589)
+||||||||+++|||||+.|++++|||.||++|.|||+.|++|.+|.|++.||++|+|+|+.+|+|+++|++|+++..
T Consensus 531 ~R~ttvyL~q~~i~MLP~~L~~~lcSL~~g~dr~aFSvvwel~~~~~i~~~~f~ksvI~s~~~lsye~Aq~~id~~~~~~ 610 (941)
T KOG2102|consen 531 RRGTTVYLVQKRIPMLPKLLSEELCSLRPGVDRLAFSVVWELDSDGSILKTWFGKSVIRSKAALSYEEAQDILDTPNSSD 610 (941)
T ss_pred hhcceEEeccccccCCchhhhhhheeccCCCceeeEEEEEEEcCCCceeeceecchhcccchhhhHHHHHHHhcCCcccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999998532
Q ss_pred -ChHHHHHHHHHHHHHHHHHHhCCCcccCCcceEEEecCCCCCCCeEEEEEecCCChHHHHHHHHHHHHHHHHHHHhhhc
Q 007798 321 -EEAELKILSEAAALRLQWRLQQGAIDTATLETRIKVANPEDPEPIINLYVEDQADPAMRLVSEMMILCGEAIATYGSFN 399 (589)
Q Consensus 321 -~~~~L~~L~~la~~l~~~R~~~Gai~~~~pe~~i~l~~~~d~~~~v~i~~~~~~~~a~~LVeE~MIlAN~~~A~~l~~~ 399 (589)
-...|..|+++|+.++++|..+|++.+..+|..+.+++. +..+..+...+ ...++.+|+|||++||..+|.++.++
T Consensus 611 ~v~~~l~~l~~ia~~lr~~R~~~gal~l~~~e~~~~~d~~--~~~p~~~e~~~-~~~~n~lveEfmllaN~~vA~~I~~~ 687 (941)
T KOG2102|consen 611 PLTSSLRLLHEIAKILRQKRLDNGALLLRSPELRFLLDEE--KPNPQDVEVKE-LTETNFLVEEFMLLANISVAEKILAS 687 (941)
T ss_pred hhhhhHHHHHHHHHHHHHHHhccCCcccccHhHHhhhccC--CCCccccceee-eehhhhHHHHHHHHHhHHHHHHHHHh
Confidence 235699999999999999999999999999999999873 22234555545 66788899999999999999998877
Q ss_pred -CCCcccccCCCCCCChh----hh-h--c----------CC------CC---cch----HHHHHHhhhcCccccC-----
Q 007798 400 -NLALPYRGQPQSNIDVS----AF-A--H----------LP------EG---PVR----SSAIVKIMRAAAIDFR----- 443 (589)
Q Consensus 400 -~ip~lyR~q~~p~~~~~----~l-~--~----------l~------~~---~~~----~~~l~r~m~~a~ys~~----- 443 (589)
.-..++|.|+.|..... ++ . . |. .+ |+. ..+..|+|.+|.|...
T Consensus 688 f~~~alLR~hp~P~~~~~~~~~~~~~~~g~~ld~sS~~~L~~Sl~r~~~~~~p~~~~~l~~l~~r~m~~A~yf~sg~~~~ 767 (941)
T KOG2102|consen 688 FPSLALLRRHPSPPPENFKPLVSLCLELGFNLDTSSSKSLADSLDRIRDDDKPYLNTLLRILATRSMTRAVYFCSGSSDT 767 (941)
T ss_pred CCchhhhccCCCCccccccHHHHHHHHcCCCccccchHHHhhhHhhhcCCchHHHHHHHHHHHhhhhhceeEEeecccCc
Confidence 55678999988854332 11 0 0 00 01 111 1334688999987551
Q ss_pred CCCCccccCCCCcccccccccchhhHHHHHHHHH-HHcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 007798 444 KPVRHGVLGLPGYVQFTSPIRRYMDLLAHYQVKA-CLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLR 522 (589)
Q Consensus 444 ~p~~HfgLgl~~YthfTSPIRRY~DLivHrqL~a-~L~g~~~~~~~~~L~~i~~~~~~~~r~a~~aer~~~~~~~~~~L~ 522 (589)
....||||+++.|||||||||||+|++|||||.+ ++...+...+...+..+|..||.+.+.++.+++++..+|.+.|++
T Consensus 768 ~~~~HygLa~p~YTHFTsPiRRY~DIivHrqL~~~~~~~~~~~~~~~~l~~i~~~~N~r~~~a~~a~~~S~~l~~~~~~k 847 (941)
T KOG2102|consen 768 PQFHHYGLASPLYTHFTSPIRRYADIIVHRQLAAAFLERSPTAPDRPNLSSLAANCNERKKAAKKAQEASTELYLCEYLK 847 (941)
T ss_pred chhhchhhcccchhhccCcccccchHHHHHHHHHHhhccCccccccccHHHHHhhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 3478999999999999999999999999999994 444443334445899999999999999999999999999999999
Q ss_pred cCCCCcEEEEEEEEEeeCeeEEEEeeccceeEEEEeC----c-c----------CCCCCEEEEE--EEeeeCCCCeEEEE
Q 007798 523 RQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWVS----V-G----------AQIGDEVEVK--VEEAHPRDDIIYLK 585 (589)
Q Consensus 523 ~~~~g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~~----~-~----------~~lGd~V~V~--I~~vD~~~~~i~~~ 585 (589)
+.. ..-+|+|+.+ +.+...|.++++|++..+... . . ++.-+.|.+. +...++....|.+.
T Consensus 848 ~~~--~~~~a~v~~V-~~~~~~v~ipe~G~e~~v~l~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~l~~~ 924 (941)
T KOG2102|consen 848 DKQ--VLEEAVVLFV-RPNGIDVVIPEYGLEGRVYLDLLKPSQTFFLDDEVSLRFEESDPVVVRIKLDKLVPQPDRLRIE 924 (941)
T ss_pred hcc--cccceEEEEE-ecCceEEEEcccCceEEEEecccCCccceeecccccccccccCCceeeecccccccCcceEEEE
Confidence 884 5678999975 445556889999998865432 1 1 1222455554 56677777888777
Q ss_pred Eec
Q 007798 586 EVV 588 (589)
Q Consensus 586 ~v~ 588 (589)
.+.
T Consensus 925 ~~~ 927 (941)
T KOG2102|consen 925 LVS 927 (941)
T ss_pred ecc
Confidence 664
No 10
>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=96.75 E-value=0.0048 Score=50.06 Aligned_cols=59 Identities=10% Similarity=0.060 Sum_probs=41.1
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
|+.++|.|+++... ..|+++++++.-+...+....|++||.++++|.++|+.+++|.|+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~v~g~i~~~~l~~~~~~~~~~~~~~Gd~i~~~V~~id~~~~~i~ls 68 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecCCcEEEEEHHHCCCccccCHHHcCCCCCEEEEEEEEEECCCCEEEEE
Confidence 57889999985322 244455544433222222345999999999999999999999986
No 11
>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=96.61 E-value=0.011 Score=48.27 Aligned_cols=60 Identities=10% Similarity=-0.031 Sum_probs=44.9
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|+++... .+|+++++++.-+...+....|++||.|+++|.++|..++++.|+.
T Consensus 4 G~iv~g~V~~v~~~gi~v~l~~~~~g~v~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~~d~~~~~i~ls~ 72 (73)
T cd05706 4 GDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSL 72 (73)
T ss_pred CCEEEEEEEEEeCCeEEEEeCCCcEEEEEhhhccCccccccccccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 78999999996432 3566676666544322333559999999999999999999999874
No 12
>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=96.57 E-value=0.0054 Score=48.76 Aligned_cols=59 Identities=17% Similarity=0.129 Sum_probs=40.0
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
|+.+.|.|+++... ..|+++.+++.-+........|++||.|+|+|.++|+.+++++|+
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~~~~g~~~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCCCCEEEEEHHHCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEecC
Confidence 47899999985432 234455444432222222234899999999999999999999873
No 13
>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=96.53 E-value=0.0058 Score=49.25 Aligned_cols=58 Identities=16% Similarity=0.053 Sum_probs=41.4
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEE-EeCccCCCCCEEEEEEEeeeCCCCeEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAA-WVSVGAQIGDEVEVKVEEAHPRDDIIYL 584 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~-~~~~~~~lGd~V~V~I~~vD~~~~~i~~ 584 (589)
|+.+.|.|.++... ..|+++++++...... .....|++||.|+|+|.++|+.+++|+|
T Consensus 1 G~~~~g~V~~i~~~G~fv~l~~~~~Glv~~~~l~~~~~~~~~~~~~~~G~~v~v~v~~id~~~~~i~l 68 (69)
T cd05690 1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEeCCCCEEEEEHHHCCCccccCChhhEECCCCEEEEEEEEEECCcCEEeC
Confidence 57889999885332 3567777766421111 1124589999999999999999999986
No 14
>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=96.49 E-value=0.011 Score=48.29 Aligned_cols=58 Identities=19% Similarity=0.148 Sum_probs=42.9
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeecccee-EEEEeCccCCCCCEEEEEEEeeeCCCCeEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQ-AAAWVSVGAQIGDEVEVKVEEAHPRDDIIYL 584 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~-~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~ 584 (589)
|+.|.|.|+++.+. ..|+++++++..+ ........|++||.|+|+|.++|+.++.|+|
T Consensus 4 g~~~~g~V~~i~~~G~fv~l~~~~~Gl~~~~~l~~~~~~~~~~~~~~~Gd~v~v~v~~id~~~~~i~~ 71 (72)
T cd05689 4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71 (72)
T ss_pred CCEEEEEEEEEEeeEEEEEcCCCCEEEEEEEeccCcccccCcccEeCCCCEEEEEEEEeeCCcCEEeC
Confidence 68999999985332 3577777777422 1112234589999999999999999999886
No 15
>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=96.47 E-value=0.0078 Score=48.04 Aligned_cols=58 Identities=22% Similarity=0.271 Sum_probs=39.9
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
|+.+.|.|+++.+. ..|+++++++.-+........|++||.|.|+|.++|+ .+.++|+
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~d~-~~~i~ls 67 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDD-RGRISLS 67 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCCCCEEEEEhHHcCCccccCHHHccCCCCEEEEEEEEECC-CCcEEee
Confidence 47889999885432 3455555554332222223458999999999999999 9999886
No 16
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=96.43 E-value=0.0089 Score=48.40 Aligned_cols=60 Identities=17% Similarity=0.117 Sum_probs=43.0
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|.++.+. ..|+++++++..+........+++||.|+|+|.++|+.++++.|+.
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~~~~gli~~s~l~~~~~~~~~~~~~~G~~i~v~v~~~d~~~~~i~ls~ 69 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSC 69 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECCCCEEEEEHHHcChhhcCCHHHcccCCCEEEEEEEEEcCCCCEEEEEe
Confidence 57788999885332 3466666666543322223458999999999999999999999874
No 17
>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=96.43 E-value=0.0079 Score=47.93 Aligned_cols=59 Identities=20% Similarity=0.156 Sum_probs=39.2
Q ss_pred CcEEEEEEEEEeeC--------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 527 ERQYRALILRFIKD--------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 527 g~~~~a~V~~~~~~--------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
|+.+.|.|+++.+. ..|+++..++........+..|++||.|+|+|.++|+.+++++|+
T Consensus 2 g~~~~g~V~~v~~~g~~v~l~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls 68 (68)
T cd05688 2 GDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68 (68)
T ss_pred CCEEEEEEEEEEeeeEEEEECCeEEEEEhHHCCCccccCHhHEECCCCEEEEEEEEEECCCCEEecC
Confidence 58899999986432 233344444331111112234899999999999999999999873
No 18
>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=96.43 E-value=0.0073 Score=48.82 Aligned_cols=59 Identities=14% Similarity=0.115 Sum_probs=41.1
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
|+.+.|.|+++... ..|+++++++.-+...+....|++||.|+++|.++|+.+++|.|+
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls 68 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEecC
Confidence 57788999885332 245555555533322233345999999999999999999998863
No 19
>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=96.36 E-value=0.022 Score=47.48 Aligned_cols=60 Identities=13% Similarity=0.121 Sum_probs=41.9
Q ss_pred CcEEEEEEEEEeeC----------eeEEEEeeccceeEE----------E-EeCccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 527 ERQYRALILRFIKD----------RTAALLLVEVGLQAA----------A-WVSVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 527 g~~~~a~V~~~~~~----------~~~~V~l~~lg~~~~----------~-~~~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
|+.++|.|+++... .+|+++++++.-+.. . +....|++||.|+|+|.++|..+++|.|+
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~gd~v~v~v~~vd~~~~~i~~~ 81 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDLDRRKIDFE 81 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecCCCcEEEcccceEEEeccCCCEEcCCCEEEEEEEEeccccCEEEEE
Confidence 58899999985322 345566655532110 0 11245899999999999999999999987
Q ss_pred E
Q 007798 586 E 586 (589)
Q Consensus 586 ~ 586 (589)
.
T Consensus 82 l 82 (83)
T cd04471 82 L 82 (83)
T ss_pred E
Confidence 4
No 20
>PRK07252 hypothetical protein; Provisional
Probab=96.36 E-value=0.014 Score=53.32 Aligned_cols=61 Identities=15% Similarity=0.076 Sum_probs=44.3
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+.+.|.|+++... ..|+++++++.-+........|++||.|+|+|.++|+..+.|.|+..
T Consensus 4 G~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSlk 73 (120)
T PRK07252 4 GDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR 73 (120)
T ss_pred CCEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence 68999999996432 24556666554332222234589999999999999999999998754
No 21
>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=96.34 E-value=0.013 Score=49.38 Aligned_cols=59 Identities=14% Similarity=0.033 Sum_probs=44.9
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
|+.+.|.|.++... ..|+++++++..+...+....|++||.|+|+|.++|..+++|.|+
T Consensus 15 G~i~~g~V~~v~~~G~fv~l~~~~~g~v~~~el~~~~~~~~~~~~~~Gd~v~vkV~~id~~~~~i~ls 82 (83)
T cd04461 15 GMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82 (83)
T ss_pred CCEEEEEEEEEeeceEEEEcCCCCEEEEEHHHCCcccccCHHHhcCCCCEEEEEEEEEcCCCCEEEEe
Confidence 79999999985332 346667766654433333456999999999999999999999886
No 22
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=96.32 E-value=0.016 Score=47.38 Aligned_cols=60 Identities=17% Similarity=0.023 Sum_probs=43.7
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|.++... ..|+++++++...........+.+||.|+|+|.++|+.++.+.|+.
T Consensus 5 G~iv~g~V~~v~~~g~~V~l~~~~~g~ip~~~l~~~~~~~~~~~~~~G~~v~v~v~~vd~~~~~i~lS~ 73 (74)
T PF00575_consen 5 GDIVEGKVTSVEDFGVFVDLGNGIEGFIPISELSDDRIDDPSEVYKIGQTVRVKVIKVDKEKGRIRLSL 73 (74)
T ss_dssp TSEEEEEEEEEETTEEEEEESTSSEEEEEGGGSSSSEESSSHGTCETTCEEEEEEEEEETTTTEEEEES
T ss_pred CCEEEEEEEEEECCEEEEEECCcEEEEEEeehhcCccccccccccCCCCEEEEEEEEEECCCCeEEEEE
Confidence 79999999986432 2455555555443222223568999999999999999999999863
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=96.31 E-value=0.013 Score=48.25 Aligned_cols=59 Identities=14% Similarity=0.073 Sum_probs=41.8
Q ss_pred CcEEEEEEEEEeeC----------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD----------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~----------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.++|.|+++.+. .+|+++++++.-....+....|++||+|+|+|.++|..+ .+.|+.
T Consensus 4 g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~~~~~~~~~~~~~Gd~v~vkv~~vd~~~-ki~ls~ 72 (73)
T cd05686 4 YQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKD-KMKLSL 72 (73)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCCCcccCHhhEECCCCEEEEEEEEECCCC-cEEEEe
Confidence 68999999985321 256667666644322222344899999999999999976 888764
No 24
>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=96.24 E-value=0.015 Score=47.63 Aligned_cols=61 Identities=18% Similarity=0.080 Sum_probs=40.7
Q ss_pred CcEEEEEEEEEeeCe----------eEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKDR----------TAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~~----------~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+.+.|.|+++...+ .|+++++++.-+........|++||.|+|+|.++|+..++++|+..
T Consensus 3 g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ls~k 73 (77)
T cd05708 3 GQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73 (77)
T ss_pred CCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCCCccCCHhHeecCCCEEEEEEEEEeCCCCEEEEEEE
Confidence 689999999864322 2333333332111111123489999999999999999999998754
No 25
>PRK08582 hypothetical protein; Provisional
Probab=96.10 E-value=0.025 Score=52.91 Aligned_cols=60 Identities=23% Similarity=0.201 Sum_probs=45.0
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+.+.|.|+++... ..|+|+++++.-+........|++||.|+|+|.++|. .+.|+|...
T Consensus 6 G~iv~G~V~~I~~fG~fV~L~~~~~GlVhiSels~~~v~~~~~~l~vGD~VkvkV~~id~-~gkI~LSlk 74 (139)
T PRK08582 6 GSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVED-DGKIGLSIK 74 (139)
T ss_pred CCEEEEEEEEEECCeEEEEECCCCEEEEEeeccCcccccccccccCCCCEEEEEEEEECC-CCcEEEEEE
Confidence 79999999995332 3577788777544433333569999999999999997 489988753
No 26
>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=95.96 E-value=0.025 Score=46.40 Aligned_cols=60 Identities=15% Similarity=0.106 Sum_probs=40.9
Q ss_pred CcEEEEEEEEEeeC-----------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD-----------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~-----------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|+++.+. ..|+++++++.-+........|++||.|+|+|.++|..+++++|+.
T Consensus 4 G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls~ 74 (76)
T cd04452 4 GELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSK 74 (76)
T ss_pred CCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEEE
Confidence 68999999985332 2344444443322111222348999999999999999999999875
No 27
>PRK05807 hypothetical protein; Provisional
Probab=95.96 E-value=0.028 Score=52.43 Aligned_cols=59 Identities=17% Similarity=0.101 Sum_probs=42.8
Q ss_pred CcEEEEEEEEEeeC--------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD--------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~--------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|+++... ..|+|+++++.-.........|++||.|+|+|.++|. .+.|+|..
T Consensus 6 G~vv~G~Vt~i~~~GafV~L~~~~Glvhiseis~~~v~~~~~~~kvGd~V~VkV~~id~-~gkI~LSl 72 (136)
T PRK05807 6 GSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSI 72 (136)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEhhhcccccccCccccCCCCCEEEEEEEEECC-CCcEEEEE
Confidence 79999999995332 3456666655433322223458999999999999998 79998875
No 28
>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=95.93 E-value=0.022 Score=45.20 Aligned_cols=59 Identities=17% Similarity=0.095 Sum_probs=37.7
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|.++... ..|+++.+++.-+........|++||.|+|+|.++|+ .++++|+.
T Consensus 1 G~~~~g~V~~i~~~g~~v~i~~~~~g~l~~~~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~ls~ 68 (69)
T cd05692 1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSI 68 (69)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCEEEEEhHHcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEEEE
Confidence 57889999985432 2233333333211110111348999999999999999 89998864
No 29
>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=95.88 E-value=0.031 Score=45.31 Aligned_cols=61 Identities=16% Similarity=0.125 Sum_probs=42.5
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+.+.|.|+++... ..|+++++++..+........|++||.|+++|.++|+.++.+.|+.-
T Consensus 1 G~~v~g~V~~v~~~g~~v~l~~~~~g~i~~~~~~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ls~k 70 (73)
T cd05691 1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70 (73)
T ss_pred CCEEEEEEEEEECCeEEEEeCCCCEEEEEHHHCCCccccCHHHccCCCCEEEEEEEEEeCCCCEEEEEEE
Confidence 47788999885322 24555555554333222234589999999999999999999988753
No 30
>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=95.73 E-value=0.039 Score=45.32 Aligned_cols=59 Identities=8% Similarity=0.052 Sum_probs=38.9
Q ss_pred CcEEE-EEEEEEeeC----------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 527 ERQYR-ALILRFIKD----------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 527 g~~~~-a~V~~~~~~----------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
|+.|+ |.|+++..+ ..|+++.+++.-+........+++||.|+++|.++|+.++.|.++
T Consensus 1 G~v~~~g~V~~v~~~~G~~V~l~~gv~G~i~~s~l~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~lS 70 (71)
T cd05696 1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLS 70 (71)
T ss_pred CcEeeeeEEEEEccCceEEEEeCCCCEEEEEHHHCCcchhcCcccccCCCCEEEEEEEEEeCCCCEEEEe
Confidence 46777 788774322 234444444432222222345999999999999999999999875
No 31
>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=95.52 E-value=0.049 Score=45.35 Aligned_cols=59 Identities=17% Similarity=0.212 Sum_probs=39.4
Q ss_pred CcEEEEEEEEEeeC------------eeEEEEeeccceeEE-EEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKD------------RTAALLLVEVGLQAA-AWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~------------~~~~V~l~~lg~~~~-~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+.|.|.|+++.+. ..|+++++++.-+.. ......|++||.|+|+|.++| ++.+.|+..
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~~~~~~~~~~~~~~Gd~v~v~v~~vd--~~~i~~s~k 72 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQ--NGKISLSMK 72 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccCCCCcCChhheeCCCCEEEEEEEEEe--CCEEEEEEE
Confidence 57889999885332 235555555532221 122234899999999999999 788888753
No 32
>PRK08059 general stress protein 13; Validated
Probab=95.35 E-value=0.056 Score=49.39 Aligned_cols=61 Identities=16% Similarity=0.062 Sum_probs=43.5
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+.+.|.|+++.+. ..|+++++++.-+........|++||.|+|+|.++|..++.++|+..
T Consensus 8 G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk 77 (123)
T PRK08059 8 GSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77 (123)
T ss_pred CCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEE
Confidence 79999999996442 23455555553332212134589999999999999999999999864
No 33
>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=95.14 E-value=0.072 Score=44.03 Aligned_cols=60 Identities=12% Similarity=0.186 Sum_probs=39.8
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeE--EEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQA--AAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~--~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|....|.|..+... .+|++++.++.-+. .......|++||.|+++|.++|+.++.|.|..
T Consensus 1 G~~V~g~V~~i~~~g~~V~l~~~i~G~i~~~~ls~~~~~~~~~~~~~~vG~~v~~kV~~id~~~~~i~Ls~ 71 (73)
T cd05703 1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSA 71 (73)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCcEEEEEHHHcCCccccccCHHHhCCCCCEEEEEEEEEeCCCCEEEEEe
Confidence 46778888875322 23444444442211 11112459999999999999999999999875
No 34
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=94.95 E-value=0.069 Score=42.18 Aligned_cols=58 Identities=21% Similarity=0.157 Sum_probs=39.3
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccceeEEEEe-----------CccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVGLQAAAWV-----------SVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~-----------~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|.++... ...|.+.. ++.+.... ...|++||.|.++|.++|+.++.+.|+.
T Consensus 3 G~~v~g~V~~v~~~-g~~v~i~~-~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls~ 71 (72)
T smart00316 3 GDVVEGTVTEITPF-GAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71 (72)
T ss_pred CCEEEEEEEEEEcc-EEEEEeCC-CCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEEe
Confidence 68899999986443 22233321 23332211 1348999999999999999999998864
No 35
>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=94.67 E-value=0.12 Score=41.72 Aligned_cols=60 Identities=17% Similarity=0.181 Sum_probs=38.0
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|.++... .+|+++..++..+........|++||.++++|.++|+..++|.|+.
T Consensus 1 G~iv~g~V~~i~~~~~~v~l~~~~~g~l~~~e~~~~~~~~~~~~~~~Gd~i~~~i~~~~~~~~~i~lS~ 69 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSK 69 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEeCCCceEEEEHHHhCccccCCHhHcCCCCCEEEEEEEEEECCCCeEEEEe
Confidence 46778888885332 2233333333211111112348999999999999999889998864
No 36
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=94.55 E-value=0.038 Score=50.25 Aligned_cols=59 Identities=19% Similarity=0.179 Sum_probs=45.4
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|...+|.|+++..- ..|+|||++..-.++.....-+..||.|+|+|.++|. ++.|.|..
T Consensus 6 G~~l~GkItgI~~yGAFV~l~~g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide-~GKisLSI 73 (129)
T COG1098 6 GSKLKGKITGITPYGAFVELEGGKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDE-NGKISLSI 73 (129)
T ss_pred cceEEEEEEeeEecceEEEecCCCcceEEehHhhhhhHHhHHHHhcCCCEEEEEEEeecc-CCCcceeh
Confidence 78899999995321 4578888877544443444568999999999999998 89988863
No 37
>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=94.49 E-value=0.12 Score=42.88 Aligned_cols=58 Identities=14% Similarity=0.104 Sum_probs=39.6
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEE---eCccCCCCCEEEEEEEeeeCCCCeEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAW---VSVGAQIGDEVEVKVEEAHPRDDIIYL 584 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~---~~~~~~lGd~V~V~I~~vD~~~~~i~~ 584 (589)
|+...|.|..+... ..|+|++.++....... ....|++||.|+++|.++|+.++.|.|
T Consensus 4 G~~V~g~V~~i~~~G~fV~l~~~v~G~v~~~~ls~~~~~~~~~~~~~~~~G~~v~~kVl~id~~~~~i~L 73 (74)
T cd05705 4 GQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVEL 73 (74)
T ss_pred CCEEEEEEEEEeCCcEEEEeCCCCEEEEEHHHccCccccChhhHhcccCCCCEEEEEEEEEECCCCEEec
Confidence 68899999885432 24455544442221111 124589999999999999999999876
No 38
>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=94.07 E-value=0.31 Score=40.52 Aligned_cols=58 Identities=22% Similarity=0.251 Sum_probs=40.6
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccceeEEEEe---CccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVGLQAAAWV---SVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~---~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+.++|.|.++.+ ....|.+.+ +.++..+. ...+++||.++|+|.++ ..++.|+|+.+
T Consensus 17 G~~~~g~V~~i~~-~G~fV~l~~-~~~Glv~~se~~~~~~iGd~v~v~I~~i-~e~~~i~l~~~ 77 (77)
T cd04473 17 GKLYKGKVNGVAK-YGVFVDLND-HVRGLIHRSNLLRDYEVGDEVIVQVTDI-PENGNIDLIPV 77 (77)
T ss_pred CCEEEEEEEeEec-ceEEEEECC-CcEEEEEchhccCcCCCCCEEEEEEEEE-CCCCcEEEEEC
Confidence 7999999998543 223344432 23322221 35689999999999999 88999999764
No 39
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=93.53 E-value=0.22 Score=59.25 Aligned_cols=65 Identities=18% Similarity=0.184 Sum_probs=48.0
Q ss_pred HhcCCCCcEEE-EEEEEEee---------CeeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 521 LRRQPKERQYR-ALILRFIK---------DRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 521 L~~~~~g~~~~-a~V~~~~~---------~~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
+...+ |+.|+ |.|+++.. ..+|+||++++.-+........|++||.|+|+|.++|+ +++|+|...
T Consensus 749 ~~~~v-G~iy~~g~V~~I~~FGaFVeL~~g~EGLVHISeLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSlK 823 (891)
T PLN00207 749 MVPTV-GDIYRNCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSRR 823 (891)
T ss_pred cCcCC-CcEEECcEEEEEeccEEEEEeCCCCEEEEEhhhcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEEe
Confidence 34556 79995 68888532 14788899888654433333569999999999999998 789998763
No 40
>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=92.97 E-value=0.34 Score=39.15 Aligned_cols=56 Identities=11% Similarity=0.144 Sum_probs=36.4
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccceeEEEEe---------CccCCCCCEEEEEEEeeeCCCCeEEE
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVGLQAAAWV---------SVGAQIGDEVEVKVEEAHPRDDIIYL 584 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~---------~~~~~lGd~V~V~I~~vD~~~~~i~~ 584 (589)
|...+|.|+.+.. ....|.+.+ ++++.... ...|++||.|+++|..+|+.++.|.|
T Consensus 1 G~~V~g~V~~i~~-~G~~v~l~~-~v~g~v~~~~l~~~~~~~~~~~~G~~i~~kVi~id~~~~~i~L 65 (66)
T cd05695 1 GMLVNARVKKVLS-NGLILDFLS-SFTGTVDFLHLDPEKSSKSTYKEGQKVRARILYVDPSTKVVGL 65 (66)
T ss_pred CCEEEEEEEEEeC-CcEEEEEcC-CceEEEEHHHcCCccCcccCcCCCCEEEEEEEEEeCCCCEEec
Confidence 4567888887532 222344432 33332211 34599999999999999999988876
No 41
>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=92.67 E-value=0.23 Score=38.37 Aligned_cols=25 Identities=48% Similarity=0.569 Sum_probs=22.5
Q ss_pred ccCCCCCEEEEEEEeeeCCCCeEEE
Q 007798 560 VGAQIGDEVEVKVEEAHPRDDIIYL 584 (589)
Q Consensus 560 ~~~~lGd~V~V~I~~vD~~~~~i~~ 584 (589)
..|++||.|+++|.++|+.++.+.+
T Consensus 40 ~~~~~G~~v~~~v~~~d~~~~~i~l 64 (65)
T cd00164 40 EVFKVGDEVEVKVLEVDPEKGRISL 64 (65)
T ss_pred hEeCCCCEEEEEEEEEcCCcCEEec
Confidence 4589999999999999999988876
No 42
>PHA02945 interferon resistance protein; Provisional
Probab=92.60 E-value=0.8 Score=39.42 Aligned_cols=57 Identities=14% Similarity=0.066 Sum_probs=42.7
Q ss_pred CcEEEEEEEEEeeCeeEEEEeecc-ceeEE------------EEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKDRTAALLLVEV-GLQAA------------AWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~l-g~~~~------------~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+..-|+|.. .+..+.|.|+++ |+++. .+....+ .|++|.++|.+||+.++.||+..
T Consensus 12 GelvigtV~~--~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l-~GqkvV~KVirVd~~kg~IDlSl 81 (88)
T PHA02945 12 GDVLKGKVYE--NGYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKL-VGKTVKVKVIRVDYTKGYIDVNY 81 (88)
T ss_pred CcEEEEEEEe--cCceEEEEecccCCcEEEEEeehhhhccceEeeeeEe-cCCEEEEEEEEECCCCCEEEeEe
Confidence 6888898886 455566778888 55542 2332235 99999999999999999999953
No 43
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=92.36 E-value=0.43 Score=53.90 Aligned_cols=66 Identities=18% Similarity=0.182 Sum_probs=47.8
Q ss_pred HhcCCCCcEEEEEEEEEeeC--------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 521 LRRQPKERQYRALILRFIKD--------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 521 L~~~~~g~~~~a~V~~~~~~--------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
+.+...|+..+|+|.++... ..|+||++++......+....+++||.|+|+|.++|..++.|.|..
T Consensus 187 ~~~l~~G~vV~G~V~~It~~GafVdigGvdGLlHiseiS~~rv~~P~~vvkvGd~VkvkVi~~D~e~~RVsLSl 260 (541)
T COG0539 187 LNKLEVGEVVEGVVKNITDYGAFVDIGGVDGLLHISEISWKRVDHPSEVVKVGDEVKVKVISLDEERGRVSLSL 260 (541)
T ss_pred HhcCCCCceEEEEEEEeecCcEEEEecCeeeEEehhhccccccCCHHHhcccCCEEEEEEEEEccCCCeEEEEe
Confidence 34433389999999986432 3577777776543222223459999999999999999999998864
No 44
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=92.26 E-value=0.42 Score=53.68 Aligned_cols=68 Identities=19% Similarity=0.147 Sum_probs=46.0
Q ss_pred HHhcCCCCcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 520 FLRRQPKERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 520 ~L~~~~~g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|.+....|+.+.|.|+++... ..|+++++++.-+........|++||+|+|+|.++|+.++.|.|...
T Consensus 287 ~~~~~~vG~vv~G~V~~I~~fGvFVeL~~gieGLvh~SeLs~~~v~~~~~~~kvGd~V~VkIi~ID~e~rrI~LSlK 363 (486)
T PRK07899 287 FARTHAIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363 (486)
T ss_pred hHHhcCCCCEEEEEEEEEeccEEEEEeCCCcEEEEEHHHcCcccccCccceeCCCCEEEEEEEEEECCCCEEEEEEE
Confidence 333333379999999985332 24555555554222212234589999999999999999999999864
No 45
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=92.15 E-value=0.42 Score=39.26 Aligned_cols=58 Identities=10% Similarity=0.032 Sum_probs=38.7
Q ss_pred CcEEEEEEEEEeeC----------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD----------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~----------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|.++..+ ..|++|++++.-+........|++||.|+++|.++|. +.|.|+.
T Consensus 4 G~iv~G~V~~i~~~~g~~v~l~~~~~Glvhis~~s~~~~~~~~~~~~~Gd~v~~kV~~~~~--~~i~LSl 71 (72)
T cd05704 4 GAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKD--GKYQLSL 71 (72)
T ss_pred CCEEEEEEEEeeCCcEEEEECCCCCEEEEEHHHhcCcccCCHHHhCCCCCEEEEEEEEecC--CEEEEEe
Confidence 68899999985432 2455666655333221112348999999999999984 7777753
No 46
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=91.86 E-value=0.32 Score=51.56 Aligned_cols=68 Identities=16% Similarity=0.240 Sum_probs=46.0
Q ss_pred HHHHhcC-C-CCcEEEEEEEEEeeCeeEEEEeecc-ceeEEE--------Ee---CccCCCCCEEEEEEEeeeCCCCeEE
Q 007798 518 IEFLRRQ-P-KERQYRALILRFIKDRTAALLLVEV-GLQAAA--------WV---SVGAQIGDEVEVKVEEAHPRDDIIY 583 (589)
Q Consensus 518 ~~~L~~~-~-~g~~~~a~V~~~~~~~~~~V~l~~l-g~~~~~--------~~---~~~~~lGd~V~V~I~~vD~~~~~i~ 583 (589)
|+|..+. + .|....|.|..+. +..++|.|.++ |+++.. +. ..-+++||.|.|+|.+||+.++.|+
T Consensus 7 cr~~~~~~P~~GdvV~g~V~~I~-d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~Id 85 (319)
T PTZ00248 7 CRFYEQKFPEEDDLVMVKVVRIT-EMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYID 85 (319)
T ss_pred ccchhhhCCCCCCEEEEEEEEEe-CCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEE
Confidence 3444443 3 2789999999853 33344555544 444432 11 1348999999999999999999999
Q ss_pred EEE
Q 007798 584 LKE 586 (589)
Q Consensus 584 ~~~ 586 (589)
|..
T Consensus 86 LS~ 88 (319)
T PTZ00248 86 LSK 88 (319)
T ss_pred EEe
Confidence 974
No 47
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=91.65 E-value=0.9 Score=53.35 Aligned_cols=62 Identities=24% Similarity=0.272 Sum_probs=46.8
Q ss_pred CCCCcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 524 QPKERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 524 ~~~g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
+. |+.|.|.|+++.+. ..|++|++++.-+...+....|++||.|+|+|.++|+. ++|.|+..
T Consensus 620 ~v-G~v~~G~V~~I~~fGafVei~~~~~GllhiSels~~~v~~~~~v~kvGD~V~VkV~~iD~~-grI~LS~k 690 (693)
T PRK11824 620 EV-GEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKR-GRIRLSRK 690 (693)
T ss_pred cC-CeEEEEEEEEEECCeEEEEECCCCEEEEEeeeccCccccCccceeCCCCEEEEEEEEECCC-CcEEEEEE
Confidence 44 79999999995332 46778888775443333345589999999999999987 99998753
No 48
>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=91.63 E-value=0.91 Score=39.54 Aligned_cols=59 Identities=10% Similarity=0.116 Sum_probs=38.2
Q ss_pred cEEEEEEEEEeeC--------eeEEEEeeccceeEEEE-----------eCccCCCCCEEEEEEEeeeCCCC-----eEE
Q 007798 528 RQYRALILRFIKD--------RTAALLLVEVGLQAAAW-----------VSVGAQIGDEVEVKVEEAHPRDD-----IIY 583 (589)
Q Consensus 528 ~~~~a~V~~~~~~--------~~~~V~l~~lg~~~~~~-----------~~~~~~lGd~V~V~I~~vD~~~~-----~i~ 583 (589)
+++.|.|+++... ..|++++.++.-+.... .+..|++||.|+|+|.++|...+ .+.
T Consensus 1 ~vv~g~V~~i~~~GifV~l~~v~G~v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~Gd~v~vkI~~vd~~~~~~~~~~i~ 80 (99)
T cd04460 1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAVSLKERRPRESKIG 80 (99)
T ss_pred CEEEEEEEEEEeccEEEEEcCeEEEEEEEEccCCceEechhheeecccCcCCEECCCCEEEEEEEEEeHHHCcCCCceEE
Confidence 3578888885332 34666666664332111 12458999999999999998753 566
Q ss_pred EEE
Q 007798 584 LKE 586 (589)
Q Consensus 584 ~~~ 586 (589)
++.
T Consensus 81 ls~ 83 (99)
T cd04460 81 LTM 83 (99)
T ss_pred EEE
Confidence 654
No 49
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=90.99 E-value=0.54 Score=48.69 Aligned_cols=59 Identities=22% Similarity=0.152 Sum_probs=42.7
Q ss_pred CcEEEEEEEEEeeCeeEEEEeecc-ceeEEEEe-----------CccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKDRTAALLLVEV-GLQAAAWV-----------SVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~l-g~~~~~~~-----------~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|+++. +....|.+.++ |+++..+. ...+++||.|.|+|.++|..++.|+|+.
T Consensus 9 GdiV~G~V~~I~-~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSl 79 (262)
T PRK03987 9 GELVVGTVKEVK-DFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSL 79 (262)
T ss_pred CCEEEEEEEEEE-CCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEE
Confidence 789999999853 33344556554 44443211 2347999999999999999999999875
No 50
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=90.62 E-value=0.71 Score=49.11 Aligned_cols=61 Identities=11% Similarity=0.044 Sum_probs=44.2
Q ss_pred CcEEEEEEEEEeeC--------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKD--------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~--------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+.+.|.|+++... ..|+++++++..+........|++||.|+|+|.++|..++.|.|...
T Consensus 197 G~vv~G~V~~I~~~G~fV~i~gv~Gllhisels~~~~~~~~~~~~vGd~VkvkVl~iD~e~~rI~LS~K 265 (318)
T PRK07400 197 GEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTK 265 (318)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHcccccccChhhccCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence 79999999985332 23555555554332222234589999999999999999999998753
No 51
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=90.03 E-value=1.4 Score=49.56 Aligned_cols=60 Identities=13% Similarity=0.164 Sum_probs=40.8
Q ss_pred CcEEEEEEEEEeeCe--------eEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKDR--------TAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~~--------~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|+++...+ .|+|+++++...........|++||.|+|+|.++|+.++.|.|..
T Consensus 209 G~iv~G~V~~i~~~G~FVdlggv~Glv~~Sels~~~v~~~~~~~kvGd~V~vkVl~iD~e~~rI~LSl 276 (486)
T PRK07899 209 GQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSL 276 (486)
T ss_pred CCEEEEEEEEEECCeEEEEECCEEEEEEHHHCCCcccCCHHHhcCCCCEEEEEEEEEECCCCEEEEEE
Confidence 799999999864322 334444444321111112348999999999999999999988875
No 52
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=89.04 E-value=1 Score=50.80 Aligned_cols=61 Identities=16% Similarity=0.138 Sum_probs=43.5
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeecccee-EEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQ-AAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~-~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+.+.|.|+++... ..|+|+++++... ...+....+++||.|+|+|.++|+.++.|.|...
T Consensus 293 G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K 363 (491)
T PRK13806 293 GDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363 (491)
T ss_pred CCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEe
Confidence 79999999985332 2456666665421 1111224589999999999999999999988753
No 53
>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=88.41 E-value=1.1 Score=52.38 Aligned_cols=57 Identities=25% Similarity=0.295 Sum_probs=42.7
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYL 584 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~ 584 (589)
|+.+.|.|+++... ..|++|++++.-+...+....|++||.|+|+|.++|. ++.|+|
T Consensus 619 G~i~~G~V~~I~~~GafVei~~g~~GllHiSei~~~~v~~~~~~~kvGD~V~VkVi~id~-~gki~L 684 (684)
T TIGR03591 619 GKIYEGKVVRIMDFGAFVEILPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDK-QGRIKL 684 (684)
T ss_pred CcEEEEEEEEEeCCEEEEEECCCcEEEEEHHHcCCCcccChhhccCCCCEEEEEEEEECC-CCCccC
Confidence 79999999995322 4677888877544333444568999999999999998 677654
No 54
>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=88.28 E-value=1.3 Score=37.37 Aligned_cols=60 Identities=17% Similarity=0.064 Sum_probs=39.0
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeecccee----EEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQ----AAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~----~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+...|.|+++... .+|+++++++..+ ........+++||.|.++|.++|.. +.+.|+..
T Consensus 7 GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~~ 79 (86)
T cd05789 7 GDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHTR 79 (86)
T ss_pred CCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEeC
Confidence 68999999985332 2344554444210 0001122489999999999999987 88888753
No 55
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=88.13 E-value=1.8 Score=46.98 Aligned_cols=62 Identities=19% Similarity=0.138 Sum_probs=40.5
Q ss_pred CCCCcEEEEEEEEEeeCe--------eEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 524 QPKERQYRALILRFIKDR--------TAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 524 ~~~g~~~~a~V~~~~~~~--------~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
.. |+.+.|.|+++...+ .|+++++++...........|++||.|+++|.++|+.++.|.|..
T Consensus 191 ~~-G~~v~g~V~~v~~~G~fV~l~~v~g~v~~sels~~~~~~~~~~~~vGd~i~~~Vl~vd~~~~~i~lS~ 260 (390)
T PRK06676 191 KE-GDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSL 260 (390)
T ss_pred CC-CCEEEEEEEEEecceEEEEeCCeEEEEEHHHcCccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 45 799999999854322 233333333221111112348999999999999999999888764
No 56
>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=88.09 E-value=3.2 Score=34.42 Aligned_cols=59 Identities=10% Similarity=-0.013 Sum_probs=39.6
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccceeEEEEe-----CccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVGLQAAAWV-----SVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~-----~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|....|.|..+.. ....|.+.--|+.+.... ...+++||.|.++|.++|..++.+.+..
T Consensus 5 G~~v~g~V~si~d-~G~~v~~g~~gv~Gfl~~~~~~~~~~~~~Gq~v~~~V~~vd~~~~~v~ls~ 68 (74)
T cd05694 5 GMVLSGCVSSVED-HGYILDIGIPGTTGFLPKKDAGNFSKLKVGQLLLCVVEKVKDDGRVVSLSA 68 (74)
T ss_pred CCEEEEEEEEEeC-CEEEEEeCCCCcEEEEEHHHCCcccccCCCCEEEEEEEEEECCCCEEEEEE
Confidence 6788899887532 222333311134443322 1458999999999999999999998865
No 57
>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=87.99 E-value=1.5 Score=42.54 Aligned_cols=67 Identities=10% Similarity=0.084 Sum_probs=42.9
Q ss_pred HHHhcCCCCcEEEEEEEEEeeCe--------eEEEEeeccceeEE----------E-EeCccCCCCCEEEEEEEeee---
Q 007798 519 EFLRRQPKERQYRALILRFIKDR--------TAALLLVEVGLQAA----------A-WVSVGAQIGDEVEVKVEEAH--- 576 (589)
Q Consensus 519 ~~L~~~~~g~~~~a~V~~~~~~~--------~~~V~l~~lg~~~~----------~-~~~~~~~lGd~V~V~I~~vD--- 576 (589)
.+++... |+.++|.|+++...+ .|+++.+++.-+.. . ..+..+++||.|+|+|.++|
T Consensus 75 i~f~p~~-gEvv~G~V~~v~~~GifV~lg~~~gi~~~~~l~~~~~~~d~~~~~~~~~~~~~~~~~Gd~VrvrV~~v~~~~ 153 (179)
T TIGR00448 75 LVFKPEL-GEIVEGEVIEIVEFGAFVSLGPFDGLFHVSQVTDDYCYYDPKESALIGKETKKVLDEGDKVRARIVALSLKD 153 (179)
T ss_pred EEEeccC-CCEEEEEEEEEEeeEEEEEeCCceEEEEcHHhCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEccC
Confidence 4566677 799999999964432 34444444421110 0 12356999999999999999
Q ss_pred --CCCCeEEEEE
Q 007798 577 --PRDDIIYLKE 586 (589)
Q Consensus 577 --~~~~~i~~~~ 586 (589)
|....|.++.
T Consensus 154 ~~~~~~~I~lt~ 165 (179)
T TIGR00448 154 RRPEGSKIGLTM 165 (179)
T ss_pred CCCCcceEEEEe
Confidence 5556665544
No 58
>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=87.85 E-value=5.3 Score=31.85 Aligned_cols=57 Identities=18% Similarity=0.184 Sum_probs=38.7
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccceeEEEEeC---------ccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVGLQAAAWVS---------VGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~~---------~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.++|.|..+.. ....|.+. |+++..... ....+||.++++|.++|...+.|.++.
T Consensus 1 G~iv~g~V~~v~~-~G~~v~l~--g~~gfip~s~~~~~~~~~~~~~vG~~i~~~i~~vd~~~~~i~lS~ 66 (67)
T cd04465 1 GEIVEGKVTEKVK-GGLIVDIE--GVRAFLPASQVDLRPVEDLDEYVGKELKFKIIEIDRERNNIVLSR 66 (67)
T ss_pred CCEEEEEEEEEEC-CeEEEEEC--CEEEEEEHHHCCCcccCChHHhCCCEEEEEEEEEeCCCCEEEEEc
Confidence 5788999988643 33345552 555543220 112489999999999999999998764
No 59
>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=87.13 E-value=1.7 Score=49.02 Aligned_cols=60 Identities=15% Similarity=0.114 Sum_probs=43.7
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.++|.|+++.+. ..|+++.+++.-+........|++||.|+++|.++|..++.|.|..
T Consensus 447 G~~v~g~V~~v~~~G~fV~l~~~~~Glv~~s~l~~~~~~~~~~~~~~Gd~v~~~V~~id~~~~~i~ls~ 515 (516)
T TIGR00717 447 GSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSV 515 (516)
T ss_pred ceEEEEEEEEEecceEEEEcCCCeEEEEEHHHcCccccccccccCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 79999999985332 2455555554433222334569999999999999999999999874
No 60
>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=86.74 E-value=2.1 Score=35.80 Aligned_cols=61 Identities=15% Similarity=-0.016 Sum_probs=38.3
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEec
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEVV 588 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v~ 588 (589)
|....|.|+++..+ .+|.+++.++..+........+++||.|.++|.++|.. +.+.|+...
T Consensus 7 GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~LS~~~ 76 (82)
T cd04454 7 GDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLLTTAD 76 (82)
T ss_pred CCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEEEECC
Confidence 68889999985322 12333333221111111123489999999999999986 888887653
No 61
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=85.85 E-value=2.1 Score=46.50 Aligned_cols=61 Identities=20% Similarity=0.137 Sum_probs=40.8
Q ss_pred CcEEEEEEEEEeeCe---------eEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKDR---------TAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~~---------~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+.+.|.|.++...+ .|+++++++.-.........|++||.|+|+|.++|+.++.|.|...
T Consensus 278 G~~v~g~V~~i~~~G~fV~l~~gi~Glv~~se~~~~~~~~~~~~~~~Gd~v~v~V~~id~e~~~i~ls~k 347 (390)
T PRK06676 278 GDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK 347 (390)
T ss_pred CcEEEEEEEEEeCceEEEEECCCCeEEEEhHHcCccccCChhhccCCCCEEEEEEEEEECCCCEEEEEEE
Confidence 799999999853321 2333443332111111123489999999999999999999999854
No 62
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=85.68 E-value=1.6 Score=49.51 Aligned_cols=60 Identities=20% Similarity=0.194 Sum_probs=44.6
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|....|.|+.+... .+|+||++++.-........-++.||.|.|+|.++|+.++.|.+..
T Consensus 278 g~~v~G~Vt~i~~~GafVei~~GvEGlvhvSEisw~~~~~P~evv~~Gq~V~V~Vl~id~e~rRIsL~i 346 (541)
T COG0539 278 GDKVEGKVTNLTDYGAFVEIEEGVEGLVHVSEISWTKKNVPSEVVKVGQEVEVKVLDIDPERRRISLGL 346 (541)
T ss_pred CCEEEEEEEEeecCcEEEEecCCccceeechhhcccccCCHHHhcccCCEEEEEEEeeCchhceEEeee
Confidence 78999999985322 4678888876322222222448999999999999999999998864
No 63
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=85.60 E-value=1.9 Score=50.35 Aligned_cols=61 Identities=15% Similarity=0.123 Sum_probs=42.1
Q ss_pred CcEEEEEEEEEeeCe---------eEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKDR---------TAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~~---------~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|+++.|.|.++...+ .|+++++++..+........|++||.|+|+|.++|+.++.|.|...
T Consensus 563 G~~v~g~V~~i~~~G~fV~l~~~i~Gli~~sel~~~~~~~~~~~~kvGd~V~vkV~~id~e~~rI~lslk 632 (647)
T PRK00087 563 GSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632 (647)
T ss_pred CeEEEEEEEEEECCeEEEEECCCCEEEEEhhhcCccccCCHhhcCCCCCEEEEEEEEEeCCCCEEEEEEe
Confidence 799999999854322 2444444433221112224589999999999999999999998753
No 64
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=85.28 E-value=2.3 Score=48.53 Aligned_cols=60 Identities=15% Similarity=0.048 Sum_probs=43.0
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEE-EEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAA-AWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~-~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|.++... ..|+++++++..... ......|++||.|+++|.++|+.++.|.|..
T Consensus 374 G~~v~g~V~~v~~~G~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd~~~~~i~ls~ 443 (565)
T PRK06299 374 GDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVDVEKERISLGI 443 (565)
T ss_pred CCEEEEEEEEEecceEEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 79999999985322 345555555543222 1223458999999999999999999998874
No 65
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=85.07 E-value=3.1 Score=49.99 Aligned_cols=68 Identities=7% Similarity=-0.021 Sum_probs=45.6
Q ss_pred HHhcCCCCcEEEEEEEEEeeC---------eeEEEEeeccceeEEE---EeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 520 FLRRQPKERQYRALILRFIKD---------RTAALLLVEVGLQAAA---WVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 520 ~L~~~~~g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~---~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|.+....|+.++|.|+++... ..|+++++++.-+... .....|++||.|+|+|.++|+.++.|.|..-
T Consensus 746 ~~~~~~vG~iV~GkV~~v~~~GvFVeL~~gVeGlI~~s~lsdd~~~~~~~~~~~f~vGD~V~v~Vl~iD~~~rkI~LSlk 825 (863)
T PRK12269 746 FANAYGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRKYAVGDRVKAVIVDMNVKDRKVAFSVR 825 (863)
T ss_pred HHhhCCCCCEEEEEEEEEecCeEEEEcCCCeEEEEEHHHcCCcccccchhhccccCCCCEEEEEEEEEEcCCCEEEEEEe
Confidence 444433379999999995332 2344555444322211 1123589999999999999999999999753
No 66
>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=84.93 E-value=1.4 Score=51.51 Aligned_cols=58 Identities=9% Similarity=0.195 Sum_probs=41.3
Q ss_pred CcEEEEEEEEEee---------CeeEEEEeeccc----eeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 527 ERQYRALILRFIK---------DRTAALLLVEVG----LQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 527 g~~~~a~V~~~~~---------~~~~~V~l~~lg----~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
|+.+.|.|..+.. ..+|+||++++. -.........+++||.|+|+|.++|. ++.|.|.
T Consensus 648 G~i~~GkV~~I~dfGaFVel~~G~eGLvHISeisdls~~~rv~~~~dv~kvGd~V~VKVl~ID~-~gKI~L~ 718 (719)
T TIGR02696 648 GERFLGTVVKTTAFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLSVGQKIQVEIADIDD-RGKLSLV 718 (719)
T ss_pred CCEEEEEEEEEECceEEEEecCCceEEEEhhhccccccccCcCCHHHcCCCCCEEEEEEEEECC-CCCeeec
Confidence 7999999998532 147888888762 11111222358999999999999995 7788764
No 67
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=84.92 E-value=5.2 Score=34.47 Aligned_cols=58 Identities=14% Similarity=0.224 Sum_probs=41.6
Q ss_pred cEEEEEEEEEeeCeeEEEEeeccceeEEE------Ee-CccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 528 RQYRALILRFIKDRTAALLLVEVGLQAAA------WV-SVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 528 ~~~~a~V~~~~~~~~~~V~l~~lg~~~~~------~~-~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
-+++|+|+..+.+....|.+++ |....+ +. ...+.+||+|.|++..-|+.++.|.+.-
T Consensus 7 ie~~G~V~e~Lp~~~frV~Len-G~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~ 71 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLEN-GVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRH 71 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeCC-CCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEEe
Confidence 4688999987666665666653 433322 22 2357899999999999999999998753
No 68
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=83.52 E-value=4.2 Score=45.89 Aligned_cols=60 Identities=17% Similarity=0.131 Sum_probs=40.3
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCC----eEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDD----IIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~----~i~~~~ 586 (589)
|+.++|.|+++... ..|+|+++++...........|++||.|+|+|.++|...+ .|.+..
T Consensus 203 G~iv~G~V~~v~~~G~fV~l~~gv~g~v~~sels~~~~~~~~~~~~vGd~i~vkVl~id~~~~~~~~ri~lS~ 275 (491)
T PRK13806 203 GDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSI 275 (491)
T ss_pred CCEEEEEEEEEeCCeEEEEcCCCcEEEEEHHHCCCccccChhHhcCCCCEEEEEEEEEecccCCcceEEEEEe
Confidence 79999999985332 2355555555433222223458999999999999999763 566653
No 69
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=81.43 E-value=22 Score=40.05 Aligned_cols=67 Identities=16% Similarity=0.083 Sum_probs=45.1
Q ss_pred HHHHHHhcCCCCcEEEEEEEEEeeCeeEEEEeeccceeEEEEe-----CccCCCCCEEEEEEEeeeCCCC--eEEEEE
Q 007798 516 WIIEFLRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWV-----SVGAQIGDEVEVKVEEAHPRDD--IIYLKE 586 (589)
Q Consensus 516 ~~~~~L~~~~~g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~-----~~~~~lGd~V~V~I~~vD~~~~--~i~~~~ 586 (589)
-...-++.+. |+...|+|.++.+.+ ..|-+. |.++.... +..|++||+|++.|.+||...+ +|-+..
T Consensus 125 ~i~~eyk~~~-GeIV~G~V~ri~~~g-iiVDLg--gvea~LP~sE~ip~E~~~~GdrIka~I~~Vd~~~kg~qIilSR 198 (470)
T PRK09202 125 RVYEEYKDRV-GEIITGVVKRVERGN-IIVDLG--RAEAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSR 198 (470)
T ss_pred HHHHHHHhhc-CCEEEEEEEEEecCC-EEEEEC--CeEEEecHHHcCCCccCCCCCEEEEEEEEEecCCCCCeEEEEe
Confidence 3344455556 699999999865432 333332 45554322 3469999999999999999877 776654
No 70
>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=81.35 E-value=4.1 Score=34.97 Aligned_cols=59 Identities=14% Similarity=0.039 Sum_probs=37.0
Q ss_pred CcEEEEEEEEEeeC-----------eeEEEEeeccceeEEEEe---CccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 527 ERQYRALILRFIKD-----------RTAALLLVEVGLQAAAWV---SVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 527 g~~~~a~V~~~~~~-----------~~~~V~l~~lg~~~~~~~---~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
|+.+.|.|+.+... ..|+++++++......+. ...++.||.|.|+|.+.........++
T Consensus 8 G~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~~~~~~K~~~lt 80 (88)
T cd04453 8 GNIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTKGPRLT 80 (88)
T ss_pred CCEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEEecCCCCCceEE
Confidence 78999999986542 245556655422110111 234899999999999977655544443
No 71
>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=81.23 E-value=4.4 Score=32.76 Aligned_cols=54 Identities=13% Similarity=0.050 Sum_probs=31.7
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeE--EEEeCccCCCCCEEEEEEEeeeCCCC
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQA--AAWVSVGAQIGDEVEVKVEEAHPRDD 580 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~--~~~~~~~~~lGd~V~V~I~~vD~~~~ 580 (589)
|....|.|+.+... .+|.+++.++..+. .......|++||.|+++|.++|..+.
T Consensus 1 G~iV~g~V~~i~~~gi~v~l~~~i~g~i~~~~i~~~~~~~~~~~~~~~~Gd~i~~kVl~~d~~~~ 65 (70)
T cd05702 1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKT 65 (70)
T ss_pred CCEEEEEEEEEECCcEEEEeCCCcEEEEEHHHhccccccccChhHhCCCCCEEEEEEEEEeCccc
Confidence 46778888875322 23334444332211 00111348999999999999997643
No 72
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=79.64 E-value=9.6 Score=45.95 Aligned_cols=60 Identities=17% Similarity=0.124 Sum_probs=41.2
Q ss_pred CcEEEEEEEEEeeC--------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD--------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~--------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|.++.+. ..|+++++++......+....+++||.|+|+|.++|+.++.|.+..
T Consensus 494 G~~V~G~Vk~i~~~G~fVdl~Gv~Gfvp~SeiS~~~v~~~~~~~kvGq~v~vkVi~iD~e~~rI~LSl 561 (863)
T PRK12269 494 EDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSL 561 (863)
T ss_pred CCEEEEEEEEEeCCcEEEEECCEEEEEEchhccccccCCHHHhccCCCEEEEEEEEEecCCCeEEEEE
Confidence 78999999985432 2345555544322111222347899999999999999999988874
No 73
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=79.50 E-value=8.4 Score=41.03 Aligned_cols=59 Identities=10% Similarity=0.038 Sum_probs=39.3
Q ss_pred CcEEEEEEEEEeeCe---------eEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 527 ERQYRALILRFIKDR---------TAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 527 g~~~~a~V~~~~~~~---------~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
|+...|.|+.+..++ .|+++++++...........+++||.|++.|.++|...+.+.+.
T Consensus 32 G~iv~G~V~~i~~~g~~Vdig~k~~g~lp~sEis~~~~~~~~~~~~~G~~v~~~Vi~~~~~~~~i~lS 99 (318)
T PRK07400 32 GDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLS 99 (318)
T ss_pred CCEEEEEEEEEECCEEEEEECCCeEEEEEHHHhccccccCHHHccCCCCEEEEEEEEEeCCCCeEEEe
Confidence 799999999854332 23344443332221111234899999999999999998888775
No 74
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=78.73 E-value=12 Score=30.77 Aligned_cols=55 Identities=15% Similarity=0.157 Sum_probs=38.9
Q ss_pred EEEEEEEEEeeCeeEEEEeeccceeEEEEe-------CccCCCCCEEEEEEEeeeCCCCeEEE
Q 007798 529 QYRALILRFIKDRTAALLLVEVGLQAAAWV-------SVGAQIGDEVEVKVEEAHPRDDIIYL 584 (589)
Q Consensus 529 ~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~-------~~~~~lGd~V~V~I~~vD~~~~~i~~ 584 (589)
++.|.|+..+......|.+++ |.+..++. ...+.+||+|.|.+..-|+.++.|-+
T Consensus 6 e~~G~V~e~L~~~~f~V~l~n-g~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd~tkgrIi~ 67 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELEN-GHEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRITY 67 (68)
T ss_pred EEEEEEEEECCCCEEEEEECC-CCEEEEEecCcchhccEEECCCCEEEEEECcccCCcEeEEe
Confidence 578999886655555566653 44433322 22378999999999999999988865
No 75
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=77.52 E-value=12 Score=43.71 Aligned_cols=58 Identities=16% Similarity=0.212 Sum_probs=38.1
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccceeEEE-----------EeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVGLQAAA-----------WVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~-----------~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+...|.|.++.++ ...|.+. .+.++.. .....|++||+|+++|.++|..++++.+..
T Consensus 303 G~iV~G~V~~v~~~-gv~Vdig-~~~~G~lp~~els~~~~~~~~~~~~vGd~V~v~V~~vd~~~g~i~LS~ 371 (647)
T PRK00087 303 GDIVKGTVVSVNEN-EVFVDVG-YKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSK 371 (647)
T ss_pred CCEEEEEEEEEECC-EEEEEEC-CCeEEEEEHHHhcccccCChhhccCCCCEEEEEEEEEECCCCcEEEEe
Confidence 79999999986443 2223331 1112211 112348999999999999998888887764
No 76
>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=76.98 E-value=42 Score=36.19 Aligned_cols=61 Identities=15% Similarity=0.074 Sum_probs=40.5
Q ss_pred cCCCCcEEEEEEEEEeeCeeEEEEeeccceeEEEEe-----CccCCCCCEEEEEEEeeeCC--CCeEEEEE
Q 007798 523 RQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWV-----SVGAQIGDEVEVKVEEAHPR--DDIIYLKE 586 (589)
Q Consensus 523 ~~~~g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~-----~~~~~lGd~V~V~I~~vD~~--~~~i~~~~ 586 (589)
.+. |+..+|+|.++.+.+...|-+. +.++.... +..|++||+|++.|.+|+.. ..+|-++.
T Consensus 129 ~k~-GeiV~G~V~~v~~~g~v~VdiG--~~ea~LP~~E~ip~E~~~~Gd~ik~~V~~V~~~~kg~qIivSR 196 (341)
T TIGR01953 129 SKE-GEIISGTVKRVNRRGNLYVELG--KTEGILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSR 196 (341)
T ss_pred hhc-CCEEEEEEEEEecCCcEEEEEC--CeEEEecHHHcCCCcCCCCCCEEEEEEEEEEcCCCCCeEEEEe
Confidence 345 6999999998654333234442 45554322 34599999999999999944 45676654
No 77
>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=76.47 E-value=4.3 Score=35.74 Aligned_cols=27 Identities=22% Similarity=0.085 Sum_probs=23.1
Q ss_pred ccCCCCCEEEEEEEeeeCC---CCeEEEEE
Q 007798 560 VGAQIGDEVEVKVEEAHPR---DDIIYLKE 586 (589)
Q Consensus 560 ~~~~lGd~V~V~I~~vD~~---~~~i~~~~ 586 (589)
..|++||.|+++|.++|.. ++.|.+..
T Consensus 65 ~~f~vGd~V~~kVi~~d~~~~~~~~i~LSl 94 (100)
T cd05693 65 DLFSVGQLVRCKVVSLDKSKSGKKRIELSL 94 (100)
T ss_pred HhccCCCEEEEEEEEccCCcCCCcEEEEEe
Confidence 3489999999999999997 78888764
No 78
>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=75.78 E-value=7.8 Score=43.72 Aligned_cols=60 Identities=15% Similarity=0.102 Sum_probs=41.3
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEE-eCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAW-VSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~-~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.+.|.|..+... ..|+|+++++....... ....|++||.|.++|.++|+.++.|.|..
T Consensus 360 G~~v~g~V~~v~~~G~fV~l~~~v~glv~~s~ls~~~~~~~~~~~~~~G~~V~~~Vl~vd~~~~~i~ls~ 429 (516)
T TIGR00717 360 GDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGV 429 (516)
T ss_pred CCEEEEEEEEEecceEEEECCCCCEEEEEHHHCcCcccCCCHhHccCCCCEEEEEEEEEeCcCCEEEEee
Confidence 79999999985322 24455555442211111 12458999999999999999999998864
No 79
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=75.57 E-value=9.7 Score=43.56 Aligned_cols=60 Identities=17% Similarity=0.189 Sum_probs=40.0
Q ss_pred CcEEEEEEEEEeeCe--------eEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKDR--------TAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~~--------~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+..+|.|+.+...+ .|+++++++...........|++||.|.|+|.++|+.++.|.|..
T Consensus 202 G~iv~g~V~~v~~~G~~V~i~g~~glv~~se~s~~~~~~~~~~~kvG~~v~v~V~~~d~~~~~i~lS~ 269 (565)
T PRK06299 202 GQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGL 269 (565)
T ss_pred CCEEEEEEEEEeCCeEEEEECCEEEEEEHHHhcccccCCHhhcCCCCCEEEEEEEEEeCCCCeEEEEE
Confidence 799999999854322 233343333221111112348999999999999999999998875
No 80
>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=75.10 E-value=15 Score=29.53 Aligned_cols=56 Identities=16% Similarity=0.109 Sum_probs=35.6
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccceeEEEEe-----CccCCCCCEEEEEEEeeeCCC--CeEEEE
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVGLQAAAWV-----SVGAQIGDEVEVKVEEAHPRD--DIIYLK 585 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~-----~~~~~lGd~V~V~I~~vD~~~--~~i~~~ 585 (589)
|+..+|.|.+..+. ...|-+. +.++.... +..+++||+|+|.|.+++... .+|.+.
T Consensus 4 g~iV~G~V~~~~~~-~~~vdig--~~eg~lp~~e~~~~~~~~~Gd~v~v~v~~v~~~~~~~~i~lS 66 (67)
T cd04455 4 GEIVTGIVKRVDRG-NVIVDLG--KVEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKGPQIILS 66 (67)
T ss_pred CCEEEEEEEEEcCC-CEEEEcC--CeEEEeeHHHCCCCCcCCCCCEEEEEEEEEecCCCCCEEEEe
Confidence 68889999985442 2233332 23333211 245899999999999999654 455543
No 81
>PHA02858 EIF2a-like PKR inhibitor; Provisional
Probab=74.67 E-value=11 Score=32.39 Aligned_cols=58 Identities=19% Similarity=0.322 Sum_probs=42.3
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccceeEEEE-----------e-CccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVGLQAAAW-----------V-SVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~-----------~-~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|....+++. +++....|.|.++|+++-.- . ++.+ .|-.+.|+|.+||..+|-||+..+
T Consensus 17 ~dvv~~Vv~--i~d~~~YV~LleY~iegmIl~~selsr~rirsi~kll-VGk~e~v~ViRVDk~KGYIDLs~~ 86 (86)
T PHA02858 17 NEVTKGIVF--VKDNIFYVKLIDYGLEALIVNYVNVNADRAEKLKKKL-VGKTINVQVIRTDKLKGYIDVRHV 86 (86)
T ss_pred CeEEEEEEE--EeccEEEEEEecCccceEEecHHHHhHHHHHhhhhhh-cCCeeEEEEEEECCCCCEEEeEcC
Confidence 355555543 46667778999998775421 1 2345 999999999999999999999753
No 82
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=74.30 E-value=4.5 Score=47.50 Aligned_cols=61 Identities=15% Similarity=0.079 Sum_probs=45.5
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEEe
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKEV 587 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~v 587 (589)
|...+|+|..+... ..|+||++.+.-.....-...+++||.|+|+|.+||..+..|.+...
T Consensus 659 Gm~leg~Vrnv~~fgafVdIgv~qDglvHis~ls~~fv~~P~~vv~vGdiV~v~V~~vD~~r~rI~Lsmr 728 (780)
T COG2183 659 GMILEGTVRNVVDFGAFVDIGVHQDGLVHISQLSDKFVKDPNEVVKVGDIVKVKVIEVDTARKRIALSMR 728 (780)
T ss_pred CCEEEEEEEEeeeccceEEeccccceeeeHHHhhhhhcCChHHhcccCCEEEEEEEEEecccCeeeeEee
Confidence 67888988875322 46778888765443332234589999999999999999999998753
No 83
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=71.45 E-value=68 Score=34.91 Aligned_cols=65 Identities=14% Similarity=0.095 Sum_probs=41.6
Q ss_pred HHHHHhcCCCCcEEEEEEEEEeeCeeEEEEeeccceeEEEE-----eCccCCCCCEEEEEEEeeeCCCC--eEEEE
Q 007798 517 IIEFLRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAW-----VSVGAQIGDEVEVKVEEAHPRDD--IIYLK 585 (589)
Q Consensus 517 ~~~~L~~~~~g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~-----~~~~~~lGd~V~V~I~~vD~~~~--~i~~~ 585 (589)
.+.-++.+. |+...|+|.++.+. ...|-+. +.++... .+..|++||+|++.|.+|+...+ +|-++
T Consensus 126 v~~ef~~k~-GeiV~G~V~~~~~~-~~~Vdlg--~vEa~LP~~E~ip~e~~~~Gd~Ika~V~~V~~~~kgp~IivS 197 (362)
T PRK12327 126 IYNEFSERE-GDIVTGVVQRRDNR-FVYVNLG--KIEAVLPPAEQIPGETYKHGDRIKVYVVKVEKTTKGPQIFVS 197 (362)
T ss_pred HHHHHHHhc-CCEEEEEEEEEeCC-cEEEEeC--CeEEEecHHHcCCCCCCCCCCEEEEEEEEEecCCCCCeEEEE
Confidence 334445556 69999999985442 2233332 3554433 13569999999999999995543 45554
No 84
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=69.36 E-value=9 Score=44.41 Aligned_cols=59 Identities=22% Similarity=0.280 Sum_probs=45.1
Q ss_pred CcEEEEEEEEEe---------eCeeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFI---------KDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~---------~~~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+.|.|.|..+. ...+|+||++.+.-....+....++.||.|.||+..+|.. +.+++..
T Consensus 620 g~iy~G~V~ri~~fGaFv~l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~-Gri~ls~ 687 (692)
T COG1185 620 GEVYEGTVVRIVDFGAFVELLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQ-GRIRLSI 687 (692)
T ss_pred ccEEEEEEEEEeecceEEEecCCcceeEEehhhhhhhhhcccceeecCceEEEEEeeeccc-CCcccee
Confidence 799999998842 2367888888776554445567799999999999999964 6666654
No 85
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=67.48 E-value=16 Score=37.63 Aligned_cols=59 Identities=17% Similarity=0.064 Sum_probs=41.4
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccc-eeEEEEe-----------CccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVG-LQAAAWV-----------SVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg-~~~~~~~-----------~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|+..-|+|..+.. -.+.|.|.+++ .++.... ..-++.|+.|-++|.+||+.++.||+..
T Consensus 12 GEiVv~tV~~V~~-~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSl 82 (269)
T COG1093 12 GEIVVGTVKQVAD-YGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSL 82 (269)
T ss_pred CcEEEEEEEEeec-cccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeeh
Confidence 5677777776433 23346677764 5543221 1347899999999999999999999974
No 86
>PRK08563 DNA-directed RNA polymerase subunit E'; Provisional
Probab=67.25 E-value=23 Score=34.41 Aligned_cols=58 Identities=7% Similarity=0.090 Sum_probs=35.7
Q ss_pred hcCCCCcEEEEEEEEEeeCe--------eEEEEeeccceeEEE-----------EeCccCCCCCEEEEEEEeeeCCCC
Q 007798 522 RRQPKERQYRALILRFIKDR--------TAALLLVEVGLQAAA-----------WVSVGAQIGDEVEVKVEEAHPRDD 580 (589)
Q Consensus 522 ~~~~~g~~~~a~V~~~~~~~--------~~~V~l~~lg~~~~~-----------~~~~~~~lGd~V~V~I~~vD~~~~ 580 (589)
+... |+.+.|.|+++.+.+ .++++.+++.-+... .....+++||.|+++|.++|...+
T Consensus 78 ~P~~-GEVv~g~V~~v~~~Gi~V~lg~~~g~v~~~~l~~~~~~~d~~~~~~~~~~~~~~i~~Gd~VrvrV~~v~~~~~ 154 (187)
T PRK08563 78 KPEL-QEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISYDPKNGRLIGKESKRVLKVGDVVRARIVAVSLKER 154 (187)
T ss_pred eccC-CCEEEEEEEEEEccEEEEEEeCceEEEEcHHcCCCceEEccccceEEEccCCeEEcCCCEEEEEEEEEEcccC
Confidence 3445 799999999864432 233333333211100 112458999999999999997654
No 87
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=58.62 E-value=29 Score=29.23 Aligned_cols=57 Identities=14% Similarity=0.149 Sum_probs=38.3
Q ss_pred cEEEEEEEEEeeCeeEEEEeeccceeEEE------Ee-CccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 528 RQYRALILRFIKDRTAALLLVEVGLQAAA------WV-SVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 528 ~~~~a~V~~~~~~~~~~V~l~~lg~~~~~------~~-~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
-+..|.|+..+-.+..-|.+++ |....+ +. ...+.+||.|.|++...|..++.|.+.
T Consensus 7 ~e~~g~V~e~L~~~~f~v~~ed-g~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~d~~kg~I~~R 70 (75)
T COG0361 7 IEMEGTVIEMLPNGRFRVELEN-GHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYR 70 (75)
T ss_pred cEEEEEEEEecCCCEEEEEecC-CcEEEEEccCcchheeEEeCCCCEEEEEecccccccccEEEE
Confidence 4678888876554444455443 333322 22 234789999999999999988888765
No 88
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=58.08 E-value=47 Score=27.80 Aligned_cols=47 Identities=26% Similarity=0.375 Sum_probs=34.5
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCC
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPR 578 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~ 578 (589)
|++++-.|..+-+.+.|..++. |+- -+-...+.||+|+|+|.+|-+.
T Consensus 16 Ge~y~V~I~d~g~~GDGiarve--Gfv---VFVp~a~~Gd~V~vkI~~v~~~ 62 (73)
T COG3269 16 GETYEVEIEDVGDQGDGIARVE--GFV---VFVPGAEVGDEVKVKITKVKPN 62 (73)
T ss_pred CCEEEEEEEEeccCCCceEEEE--EEE---EEeCCCCCCCeeeEEEEEeecc
Confidence 6788888887766677766666 432 2334679999999999998654
No 89
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=55.72 E-value=1.7e+02 Score=31.96 Aligned_cols=62 Identities=11% Similarity=0.185 Sum_probs=39.8
Q ss_pred HhcCCCCcEEEEEEEEEeeCeeEEEEeeccceeEEEEe-----CccCCCCCEEEEEEEeeeCCCC---eEEEE
Q 007798 521 LRRQPKERQYRALILRFIKDRTAALLLVEVGLQAAAWV-----SVGAQIGDEVEVKVEEAHPRDD---IIYLK 585 (589)
Q Consensus 521 L~~~~~g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~-----~~~~~lGd~V~V~I~~vD~~~~---~i~~~ 585 (589)
+..+. |+...|+|.++...+...|-+. +.+..... +..|++||++++-|.+|+...+ +|-+.
T Consensus 134 y~~~~-Geiv~g~V~r~~~~~~i~vdlg--~~ea~LP~~eqip~E~~~~Gdrik~~i~~V~~~~k~gp~IilS 203 (374)
T PRK12328 134 YKKKV-GKIVFGTVVRVDNEENTFIEID--EIRAVLPMKNRIKGEKFKVGDVVKAVLKRVKIDKNNGILIELS 203 (374)
T ss_pred HHHhc-CcEEEEEEEEEecCCCEEEEcC--CeEEEeCHHHcCCCCcCCCCCEEEEEEEEEecCCCCCCEEEEE
Confidence 34455 6999999998543232233332 34443322 3569999999999999997665 55444
No 90
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=48.18 E-value=41 Score=32.91 Aligned_cols=57 Identities=19% Similarity=0.166 Sum_probs=36.1
Q ss_pred CcEEEEEEEEEeeCeeEEEEeecc---------ceeEEEEe-----------CccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKDRTAALLLVEV---------GLQAAAWV-----------SVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~l---------g~~~~~~~-----------~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|....|.|+++.. ....|.|... +++...+. ...|++||.|.++|.++| +.+.|..
T Consensus 65 GdiV~GkV~~i~~-~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~~~~~~~~~~~~~~GD~V~akV~~i~---~~i~LS~ 140 (189)
T PRK09521 65 GDIVYGRVVDVKE-QRALVRIVSIEGSERELATSKLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYT---DPLQLST 140 (189)
T ss_pred CCEEEEEEEEEcC-CeEEEEEEEecccccccCCCceeeEEhhHcChhhhhhHHhccCCCCEEEEEEEecC---CcEEEEE
Confidence 7899999998643 3333444321 22222211 234899999999999999 5676654
Q ss_pred e
Q 007798 587 V 587 (589)
Q Consensus 587 v 587 (589)
.
T Consensus 141 k 141 (189)
T PRK09521 141 K 141 (189)
T ss_pred e
Confidence 3
No 91
>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=48.10 E-value=70 Score=25.02 Aligned_cols=50 Identities=14% Similarity=0.106 Sum_probs=27.8
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccceeEEEEeCccCCCCCEEEEEEEeeeCC
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVGLQAAAWVSVGAQIGDEVEVKVEEAHPR 578 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~~~~~~lGd~V~V~I~~vD~~ 578 (589)
|++.+-.|.+...++.+.-+.+. +.........+. +|+.|+|+|.++...
T Consensus 5 G~~~~VlVe~~~~~g~~~gr~~~-~~~V~v~~~~~~-iG~~v~v~I~~~~~~ 54 (61)
T PF01938_consen 5 GKTLEVLVEELGDEGQGIGRTDN-GKVVFVPGGLPL-IGEFVKVRITKAKKN 54 (61)
T ss_dssp TEEEEEEEEEE-TTSEEEEEET--TEEEEETT--T---TEEEEEEEEEE-SS
T ss_pred CcEEEEEEEEecCCCEEEEEeCC-CeEEEECCCCCC-CCCEEEEEEEEeeCC
Confidence 68888888875433555555553 211122222334 799999999999863
No 92
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=34.28 E-value=1.3e+02 Score=31.51 Aligned_cols=57 Identities=16% Similarity=0.269 Sum_probs=40.1
Q ss_pred CcEEEEEEEEEeeCeeEEEEeeccceeEEEEeC---ccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKDRTAALLLVEVGLQAAAWVS---VGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~~---~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
++.++|+|-++...+ ..|.+ +-++-+..+.. ..+++|++++++|.++.. ++.|+++.
T Consensus 156 nq~v~~tVYr~~~~G-~fv~~-e~~~~GfIh~sEr~~~prlG~~l~~rVi~~re-Dg~lnLSl 215 (287)
T COG2996 156 NQEVDATVYRLLESG-TFVIT-ENGYLGFIHKSERFAEPRLGERLTARVIGVRE-DGKLNLSL 215 (287)
T ss_pred cCeeeeEEEEEeccc-eEEEE-cCCeEEEEcchhhcccccCCceEEEEEEEEcc-CCeeeccc
Confidence 588999999864323 23344 44555544332 347899999999999998 89998864
No 93
>PF05800 GvpO: Gas vesicle synthesis protein GvpO; InterPro: IPR008634 This family consists of archaeal GvpO proteins which are required for gas vesicle synthesis []. The family also contain related sequences from bacteria.; GO: 0031412 gas vesicle organization
Probab=34.19 E-value=87 Score=27.87 Aligned_cols=24 Identities=25% Similarity=0.397 Sum_probs=18.5
Q ss_pred cceeEEEEecCCeEEEEEEEcCCc
Q 007798 205 DDALSAMRLQDGRIKVYIHVADPT 228 (589)
Q Consensus 205 DDAiSie~~~dG~~~l~VHIADvs 228 (589)
+-.+++++.+||+|++.|-|-...
T Consensus 39 e~V~~~~~~edgGW~v~VEVvE~~ 62 (100)
T PF05800_consen 39 EGVSSVERTEDGGWRVVVEVVEDR 62 (100)
T ss_pred ceEEEEeecCCCCeEEEEEEeeec
Confidence 335789999997899999876554
No 94
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=33.74 E-value=6.4e+02 Score=28.38 Aligned_cols=68 Identities=16% Similarity=0.173 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCcEEEEEEEEEeeCeeEEEEee-ccc---eeEEEEe-----CccCCCCCEEEEEEEee
Q 007798 505 ARRLSNTSLRYWIIEFLRRQPKERQYRALILRFIKDRTAALLLV-EVG---LQAAAWV-----SVGAQIGDEVEVKVEEA 575 (589)
Q Consensus 505 a~~aer~~~~~~~~~~L~~~~~g~~~~a~V~~~~~~~~~~V~l~-~lg---~~~~~~~-----~~~~~lGd~V~V~I~~v 575 (589)
.+++||+. ...-++.+. |+...|+|.++-+. ...|-+. ++| .+..... +..|++||+|++-|.+|
T Consensus 136 ire~ER~~----i~~ef~~~~-GeIV~G~V~r~e~~-~viv~l~~~~g~~~~EaiLP~~Eqip~E~y~~Gdrika~i~~V 209 (449)
T PRK12329 136 LRDQQRKM----IQEEFQDLE-DTVLTARVLRFERQ-SVIMAVSSGFGQPEVEAELPKREQLPNDNYRANATFKVFLKEV 209 (449)
T ss_pred HHHHHHHH----HHHHHHHhc-CcEEEEEEEEEcCC-CEEEEecccCCCcceEEEecHHHcCCCCcCCCCCEEEEEEEEe
Confidence 33445544 333445556 69999999985333 2223332 234 3433221 35699999999999999
Q ss_pred eCC
Q 007798 576 HPR 578 (589)
Q Consensus 576 D~~ 578 (589)
...
T Consensus 210 ~~~ 212 (449)
T PRK12329 210 SEG 212 (449)
T ss_pred ecC
Confidence 865
No 95
>PF03544 TonB_C: Gram-negative bacterial TonB protein C-terminal; InterPro: IPR006260 The sequences in this set all contain a conserved C-terminal domain which is characteristic of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria []. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetitive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to span the periplasm. Iron is essential for growth in both bacteria and mammals. Controlling the amount of free iron in solution is often used as a tactic by hosts to limit invasion of pathogenic microbes; binding iron tightly within protein molecules can accomplish this. Some bacteria express surface receptors to capture eukaryotic iron-binding compounds, while others have evolved siderophores to scavenge iron from iron-binding host proteins []. The absence of free iron molecules in the surrounding environment triggers transcription of gene clusters that encode both siderophore-synthesis ezymes, and receptors that recognise iron-bound siderophores []. An example of the latter is Escherichia coli fepA, which resides in the outer envelope and captures iron-bound enterobactin []. To complete transport of bound iron across the inner membrane, a second receptor complex is needed. The major component of this is tonB, a 27kDa protein that facilitates energy transfer from the proton motive force to outer receptors. B-12 and colicin receptors also make use of the tonB system to drive active transport at the outer membrane.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016020 membrane, 0030288 outer membrane-bounded periplasmic space; PDB: 1U07_B 1IHR_A 2GRX_C 2GSK_B 1QXX_A 1XX3_A 2K9K_A.
Probab=32.45 E-value=77 Score=25.52 Aligned_cols=24 Identities=25% Similarity=0.389 Sum_probs=19.5
Q ss_pred eeEEEEEEEECCCCeEeEEEEEEE
Q 007798 275 CNAVTVSVVLHSDGSIAEYSVDNS 298 (589)
Q Consensus 275 r~AlS~~~~ld~~G~I~~~~~~~s 298 (589)
.-.+.+.+.||++|+|.+.++..+
T Consensus 15 ~G~v~v~~~I~~~G~v~~~~v~~s 38 (79)
T PF03544_consen 15 EGTVVVEFTIDPDGRVSDVRVIQS 38 (79)
T ss_dssp EEEEEEEEEEETTTEEEEEEEEEE
T ss_pred eEEEEEEEEEeCCCCEEEEEEEEc
Confidence 346889999999999999876554
No 96
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=31.94 E-value=69 Score=26.47 Aligned_cols=24 Identities=21% Similarity=0.306 Sum_probs=16.7
Q ss_pred eeeEEEEEEEECCCCeEeEEEEEE
Q 007798 274 VCNAVTVSVVLHSDGSIAEYSVDN 297 (589)
Q Consensus 274 ~r~AlS~~~~ld~~G~I~~~~~~~ 297 (589)
......+.++||++|+|.++++.+
T Consensus 24 ~~~~~~V~i~i~~dG~v~~~~i~~ 47 (85)
T PF13103_consen 24 GGLSVTVRITIDPDGRVISVRIVK 47 (85)
T ss_dssp TT--EEEEEEE-TTSBEEEEEEEE
T ss_pred CCcEEEEEEEECCCCCEEEEEEec
Confidence 345678999999999998776654
No 97
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=28.41 E-value=2.6e+02 Score=22.97 Aligned_cols=56 Identities=14% Similarity=0.130 Sum_probs=34.0
Q ss_pred cEEEEEEEEEeeCeeEEEEeeccceeEEE------Ee-CccCCCCCEEEEEEEeeeCCCCeEEE
Q 007798 528 RQYRALILRFIKDRTAALLLVEVGLQAAA------WV-SVGAQIGDEVEVKVEEAHPRDDIIYL 584 (589)
Q Consensus 528 ~~~~a~V~~~~~~~~~~V~l~~lg~~~~~------~~-~~~~~lGd~V~V~I~~vD~~~~~i~~ 584 (589)
-+..|.|+..+..+...|..++ |..... +. .....+||.|.|.+...|..++.|-+
T Consensus 7 ~~~~G~Vi~~~~~~~y~V~~~~-g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 7 IEMEGTVVEALPNAMFRVELEN-GHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred EEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEccceeeCCcccCCCCEEEEEEcccCCCeEEEEE
Confidence 3568999876544345554322 323222 21 22367899999998777776676654
No 98
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=28.18 E-value=1.5e+02 Score=30.13 Aligned_cols=59 Identities=19% Similarity=0.077 Sum_probs=35.3
Q ss_pred CcEEEEEEEEEeeC---------eeEEEEeeccceeEE----EEeCccCCCCCEEEEEEEeeeCCCCeEEEEE
Q 007798 527 ERQYRALILRFIKD---------RTAALLLVEVGLQAA----AWVSVGAQIGDEVEVKVEEAHPRDDIIYLKE 586 (589)
Q Consensus 527 g~~~~a~V~~~~~~---------~~~~V~l~~lg~~~~----~~~~~~~~lGd~V~V~I~~vD~~~~~i~~~~ 586 (589)
|....|.|+++..+ ..|++++.++.-... ......|++||.|..+|.++|+... +.|..
T Consensus 64 GDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~~~~~-~~LS~ 135 (235)
T PRK04163 64 GDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVDRTRD-VVLTL 135 (235)
T ss_pred CCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEECCCCc-EEEEE
Confidence 68889999985332 134444443311110 1112348999999999999997543 55543
No 99
>PRK11570 peptidyl-prolyl cis-trans isomerase; Provisional
Probab=27.73 E-value=6.2e+02 Score=25.20 Aligned_cols=51 Identities=14% Similarity=0.244 Sum_probs=33.2
Q ss_pred HHHHHcCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 007798 475 VKACLRGESPPFSAGQLEGMASIVNMQTRIARRLSNTSLRYWIIEFLRRQP 525 (589)
Q Consensus 475 L~a~L~g~~~~~~~~~L~~i~~~~~~~~r~a~~aer~~~~~~~~~~L~~~~ 525 (589)
|+..+.|+++.++.+++...+..++.+.....+....-..-.--.||..+.
T Consensus 42 ~~d~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fl~~~~ 92 (206)
T PRK11570 42 LADALEGKHPAVPVDVVHRALREIHERADAVRRERQQAMAAEGVKFLEENA 92 (206)
T ss_pred HHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 667778887778989998888888765554443332333334456777654
No 100
>TIGR01352 tonB_Cterm TonB family C-terminal domain. This model represents the C-terminal of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to help span the periplasm.
Probab=26.85 E-value=1e+02 Score=24.41 Aligned_cols=21 Identities=29% Similarity=0.428 Sum_probs=17.7
Q ss_pred EEEEEEEECCCCeEeEEEEEE
Q 007798 277 AVTVSVVLHSDGSIAEYSVDN 297 (589)
Q Consensus 277 AlS~~~~ld~~G~I~~~~~~~ 297 (589)
.+.+.+.|+++|+|.+.++..
T Consensus 11 ~v~v~~~i~~~G~v~~~~i~~ 31 (74)
T TIGR01352 11 TVVVRFTVDADGRVTSVSVLK 31 (74)
T ss_pred EEEEEEEECCCCCEEEEEEEE
Confidence 478899999999999887754
No 101
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=24.83 E-value=1.5e+02 Score=29.13 Aligned_cols=22 Identities=14% Similarity=0.277 Sum_probs=18.6
Q ss_pred CccCCCCCEEEEEEEeeeCCCC
Q 007798 559 SVGAQIGDEVEVKVEEAHPRDD 580 (589)
Q Consensus 559 ~~~~~lGd~V~V~I~~vD~~~~ 580 (589)
++.++.||.|+++|..++....
T Consensus 133 k~~i~~gd~VR~RIv~~s~~~~ 154 (183)
T COG1095 133 KRVLKVGDKVRARIVGVSLKSR 154 (183)
T ss_pred ceEEecCCEEEEEEEEEecccC
Confidence 4568999999999999997664
No 102
>CHL00010 infA translation initiation factor 1
Probab=24.70 E-value=3.9e+02 Score=22.37 Aligned_cols=56 Identities=16% Similarity=0.245 Sum_probs=32.7
Q ss_pred EEEEEEEEEeeCeeEEEEeeccceeEEEEe----C---ccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 529 QYRALILRFIKDRTAALLLVEVGLQAAAWV----S---VGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 529 ~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~----~---~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
+..|.|+..+..+...|.+++ |-....+. . ....+||.|.|.+...+..++.|-+.
T Consensus 8 ~~~G~Vik~lg~~~y~V~~~~-g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r 70 (78)
T CHL00010 8 EMEGLVTESLPNGMFRVRLDN-GCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYR 70 (78)
T ss_pred EEEEEEEEEcCCCEEEEEeCC-CCEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEEE
Confidence 467888875533444454321 32222211 1 23568999999987777766766543
No 103
>PF06345 Drf_DAD: DRF Autoregulatory Domain; InterPro: IPR010465 This domain is found in Diaphanous-related formins (Drfs). It binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of diaphanous activating domains (DAD) to mammalian cells induces actin filament formation, stabilises microtubules, and activates serum-response mediated transcription [].; PDB: 3O4X_H 3OBV_E 2BAP_C 2F31_B.
Probab=24.19 E-value=75 Score=18.29 Aligned_cols=12 Identities=25% Similarity=0.559 Sum_probs=8.7
Q ss_pred chHHHHHHHHHH
Q 007798 71 SLVDSVMQELVA 82 (589)
Q Consensus 71 ~~~~~~~~~l~~ 82 (589)
|..|+|.+||..
T Consensus 1 gvmdsllealqt 12 (15)
T PF06345_consen 1 GVMDSLLEALQT 12 (15)
T ss_dssp -HHHHHHHHHHH
T ss_pred CcHHHHHHHHHc
Confidence 567899888864
No 104
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=23.97 E-value=80 Score=36.38 Aligned_cols=61 Identities=23% Similarity=0.292 Sum_probs=40.2
Q ss_pred CcEEEEEEEEEeeCeeEEEEeec--cceeEEEEe--CccCCCCCEEEEEEEeeeCCCCeEEEEEec
Q 007798 527 ERQYRALILRFIKDRTAALLLVE--VGLQAAAWV--SVGAQIGDEVEVKVEEAHPRDDIIYLKEVV 588 (589)
Q Consensus 527 g~~~~a~V~~~~~~~~~~V~l~~--lg~~~~~~~--~~~~~lGd~V~V~I~~vD~~~~~i~~~~v~ 588 (589)
|+.|.|+|+++.+- ..+|.+.+ .|+--.... ...+..||.+-|+++.|-+.++.|||+-+.
T Consensus 123 g~~Y~g~v~~v~~~-GvFv~Ln~~v~GL~~~~d~~~~~~~~vgdeiiV~v~~vr~~~geidf~~~~ 187 (715)
T COG1107 123 GKYYKGIVSRVEKY-GVFVELNSHVRGLIHRRDLGGDPDYAVGDEIIVQVSDVRPEKGEIDFEPVG 187 (715)
T ss_pred ceeeeccccchhhh-cceeecChhhhccccccccCCCCCCCCCCeEEEEeeccCCCCCccceeecC
Confidence 68899999974221 12233321 122111111 256999999999999999999999998753
No 105
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=21.91 E-value=3.9e+02 Score=21.40 Aligned_cols=54 Identities=13% Similarity=0.074 Sum_probs=33.5
Q ss_pred EEEEEEEEEeeCeeEEEEeeccceeEEEEe------CccCCCCCEEEEEEEeeeCCCCeEE
Q 007798 529 QYRALILRFIKDRTAALLLVEVGLQAAAWV------SVGAQIGDEVEVKVEEAHPRDDIIY 583 (589)
Q Consensus 529 ~~~a~V~~~~~~~~~~V~l~~lg~~~~~~~------~~~~~lGd~V~V~I~~vD~~~~~i~ 583 (589)
+..|.|+.....+...|.+++ |....++. ...+..||.|.|.+..-|..++.|-
T Consensus 4 e~~~~V~~~lG~~~~~V~~~d-g~~~l~~i~gK~r~~iwI~~GD~V~V~~~~~d~~kG~Ii 63 (65)
T PF01176_consen 4 EVIGRVTEMLGNNLFEVECED-GEERLARIPGKFRKRIWIKRGDFVLVEPSPYDKVKGRII 63 (65)
T ss_dssp EEEEEEEEEESSSEEEEEETT-SEEEEEEE-HHHHTCC---TTEEEEEEESTTCTTEEEEE
T ss_pred EEEEEEEEECCCCEEEEEeCC-CCEEEEEeccceeeeEecCCCCEEEEEecccCCCeEEEE
Confidence 467888876555565566653 44433322 2347899999999988887776664
No 106
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=20.85 E-value=4.7e+02 Score=23.16 Aligned_cols=57 Identities=11% Similarity=0.090 Sum_probs=36.5
Q ss_pred cEEEEEEEEEeeCeeEEEEeeccceeEEE------EeCccCCCCCEEEEEEEeeeCCCCeEEEE
Q 007798 528 RQYRALILRFIKDRTAALLLVEVGLQAAA------WVSVGAQIGDEVEVKVEEAHPRDDIIYLK 585 (589)
Q Consensus 528 ~~~~a~V~~~~~~~~~~V~l~~lg~~~~~------~~~~~~~lGd~V~V~I~~vD~~~~~i~~~ 585 (589)
.+..|.|+...-.+...|.+++ |....+ +....+..||.|.|.+..-|+.++.|.+.
T Consensus 21 ~e~~g~V~~~lG~~~~~V~~~d-G~~~la~i~GK~Rk~IwI~~GD~VlVe~~~~~~~kg~Iv~r 83 (100)
T PRK04012 21 GEVFGVVEQMLGANRVRVRCMD-GVERMGRIPGKMKKRMWIREGDVVIVAPWDFQDEKADIIWR 83 (100)
T ss_pred CEEEEEEEEEcCCCEEEEEeCC-CCEEEEEEchhhcccEEecCCCEEEEEecccCCCEEEEEEE
Confidence 4567888875444554455543 433322 22234789999999999999887777653
Done!