Query 021563
Match_columns 311
No_of_seqs 137 out of 579
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 03:58:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021563.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021563hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2869 Meiotic cell division 100.0 2.5E-89 5.5E-94 623.6 26.1 308 3-310 17-324 (379)
2 TIGR00111 pelota probable tran 100.0 9.5E-84 2.1E-88 614.5 37.1 288 3-304 16-304 (351)
3 COG1537 PelA Predicted RNA-bin 100.0 1.1E-79 2.4E-84 570.9 33.6 292 3-310 14-305 (352)
4 TIGR00108 eRF peptide chain re 100.0 4.4E-51 9.6E-56 396.3 15.5 273 15-304 27-319 (409)
5 TIGR03676 aRF1/eRF1 peptide ch 100.0 2.1E-46 4.5E-51 362.6 28.0 227 59-303 74-314 (403)
6 PRK04011 peptide chain release 100.0 1.3E-45 2.9E-50 358.2 27.8 229 61-305 83-324 (411)
7 PF03463 eRF1_1: eRF1 domain 1 100.0 5.6E-36 1.2E-40 248.8 7.7 114 3-116 17-131 (132)
8 COG1503 eRF1 Peptide chain rel 100.0 1.3E-34 2.8E-39 275.3 16.8 229 59-304 81-322 (411)
9 PF03464 eRF1_2: eRF1 domain 2 100.0 2.3E-29 5E-34 209.4 15.2 126 122-254 1-133 (133)
10 KOG0688 Peptide chain release 100.0 4.7E-30 1E-34 234.4 7.2 227 61-304 84-323 (431)
11 PF03465 eRF1_3: eRF1 domain 3 99.4 1.6E-13 3.5E-18 111.0 5.7 52 257-308 1-52 (113)
12 PF10116 Host_attach: Protein 95.5 0.049 1.1E-06 45.2 6.8 91 124-214 2-117 (138)
13 TIGR03677 rpl7ae 50S ribosomal 71.2 9.4 0.0002 30.9 5.0 30 274-303 23-52 (117)
14 PF01248 Ribosomal_L7Ae: Ribos 71.1 10 0.00022 28.9 5.0 38 266-304 5-42 (95)
15 PRK07283 hypothetical protein; 70.4 5.3 0.00011 31.2 3.3 32 272-303 13-44 (98)
16 PRK07714 hypothetical protein; 70.0 5.2 0.00011 31.3 3.2 36 267-303 9-44 (100)
17 PRK05583 ribosomal protein L7A 68.7 5.8 0.00013 31.4 3.2 32 272-303 12-43 (104)
18 PRK04175 rpl7ae 50S ribosomal 64.6 18 0.0004 29.4 5.5 40 264-304 18-57 (122)
19 PTZ00106 60S ribosomal protein 64.5 15 0.00032 29.3 4.8 39 264-303 13-51 (108)
20 PRK13602 putative ribosomal pr 63.3 15 0.00031 27.8 4.3 28 276-303 10-37 (82)
21 PRK09190 hypothetical protein; 62.2 33 0.00072 31.0 7.1 32 272-303 106-137 (220)
22 PRK01018 50S ribosomal protein 61.1 21 0.00045 27.9 5.0 29 275-303 14-42 (99)
23 TIGR01175 pilM type IV pilus a 60.6 1.1E+02 0.0025 28.7 11.1 89 123-211 190-306 (348)
24 PF08032 SpoU_sub_bind: RNA 2' 59.7 12 0.00027 26.9 3.3 24 279-302 2-26 (76)
25 PF03485 Arg_tRNA_synt_N: Argi 58.1 12 0.00025 28.1 3.0 29 171-199 52-81 (85)
26 PRK13601 putative L7Ae-like ri 56.6 18 0.00039 27.4 3.8 29 275-303 6-34 (82)
27 PRK06683 hypothetical protein; 56.3 23 0.00051 26.7 4.4 30 274-303 8-37 (82)
28 PRK13600 putative ribosomal pr 53.4 23 0.0005 27.0 3.9 27 277-303 13-39 (84)
29 PRK09557 fructokinase; Reviewe 48.6 64 0.0014 29.8 7.0 47 167-213 224-270 (301)
30 PRK05082 N-acetylmannosamine k 47.9 41 0.00089 30.9 5.6 46 168-213 214-259 (291)
31 COG1855 ATPase (PilT family) [ 46.1 1.7E+02 0.0036 29.8 9.5 130 60-213 146-289 (604)
32 COG1358 RPL8A Ribosomal protei 45.0 45 0.00097 27.0 4.6 30 274-303 24-53 (116)
33 COG1105 FruK Fructose-1-phosph 43.7 90 0.002 29.7 7.1 64 165-246 113-178 (310)
34 PRK13310 N-acetyl-D-glucosamin 35.6 1.2E+02 0.0026 28.0 6.7 47 167-213 225-271 (303)
35 COG0018 ArgS Arginyl-tRNA synt 35.5 72 0.0016 33.0 5.5 27 173-199 57-84 (577)
36 COG4972 PilM Tfp pilus assembl 34.9 76 0.0017 30.5 5.1 47 165-211 258-311 (354)
37 COG1911 RPL30 Ribosomal protei 32.4 75 0.0016 25.0 3.8 33 272-304 14-46 (100)
38 PF04628 Sedlin_N: Sedlin, N-t 32.3 2.7E+02 0.0058 22.6 7.5 71 106-183 35-106 (132)
39 PTZ00288 glucokinase 1; Provis 28.8 4.3E+02 0.0093 26.1 9.5 87 104-196 5-101 (405)
40 PRK15080 ethanolamine utilizat 27.9 1.3E+02 0.0029 27.5 5.5 44 168-211 202-245 (267)
41 PF07116 DUF1372: Protein of u 27.8 89 0.0019 24.7 3.6 37 67-106 56-92 (104)
42 KOG0283 WD40 repeat-containing 23.8 6E+02 0.013 27.1 9.8 84 55-153 412-495 (712)
43 PF09345 DUF1987: Domain of un 23.8 67 0.0015 25.2 2.3 21 57-77 2-22 (99)
44 COG1940 NagC Transcriptional r 22.5 2E+02 0.0042 26.7 5.7 46 168-213 228-275 (314)
45 PF14213 DUF4325: Domain of un 22.4 92 0.002 22.6 2.7 68 169-243 4-72 (74)
46 cd05791 S1_CSL4 S1_CSL4: CSL4, 22.2 85 0.0019 24.0 2.6 19 11-29 53-71 (92)
47 PTZ00222 60S ribosomal protein 21.2 2.8E+02 0.006 25.8 6.0 31 273-303 128-158 (263)
48 PF11215 DUF3010: Protein of u 21.1 5E+02 0.011 21.7 7.8 61 123-193 3-67 (138)
49 TIGR00744 ROK_glcA_fam ROK fam 20.9 3E+02 0.0066 25.3 6.6 47 167-213 231-278 (318)
50 PF12984 DUF3868: Domain of un 20.6 2E+02 0.0044 23.0 4.6 39 52-92 29-67 (115)
51 PF14801 GCD14_N: tRNA methylt 20.4 77 0.0017 22.1 1.8 19 81-99 17-35 (54)
52 PRK09698 D-allose kinase; Prov 20.2 3.4E+02 0.0073 24.9 6.7 47 167-213 216-263 (302)
No 1
>KOG2869 consensus Meiotic cell division protein Pelota/DOM34 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-89 Score=623.60 Aligned_cols=308 Identities=57% Similarity=0.896 Sum_probs=303.4
Q ss_pred cccccCCchhhhHhhhcCCCCEEEEEeEEEEEeccCCCCccceEEEEEEEEEEEEEeecCCCCEEEEEEEEeecCccccc
Q 021563 3 LMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERVKLKLEIKVEVVDYDKEGSVLRIRGKNILENEHVKI 82 (311)
Q Consensus 3 ~l~~E~~dDlw~lynli~~GD~V~~~T~Rkv~~~~~~g~~~~~r~~~~L~i~Ve~ief~~~~~~Lri~G~i~~~~e~v~~ 82 (311)
|++||+.|||||+||+|++||.|+|.|.|||+.+.++|+++++|+.++|+|+||+++||+.++.||++|+++++|++|++
T Consensus 17 tmvpEe~eDmw~~ynli~~gD~v~a~T~rkvq~e~a~G~~~s~rv~~~L~i~VesidfD~~~~~L~~KGrti~eNe~Vk~ 96 (379)
T KOG2869|consen 17 TMVPEESEDLWHLYNLIQVGDSVIASTIRKVQKEEATGKTKSSRVLLKLKIKVESIDFDTKACVLRLKGRTIEENEYVKM 96 (379)
T ss_pred EECcCchhHHHHHHhhccCCceeEEEEEEEeeeccccCcccceEEEEEEEEEEEEeeccccccEEEEeeeeeeecccccc
Confidence 78999999999999999999999999999999998889888899999999999999999999999999999999999999
Q ss_pred ccEEEEEEccCCceEEEEccCChhhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCCCCcc
Q 021563 83 GAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIA 162 (311)
Q Consensus 83 G~~HTl~i~~~~~i~i~K~~wd~~~le~L~ea~~~~~~~~~~~vvid~g~a~i~ll~~~~~~~~~~i~~~ip~K~~~~~s 162 (311)
|+|||++|+++++|++.|.+||++.+++|++||++..++++++|++++|.|+||+++.++|..+++++.+||+||+++-|
T Consensus 97 GaYHTidlel~r~FtL~K~ewds~al~~l~~A~dp~~~ad~aaVvlqEGla~IcLvt~s~tilr~kIe~siPrKr~~~~s 176 (379)
T KOG2869|consen 97 GAYHTIDLELNRPFTLRKEEWDSMALKLLKEACDPAPSADVAAVVLQEGLAHICLVTKSSTILRAKIEVSIPRKRKGDVS 176 (379)
T ss_pred cceeEEEeccCCceEEEhhhchHHHHHHHHHhhCcccccceeeeehhcCceeEEEechhHHHHHHhhhcccccccCcchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999888888
Q ss_pred hhhHHHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHhcccccccccCCcEEEEEcCCCccccHHHH
Q 021563 163 GYESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREV 242 (311)
Q Consensus 163 ~~~~~~~~f~~~v~~~l~~~~~~~~~~~iIIaGPGf~k~~f~~~l~~~~~~~~~~~~~~~~~k~~~~~~s~~~~~gl~Ev 242 (311)
++++.+++||++|.+++.++++|+.++|+|||||||+++.|++|+.+.+.+..+|.++.|++||.++|+|+|+.++|+|+
T Consensus 177 ~~e~~l~kfye~V~qA~~k~v~fd~vk~~vvASpgF~~~~~~d~~~q~A~~~~~k~il~nk~kf~~~h~ssg~~hslnev 256 (379)
T KOG2869|consen 177 QHEEGLEKFYENVVQAILKHVNFDVVKCVVVASPGFVKDQFMDYLFQQAVKLDLKLILENKSKFPLVHASSGYKHSLNEV 256 (379)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCcceEEEEEEcCCchhHHHHHHHHHHHHHHhchhhhhhcccceeEEecCCchHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCchhHHhhhhhhHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHHHHhcCCccEEEEecCCcccCCCC
Q 021563 243 LDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFRLVCSK 310 (311)
Q Consensus 243 l~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l~r~~d~~ 310 (311)
|.+|.|.+.|+|+|+++|+++||+|+.+|+++|++||||++||.+|+|+|||++|||||++||+.|++
T Consensus 257 L~dp~v~~~l~dtK~~~EvkalddF~~~l~~~~drA~yG~khV~~A~e~~AI~tLLitD~lfr~~DV~ 324 (379)
T KOG2869|consen 257 LKDPAVASKLQDTKAAKEVKALDDFYVMLSKDPDRACYGPKHVEKANEYGAIETLLITDELFRSQDVA 324 (379)
T ss_pred hcChHHHHHhhchhhHHHHHHHHHHHHHhccCccccccCHHHHHHHHhhcchhheehhhhhcccccHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999975
No 2
>TIGR00111 pelota probable translation factor pelota. This model describes the Drosophila protein Pelota, the budding yeast protein DOM34 which it can replace, and a set of closely related archaeal proteins. Members contain a proposed RNA binding motif. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A. This family is homologous to a family of peptide chain release factors. Pelota is proposed to act in protein translation.
Probab=100.00 E-value=9.5e-84 Score=614.53 Aligned_cols=288 Identities=28% Similarity=0.487 Sum_probs=273.0
Q ss_pred cccccCCchhhhHhhhcCCCCEEEEEeEEEEEeccCCCCccceEEEEEEEEEEEEEeecCCCCEEEEEEEEeecC-cccc
Q 021563 3 LMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERVKLKLEIKVEVVDYDKEGSVLRIRGKNILEN-EHVK 81 (311)
Q Consensus 3 ~l~~E~~dDlw~lynli~~GD~V~~~T~Rkv~~~~~~g~~~~~r~~~~L~i~Ve~ief~~~~~~Lri~G~i~~~~-e~v~ 81 (311)
+|+||++||||||||||++||+|+|+|+|+|+++..+|+++ +|++++|+|+||+++|||++++|||+|+|+++| ++|+
T Consensus 16 ~l~pe~~dDlw~l~nli~~GD~V~~~T~Rkv~~~~~~g~~~-er~~~~l~i~Ve~ief~~~~~~Lri~G~i~~~~e~~v~ 94 (351)
T TIGR00111 16 KLLPETLDDLWHLYQIIEKGDVEFAFTKRRTQDLDKIRSDK-SKDTVKLGIEVESVEFDMKTERLRYKGVIVTGPEDDVP 94 (351)
T ss_pred EEEeCChHHHHHHHHhCCCCCEEEEEEEEEEeccccCCCcc-eEEEEEEEEEEEEEEecCCCCEEEEEEEEecCCccccc
Confidence 68999999999999999999999999999999887788777 999999999999999999999999999999998 7999
Q ss_pred cccEEEEEEccCCceEEEEccCChhhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCCCCc
Q 021563 82 IGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAI 161 (311)
Q Consensus 82 ~G~~HTl~i~~~~~i~i~K~~wd~~~le~L~ea~~~~~~~~~~~vvid~g~a~i~ll~~~~~~~~~~i~~~ip~K~~~~~ 161 (311)
+|+|||++|+||++|+|+|++||+|++++|++|++++.++.+++|+||+|+|+||+|+++++++++++++++|+||++
T Consensus 95 ~G~~HTl~ie~~~~i~i~K~~w~~~~le~L~ea~~~~~~~~~~~vv~d~g~A~i~ll~~~~~~~~~~i~~~iP~K~~~-- 172 (351)
T TIGR00111 95 VGSYHTLEIKYVYPLSIIKQNWKKWQLKRLREAVEISKRPKTAAVVMEEGIAHVGLVRQYSVEEIQKIEYHMPGKKRT-- 172 (351)
T ss_pred ccceEEEEEcCCCcEEEEEecCCHHHHHHHHHHhccccCCcEEEEEEeCCcEEEEEEcCCEEEEEEEEEEeCCCCccc--
Confidence 999999999999999999999999999999999999988899999999999999999999999999999999999854
Q ss_pred chhhHHHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHhcccccccccCCcEEEEEcCCCccccHHH
Q 021563 162 AGYESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLRE 241 (311)
Q Consensus 162 s~~~~~~~~f~~~v~~~l~~~~~~~~~~~iIIaGPGf~k~~f~~~l~~~~~~~~~~~~~~~~~k~~~~~~s~~~~~gl~E 241 (311)
+.+++++++||++|++++.+ +.++++||||||||+|++|++||++++++.. .+.++.++|+|+.+||+|
T Consensus 173 ~~~e~~~~~Ff~~v~~~l~~---~~~v~~iIiaGPGf~k~~f~~~l~~~~~~~~--------~k~ii~~~s~g~~~gl~E 241 (351)
T TIGR00111 173 LKFGELRKEFYKEIAKKLLN---FDDLKTIIVAGPGFYKNDFYDFIFERYPEEA--------NKAVLENCSTGGRAGINE 241 (351)
T ss_pred chhHHHHHHHHHHHHHHHhh---hcccCEEEEECCHHHHHHHHHHHHHHhhhhh--------CCcEEEecCCCchhHHHH
Confidence 55888999999999999854 4689999999999999999999999987632 345667999999999999
Q ss_pred HhcCchhHHhhhhhhHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHHHHhcCCccEEEEecCCc
Q 021563 242 VLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLF 304 (311)
Q Consensus 242 vl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l~ 304 (311)
+|++|.++++|+|+++++|.++||+||++|++|+++||||+++|.+|+++|||++|||||++|
T Consensus 242 vL~~~~v~~~l~d~k~~~E~~~l~~f~~~l~kd~~~~~YG~~eV~~Ale~GAVetLLIsD~l~ 304 (351)
T TIGR00111 242 VLKRGLVARILQETRYAKEIMVIDEFLEHLAKDGDKAVYGEDEVVKAAEYGAIEYLLVTDKVL 304 (351)
T ss_pred HHhChHHHHHHhhhhHHHHHHHHHHHHHHHhcCCCeEEECHHHHHHHHHcCCceEEEEecchh
Confidence 999999999999999999999999999999999999999999999999999999999999996
No 3
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=100.00 E-value=1.1e-79 Score=570.86 Aligned_cols=292 Identities=32% Similarity=0.513 Sum_probs=272.3
Q ss_pred cccccCCchhhhHhhhcCCCCEEEEEeEEEEEeccCCCCccceEEEEEEEEEEEEEeecCCCCEEEEEEEEeecCccccc
Q 021563 3 LMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQMASGSRDAERVKLKLEIKVEVVDYDKEGSVLRIRGKNILENEHVKI 82 (311)
Q Consensus 3 ~l~~E~~dDlw~lynli~~GD~V~~~T~Rkv~~~~~~g~~~~~r~~~~L~i~Ve~ief~~~~~~Lri~G~i~~~~e~v~~ 82 (311)
+|+||++||||||||+|++||.|+|+|+|+.++....++++++|++|+|+|+||++|||+|+++|||+|+++++|+.+++
T Consensus 14 ~l~pE~lDDLw~L~~Ii~~GD~v~a~T~Rr~~~~d~~r~~~~eri~m~L~IkVe~ieF~~f~nrLRi~G~i~~~~e~~~~ 93 (352)
T COG1537 14 KLVPETLDDLWHLYNIIEKGDKVFAKTTRRDESSDVIRSKKGERIPMTLGIKVEKIEFDKFANRLRIKGPIVEGPEEVVK 93 (352)
T ss_pred EEecCChHHHHHHHHhcCCCCEEEEEEEEecccccccccCcceEEEEEEEEEEEEEEeeecccEEEEEEEEEEcCccccc
Confidence 68999999999999999999999999999933322334788899999999999999999999999999999999999889
Q ss_pred ccEEEEEEccCCceEEEEccCChhhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCCCCcc
Q 021563 83 GAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIA 162 (311)
Q Consensus 83 G~~HTl~i~~~~~i~i~K~~wd~~~le~L~ea~~~~~~~~~~~vvid~g~a~i~ll~~~~~~~~~~i~~~ip~K~~~~~s 162 (311)
|+|||++|++|++|+|.|.+|+++++++|++|++++.++.+++|+||+|+|+||++++|++.++.+++.+.|+|+....
T Consensus 94 G~yHTi~v~~g~~i~I~K~~W~~~~lerLkeA~~~~~~~~~~~v~~degea~i~iv~~ygi~~~~~i~~~~~gK~~~~~- 172 (352)
T COG1537 94 GSYHTINVTIGTEIEIEKEEWNKDQLERLKEAVEASKRPEVAIVVVDEGEAAIAIVRDYGIIILGKIRSGIPGKREGDI- 172 (352)
T ss_pred ccceEEEeccCceEEEEEccCCHHHHHHHHHHhhcccCCceEEEEEecCceEEEEEeccceEEEEEEeccCCCCcccch-
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999998875443
Q ss_pred hhhHHHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHhcccccccccCCcEEEEEcCCCccccHHHH
Q 021563 163 GYESALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREV 242 (311)
Q Consensus 163 ~~~~~~~~f~~~v~~~l~~~~~~~~~~~iIIaGPGf~k~~f~~~l~~~~~~~~~~~~~~~~~k~~~~~~s~~~~~gl~Ev 242 (311)
+ +..+||..|++++.+.. +++.||||||||+|++|++|+.++.++. .++++.++|++|.+|++|+
T Consensus 173 -~--~~~k~~~~i~~~~~~~~---~~~~iIvaGPGF~k~~~~~~~~~~~p~~---------~~~~~~~~s~~g~~gi~Ev 237 (352)
T COG1537 173 -R--AERKFFDEIAKALKEYA---NLDIIIVAGPGFAKEDFYDFLRERYPEL---------ANIVIEDTSTGGRAGINEV 237 (352)
T ss_pred -h--hHHHHHHHHHHHHHHhh---CCCeEEEeCCchHHHHHHHHHHHhcccc---------cceEEEeccCcchHHHHHH
Confidence 2 12899999999999987 6889999999999999999999998763 1378999999999999999
Q ss_pred hcCchhHHhhhhhhHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHHHHhcCCccEEEEecCCcccCCCC
Q 021563 243 LDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFRLVCSK 310 (311)
Q Consensus 243 l~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l~r~~d~~ 310 (311)
|++|.+.++++++++++|.++||+|++.|++++++||||+++|.+|++||||++|||+|++||+.+++
T Consensus 238 Lkr~~v~ki~~e~ria~e~~~~e~fl~~iak~~~~v~YG~~eV~~A~e~GAve~LLv~De~lr~~~~~ 305 (352)
T COG1537 238 LKRGAVDKILSETRIAEEIELVEEFLERLAKDDDKVAYGLEEVEKAAEYGAVETLLVTDELLRSDDVE 305 (352)
T ss_pred HhhhhHHhHhhhhHHHHHHHHHHHHHHHHhcCCCceeEcHHHHHHHHhcCcceeEEeehhhhcccchh
Confidence 99999999999999999999999999999999999999999999999999999999999999997653
No 4
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=100.00 E-value=4.4e-51 Score=396.30 Aligned_cols=273 Identities=21% Similarity=0.277 Sum_probs=236.6
Q ss_pred HhhhcCCCCEE--EEEeEEEEEeccCCCCccceEEEEEEEEEEEE-----EeecCCCCEEEEEEEEeecCcccccccEEE
Q 021563 15 AYNLIAPGDSV--MAVTVRKVLRQMASGSRDAERVKLKLEIKVEV-----VDYDKEGSVLRIRGKNILENEHVKIGAFHT 87 (311)
Q Consensus 15 lynli~~GD~V--~~~T~Rkv~~~~~~g~~~~~r~~~~L~i~Ve~-----ief~~~~~~Lri~G~i~~~~e~v~~G~~HT 87 (311)
++.+|.|||.| .+.+.|+-...++.-..++.|.+|...|++.. ..--|.++.++++|.|..++. .|+|||
T Consensus 27 isl~ipp~~~i~~~~~~l~~e~~~a~niks~~~r~~v~~ai~~~~~~lk~~~~~p~nglv~~~G~v~~~~~---~~~~~t 103 (409)
T TIGR00108 27 ISLYIPPDRQISDVAKHLREELSQASNIKSKQTRKNVLSAIEAILQRLKLFNKPPENGLVIFCGMVPREGP---TEKMET 103 (409)
T ss_pred EEEEeCCCCcHHHHHHHHHHHHhhhhcccccchhhhHHHHHHHHHHHhhccCCCCCCcEEEEEeEeccCCC---cccEEE
Confidence 46789999999 88888873332233323356777766665443 345667899999999998873 389999
Q ss_pred EEEccCCceEEEEccCC-hhhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCCC-Ccch--
Q 021563 88 LEIELHRAFVLRKDLWD-SLALDTLHQAADPTASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGP-AIAG-- 163 (311)
Q Consensus 88 l~i~~~~~i~i~K~~wd-~~~le~L~ea~~~~~~~~~~~vvid~g~a~i~ll~~~~~~~~~~i~~~ip~K~~~-~~s~-- 163 (311)
++|+||+||+++||.|| +||+++|++|++... .+++|+||+|+|.||+++++++++++++++++|+||++ |||+
T Consensus 104 ~~iep~~pi~~~~y~~d~~f~le~L~e~~~~~~--~~g~VvvD~~~A~i~~l~g~~~~~~~~i~~~vp~K~~~GGqS~~R 181 (409)
T TIGR00108 104 YVIEPPEPIKTYIYHCDSKFYLEPLSEMLEEKD--KYGLIVLDRQEATIGLVKGKRITVLKKLTSGVPGKHKAGGQSARR 181 (409)
T ss_pred EEEeCCCceEEEEEccCChhHHHHHHHHhcCCC--CEEEEEEecCCEEEEEEcCCEEEEEEEEeeeCCCcccCCCcchhh
Confidence 99999999999999655 799999999999765 99999999999999999999999999999999999977 7876
Q ss_pred ----hhHHHHHHHHHHHHHHHhcc---cccCccEEEEECCcccHHHHHH--HHHHHHHhcccccccccCCcEEEEEcCCC
Q 021563 164 ----YESALNKFFENVLQAFLKHV---DFNVVRCAVIASPGFTKDQFHR--HLLLEAERRQLRPIIENKSRIILVHTSSG 234 (311)
Q Consensus 164 ----~~~~~~~f~~~v~~~l~~~~---~~~~~~~iIIaGPGf~k~~f~~--~l~~~~~~~~~~~~~~~~~k~~~~~~s~~ 234 (311)
+++++++||++|++.+.++| +..++++||||||||+|++|.+ ||.+++.++ -+.++++|+|
T Consensus 182 f~r~~e~~~~~f~~~Vae~~~~~f~~~~~~~v~~IIlaGpg~~K~~f~~~~~l~~~l~~k----------vi~~vdvs~g 251 (409)
T TIGR00108 182 FERLRELAAHEFLKKVGEVANEAFLPNDDVKLKGIILGGPGHTKEEFAEGEYLHHELKKK----------VISTVDVSYT 251 (409)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhcccccceEEEEeccHHHHHHhhhhhhHHHHhhhh----------EEEEEEcCCC
Confidence 68889999999999999886 2337999999999999999998 999988542 1357899999
Q ss_pred ccccHHHHhcCchhHHhhhhhhHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHHHHhcCCccEEEEecCCc
Q 021563 235 YKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLF 304 (311)
Q Consensus 235 ~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l~ 304 (311)
|.+|++|++++. +++|+++++++|.++|++|++++++|++++|||+++|.+|+++|||+||||+|+|.
T Consensus 252 g~~gl~E~l~~~--~~~L~~~k~~~E~~lle~F~~ei~~d~G~avyG~~eV~~ALe~GAVetLLV~d~l~ 319 (409)
T TIGR00108 252 GEFGIRELIEKS--ADVLAEVDYMREKKLVQRFLKELIQEDGLACYGEDEVLKALDLGAVETLIVSEDLE 319 (409)
T ss_pred cccCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhcCCCcEEeCHHHHHHHHHhCCCcEEEEecccc
Confidence 999999999976 99999999999999999999999999999999999999999999999999999993
No 5
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=100.00 E-value=2.1e-46 Score=362.57 Aligned_cols=227 Identities=24% Similarity=0.291 Sum_probs=208.2
Q ss_pred eecCCCCEEEEEEEEeecCcccccccEEEEEEccCCceEEEEccCC-hhhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEE
Q 021563 59 DYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWD-SLALDTLHQAADPTASADLAVVLMQEGLAHILL 137 (311)
Q Consensus 59 ef~~~~~~Lri~G~i~~~~e~v~~G~~HTl~i~~~~~i~i~K~~wd-~~~le~L~ea~~~~~~~~~~~vvid~g~a~i~l 137 (311)
.--|.+|..-++|.+..+. ...+|||++|+||+||+++||.|| +||+++|++|++... .+++|+||+++|.||+
T Consensus 74 ~~~p~nGlv~f~g~~~~~~---~~~~~~t~~iep~~pi~~~~y~cd~~f~lepL~e~l~~~~--~~g~VvvD~~~A~i~~ 148 (403)
T TIGR03676 74 KKPPENGLVLFAGMVPTGG---GTEKMETYVIEPPEPINTYLYRCDSKFYLEPLEEMLEEKD--VYGLIVLDRREATIGL 148 (403)
T ss_pred CCCCCCeEEEEEeeecCCC---CceeEEEEEEeCCCceEEEEecCCChHHHHHHHHHhcCCC--CEEEEEEecCceEEEE
Confidence 3468999999999998754 346999999999999999999766 699999999999755 9999999999999999
Q ss_pred EecceEEEEEEEEEecCCCCCC-Ccch------hhHHHHHHHHHHHHHHHhccc---ccCccEEEEECCcccHHHHHH--
Q 021563 138 VGRSMTITRSRIETSIPRKHGP-AIAG------YESALNKFFENVLQAFLKHVD---FNVVRCAVIASPGFTKDQFHR-- 205 (311)
Q Consensus 138 l~~~~~~~~~~i~~~ip~K~~~-~~s~------~~~~~~~f~~~v~~~l~~~~~---~~~~~~iIIaGPGf~k~~f~~-- 205 (311)
++++++++++++++++|+||+. |||+ +++++++||++|++.+.++|. ..++++||||||||+|++|.+
T Consensus 149 l~g~~~e~~~~i~~~vp~K~~~GGqS~~Rf~R~~e~~~~~f~~~Vae~~~~~f~~~~~~~v~~lILaGpg~~K~~f~~~~ 228 (403)
T TIGR03676 149 LKGKRIEVLKELTSGVPGKHRAGGQSARRFERLIEIAAHEFYKRVGEAANEAFLPLKDKKLKGILIGGPGPTKEEFAEGD 228 (403)
T ss_pred EcCCEEEEEEEEEeeCCCCccCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccEEEEeCCHHHHHHHhhhh
Confidence 9999999999999999999875 7887 788999999999999988763 226999999999999999999
Q ss_pred HHHHHHHhcccccccccCCcE-EEEEcCCCccccHHHHhcCchhHHhhhhhhHHHHHHHHHHHHHHHhcCCCcEEEcHHH
Q 021563 206 HLLLEAERRQLRPIIENKSRI-ILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKH 284 (311)
Q Consensus 206 ~l~~~~~~~~~~~~~~~~~k~-~~~~~s~~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~~~YG~~e 284 (311)
||++++.+ ++ .++++|+++.+|++|++++. +++|++.++++|.++|++||+++++|++++|||+++
T Consensus 229 ~L~~~l~~-----------kvi~~vd~s~~~~~Gl~Evl~~~--~~~L~~~k~~~E~~lle~f~~el~~d~g~avyG~~e 295 (403)
T TIGR03676 229 YLHHELKK-----------KILGLFDVSYTGESGLRELVEKA--EDLLKDLELMKEKKLMERFFKELVKDGGLAAYGEEE 295 (403)
T ss_pred hhhHHHHh-----------hEEEEEecCCCCccCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhcCCCcEEEcHHH
Confidence 99998754 34 68899999999999999984 999999999999999999999999999999999999
Q ss_pred HHHHHhcCCccEEEEecCC
Q 021563 285 VEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 285 V~~A~e~GAVetLLIsD~l 303 (311)
|.+|+++|||+||||+|+|
T Consensus 296 V~~ALe~GAVetLLV~d~l 314 (403)
T TIGR03676 296 VRKALEMGAVDTLLISEDL 314 (403)
T ss_pred HHHHHHhCCCcEEEEEccc
Confidence 9999999999999999999
No 6
>PRK04011 peptide chain release factor 1; Provisional
Probab=100.00 E-value=1.3e-45 Score=358.21 Aligned_cols=229 Identities=23% Similarity=0.282 Sum_probs=210.2
Q ss_pred cCCCCEEEEEEEEeecCcccccccEEEEEEccCCceEEEEccCCh-hhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEe
Q 021563 61 DKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDS-LALDTLHQAADPTASADLAVVLMQEGLAHILLVG 139 (311)
Q Consensus 61 ~~~~~~Lri~G~i~~~~e~v~~G~~HTl~i~~~~~i~i~K~~wd~-~~le~L~ea~~~~~~~~~~~vvid~g~a~i~ll~ 139 (311)
.|.+|+.-++|.+..+.+ ..|.|||++|+||+||+++||.||+ ||+++|++|+++. +.+++|+||+++|.||+++
T Consensus 83 ~p~nGl~~f~g~~~~~~~--~~~~~~t~~i~p~~~i~~~~y~~d~~f~le~L~e~~~~~--~~~~~VvvD~~~A~i~~l~ 158 (411)
T PRK04011 83 PPENGLVIFCGAVPIGGP--GTEDMETYVIEPPEPVPTFFYRCDSEFHTEPLEDMLEDK--EVYGLIVVDRREATIGLLK 158 (411)
T ss_pred CCCCeEEEEEeecccCCC--CCceEEEEEEcCCCccEEEEecCCcHHHHHHHHHHhcCC--CCEEEEEEecCceEEEEEe
Confidence 678999999999887541 3489999999999999999998776 9999999999974 4999999999999999999
Q ss_pred cceEEEEEEEEEecCCCCCC-Ccch------hhHHHHHHHHHHHHHHHhccc---ccCccEEEEECCcccHHHHHH--HH
Q 021563 140 RSMTITRSRIETSIPRKHGP-AIAG------YESALNKFFENVLQAFLKHVD---FNVVRCAVIASPGFTKDQFHR--HL 207 (311)
Q Consensus 140 ~~~~~~~~~i~~~ip~K~~~-~~s~------~~~~~~~f~~~v~~~l~~~~~---~~~~~~iIIaGPGf~k~~f~~--~l 207 (311)
++++++++++++++|+||++ |||+ +++++++||++|++.+.++|. +.++++||||||||+|++|.+ ||
T Consensus 159 g~~~~~~~~i~~~vp~K~~~GG~S~~Rf~r~~e~~~~~f~k~Vae~~~~~f~~~~~~~v~~IvlaGpg~~K~~f~~~~~L 238 (411)
T PRK04011 159 GKRIEVLKELTSFVPGKHRKGGQSARRFERLIEQAAHEFYKRVGEKANEAFLPLLEGKLKGILIGGPGPTKEEFLEGDYL 238 (411)
T ss_pred CCEEEEEEEEEeeCCCCccCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccEEEEECChhHHHHHhhhhhh
Confidence 99999999999999999885 7876 588999999999999998875 478999999999999999999 99
Q ss_pred HHHHHhcccccccccCCcEEEEEcCCCccccHHHHhcCchhHHhhhhhhHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHH
Q 021563 208 LLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEV 287 (311)
Q Consensus 208 ~~~~~~~~~~~~~~~~~k~~~~~~s~~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~~~YG~~eV~~ 287 (311)
.+++.++ .+.++++|+++.+|++|++++. +++|+++++++|.++|++||++++++++++|||+++|.+
T Consensus 239 ~~~l~~~----------vv~~~~~s~~~~~Gl~E~l~~~--~~~L~~~k~~~e~~lle~f~~~l~~d~g~avyG~~~V~~ 306 (411)
T PRK04011 239 HYELKKK----------ILGLFDVSYTGESGLRELVDKA--SDLLKEQELVKEKKLMEEFFKELAKDGGLAVYGEEEVRK 306 (411)
T ss_pred hHHHHhh----------eEEEEecCCCCccCHHHHHHHH--HHHHHHhHHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHH
Confidence 9998542 2257899999999999999984 999999999999999999999999999999999999999
Q ss_pred HHhcCCccEEEEecCCcc
Q 021563 288 AHERMAVQTLLITDDLFR 305 (311)
Q Consensus 288 A~e~GAVetLLIsD~l~r 305 (311)
|+++|||+||||+|+++|
T Consensus 307 Ale~GAVetLLV~d~l~~ 324 (411)
T PRK04011 307 ALEMGAVDTLLISEDLRK 324 (411)
T ss_pred HHHcCCceEEEEeccccc
Confidence 999999999999999987
No 7
>PF03463 eRF1_1: eRF1 domain 1; InterPro: IPR005140 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.; PDB: 2VGN_A 2VGM_A 3J16_A 3IZQ 3AGK_A 3AGJ_B 3OBW_A 3E1Y_D 1DT9_A 2LLX_A ....
Probab=100.00 E-value=5.6e-36 Score=248.80 Aligned_cols=114 Identities=50% Similarity=0.793 Sum_probs=108.0
Q ss_pred cccccCCchhhhHhhhcCCCCEEEEEeEEEEEec-cCCCCccceEEEEEEEEEEEEEeecCCCCEEEEEEEEeecCcccc
Q 021563 3 LMEPVDSDDLWFAYNLIAPGDSVMAVTVRKVLRQ-MASGSRDAERVKLKLEIKVEVVDYDKEGSVLRIRGKNILENEHVK 81 (311)
Q Consensus 3 ~l~~E~~dDlw~lynli~~GD~V~~~T~Rkv~~~-~~~g~~~~~r~~~~L~i~Ve~ief~~~~~~Lri~G~i~~~~e~v~ 81 (311)
+++||+.||||||||||.|||.|.|.|+|+|+.+ +.+++.++++++++|+|+|++++|+|+++.|||+|+|+++|++++
T Consensus 17 ~ll~e~~dDlw~L~~li~~gD~v~~~t~Rkv~~~~~~~~~~~~~~v~~~L~i~ve~v~~~~~~~~Lri~G~i~~~~~~~~ 96 (132)
T PF03463_consen 17 KLLPEEKDDLWHLYNLIIPGDEVISKTTRKVQEASNIKGSKTRERVQIALTIKVEKVEFDPENGLLRISGKIVEENEDVK 96 (132)
T ss_dssp EEETTSHHHHHHHHHHEETTTEEEECCHCHHHHCTCESSHHHHHCEEEEEEEEEEEEEEETTTTEEEEEEEEEEGSCGGG
T ss_pred EEcccccCCcEEEEEEEECCCEEEEEEEEeeeecccccCCcceEEEEEEEEEEEEEeEecCCCCEEEEEeEEccCCCCCC
Confidence 5899999999999999999999999999999443 456677889999999999999999999999999999999999999
Q ss_pred cccEEEEEEccCCceEEEEccCChhhHHHHHHhcC
Q 021563 82 IGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAAD 116 (311)
Q Consensus 82 ~G~~HTl~i~~~~~i~i~K~~wd~~~le~L~ea~~ 116 (311)
+|+|||++|+||+||+|+|+.||++++++|++|++
T Consensus 97 ~G~~hT~~i~~~~~~ti~K~~wd~~~~~~l~ea~~ 131 (132)
T PF03463_consen 97 LGKYHTLDIEPGRPFTIIKYRWDSYFLDRLKEAMD 131 (132)
T ss_dssp TTSEEEEEEETSSEEEEEEEEEEHHHHHHHHHHTS
T ss_pred cceEEEEEEeCCCceEEEEecCCHHHHHHHHHHhc
Confidence 99999999999999999999999999999999986
No 8
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-34 Score=275.33 Aligned_cols=229 Identities=24% Similarity=0.280 Sum_probs=208.4
Q ss_pred eecCCCCEEEEEEEEeecCcccccccEEEEEEccCCceEEEEccCCh-hhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEE
Q 021563 59 DYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDS-LALDTLHQAADPTASADLAVVLMQEGLAHILL 137 (311)
Q Consensus 59 ef~~~~~~Lri~G~i~~~~e~v~~G~~HTl~i~~~~~i~i~K~~wd~-~~le~L~ea~~~~~~~~~~~vvid~g~a~i~l 137 (311)
.=.|.+|...++|.+..+-.. ...-|..++|+.|++.+.|.||+ |++++|++++.+.. .|++++||.++|.+++
T Consensus 81 ~~~P~nGlv~f~g~v~~~~~~---t~~~~~~~~PP~Pi~~~ly~cDs~F~~e~L~~~l~~~~--~ygliv~dr~ea~ig~ 155 (411)
T COG1503 81 CKTPENGLVLFVGDVLGGGGK---TKKVTVVIEPPEPINTFLYRCDSKFYLEPLEEMLEDKD--LYGLIVLDRIEATIGL 155 (411)
T ss_pred ccCCCCCeEEEEeeeccCCCc---cceeeecccCCCCcceeeeccccHHHHHHHHHHhhhcc--cccEEEEecccceeee
Confidence 346789999999988765322 24567777999999999999999 99999999998888 9999999999999999
Q ss_pred EecceEEEEEEEEEecCCCCCC-Ccch------hhHHHHHHHHHHHHHHHhccc---ccCccEEEEECCcccHHHHHH--
Q 021563 138 VGRSMTITRSRIETSIPRKHGP-AIAG------YESALNKFFENVLQAFLKHVD---FNVVRCAVIASPGFTKDQFHR-- 205 (311)
Q Consensus 138 l~~~~~~~~~~i~~~ip~K~~~-~~s~------~~~~~~~f~~~v~~~l~~~~~---~~~~~~iIIaGPGf~k~~f~~-- 205 (311)
|.+..+.++.++++.+||||++ |||+ ++.+.+.||+.|.+++.+.|. ..++++|+|+|||.+|++|++
T Consensus 156 l~g~r~evl~~~~s~vpgKh~~Ggqsa~rferl~ee~~h~f~k~vge~A~e~f~~~~~~~~kgIilgGp~~tk~ef~e~~ 235 (411)
T COG1503 156 LKGKRIEVLKELTSDVPGKHRAGGQSARRFERLIEEAAHEFYKKVGEAASEAFLPIAKKELKGIILGGPGPTKEEFVEGD 235 (411)
T ss_pred eccceeeHhhhhcccCcchhhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhcceEeeCCcccchhhhccc
Confidence 9999999999999999999988 7887 778899999999999999885 226899999999999999997
Q ss_pred HHHHHHHhcccccccccCCcEEEEEcCCCccccHHHHhcCchhHHhhhhhhHHHHHHHHHHHHHHHhcCCCcEEEcHHHH
Q 021563 206 HLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHV 285 (311)
Q Consensus 206 ~l~~~~~~~~~~~~~~~~~k~~~~~~s~~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~~~YG~~eV 285 (311)
||.++++.+.. -++++++++.+|++|++..+ .+.|++.++.+|.++|++|++.+.+++++++||.++|
T Consensus 236 yL~~~lk~kv~----------~lvDv~y~~esg~~eli~~A--~d~L~~~~~~~eK~l~e~f~~e~~~~~Gla~yG~~~v 303 (411)
T COG1503 236 YLHHELKKKVL----------GLVDVSYTGESGLRELIEKA--EDALKDVDYVREKKLMEEFFKELAKDSGLAVYGEEEV 303 (411)
T ss_pred ccchHHHHHHH----------hhccccccccccHHHHHHHh--HHHHHhhhhhcchhHHHHHHHHhccCcceeecchHHH
Confidence 99999865321 47999999999999999999 9999999999999999999999999999999999999
Q ss_pred HHHHhcCCccEEEEecCCc
Q 021563 286 EVAHERMAVQTLLITDDLF 304 (311)
Q Consensus 286 ~~A~e~GAVetLLIsD~l~ 304 (311)
++|+++|||++|||+.++-
T Consensus 304 r~aL~~gaVd~llv~Edl~ 322 (411)
T COG1503 304 REALEMGAVDTLLVSEDLE 322 (411)
T ss_pred HHHHHhcccceEEeecccc
Confidence 9999999999999999876
No 9
>PF03464 eRF1_2: eRF1 domain 2; InterPro: IPR005141 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination ; PDB: 3AGK_A 2VGN_A 2VGM_A 3J16_A 3IZQ 3IR9_A 3OBW_A 3MCA_B 2QI2_A 3E1Y_D ....
Probab=99.96 E-value=2.3e-29 Score=209.40 Aligned_cols=126 Identities=42% Similarity=0.664 Sum_probs=114.7
Q ss_pred cEEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCCC-Ccchh----hHHHHHHHHHHHHHHHhc--ccccCccEEEEE
Q 021563 122 DLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGP-AIAGY----ESALNKFFENVLQAFLKH--VDFNVVRCAVIA 194 (311)
Q Consensus 122 ~~~~vvid~g~a~i~ll~~~~~~~~~~i~~~ip~K~~~-~~s~~----~~~~~~f~~~v~~~l~~~--~~~~~~~~iIIa 194 (311)
++++|+||+|+|+||+++++++++++++++++|+||++ |+|+. ++++++||++|++++.++ .++.++++||||
T Consensus 1 ~v~~v~id~g~A~i~~l~~~~~~~~~~i~~~ip~K~~~Gg~s~~rf~r~~~~~~f~~~i~~~l~~~f~~~~~~~~~iIia 80 (133)
T PF03464_consen 1 KVGIVVIDEGEANICLLRGYGTEILQRIESNIPGKHKKGGQSQRRFEREKALEKFFKEIAEALKKYFLVNFDDVKCIIIA 80 (133)
T ss_dssp EEEEEEEETTEEEEEEEETTEEEEEEEEE-GHCCCSSTTCSHHHHHHHHHHHHHHHHHHHHHHHHHCCCHTTTCSEEEEE
T ss_pred CEEEEEEeCCCEEEEEEcCCEEEEEEEEEecCCCccCCCCcchhhHHHHHHHHHHHHHHHHHHHHHhhhccccccEEEEE
Confidence 48999999999999999999999999999999999986 67764 899999999999999999 779999999999
Q ss_pred CCcccHHHHHHHHHHHHHhcccccccccCCcEEEEEcCCCccccHHHHhcCchhHHhhhh
Q 021563 195 SPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIKD 254 (311)
Q Consensus 195 GPGf~k~~f~~~l~~~~~~~~~~~~~~~~~k~~~~~~s~~~~~gl~Evl~~~~v~~~l~d 254 (311)
||||+|++|++|+....+.+. +.++.++++|+++++||+|+|++|+++++|+|
T Consensus 81 GPGf~k~~f~~~l~~~~~~~~-------~~~i~~~~~s~~~~~gl~Evl~~~~v~~~l~d 133 (133)
T PF03464_consen 81 GPGFTKEEFYKYLKAEARRKD-------KKKIVVVDTSSGGESGLNEVLKRPEVQKILKD 133 (133)
T ss_dssp ESTTHHHHHHHHHHHHHHHHT-------CCEEEEEE-SSSCHHHHHHHHHSHHHHHHHCT
T ss_pred CCHHHHHHHHHHHHHhhHhhc-------CCEEEEEECCCCCHHHHHHHHHhhhHHHHhcC
Confidence 999999999999999987642 25789999999999999999999999999976
No 10
>KOG0688 consensus Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=4.7e-30 Score=234.41 Aligned_cols=227 Identities=14% Similarity=0.222 Sum_probs=204.9
Q ss_pred cCCCCEEEEEEEEeecCcccccccEEEEEEccCCceEEEEccCCh-hhHHHHHHhcCCCCCCcEEEEEEeCCeEEEEEEe
Q 021563 61 DKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDS-LALDTLHQAADPTASADLAVVLMQEGLAHILLVG 139 (311)
Q Consensus 61 ~~~~~~Lri~G~i~~~~e~v~~G~~HTl~i~~~~~i~i~K~~wd~-~~le~L~ea~~~~~~~~~~~vvid~g~a~i~ll~ 139 (311)
-|.++..-.+|.++.+. ...+..++++||.+||....|.||. ||++.|.+++.+.. .+|+++||...+.++++.
T Consensus 84 vPpnglvly~gti~ted---gkekkv~idfepfkpintslyLcdNkfhte~l~~Ll~sd~--kfgfivmDg~~tlfgtl~ 158 (431)
T KOG0688|consen 84 VPPNGLVLYTGTIVTED---GKEKKVNIDFEPFKPINTSLYLCDNKFHTEALKELLESDN--KFGFIVMDGNGTLFGTLQ 158 (431)
T ss_pred CCCCceEEEeeeeEccC---CceeeeecccccccccccceEecCCccchHHHHHHHhhcc--cccEEEEcCCceeEEEec
Confidence 47789999999999876 3446789999999999999999987 99999999999888 899999999999999999
Q ss_pred cceEEEEEEEEEecCCCCCC-Ccch------hhHHHHHHHHHHHHHHHhccc---ccCccEEEEECCcccHHHHHH--HH
Q 021563 140 RSMTITRSRIETSIPRKHGP-AIAG------YESALNKFFENVLQAFLKHVD---FNVVRCAVIASPGFTKDQFHR--HL 207 (311)
Q Consensus 140 ~~~~~~~~~i~~~ip~K~~~-~~s~------~~~~~~~f~~~v~~~l~~~~~---~~~~~~iIIaGPGf~k~~f~~--~l 207 (311)
++...+++++++.+|+||++ |||+ |.+.++.|.+.+++...+++. ..++.++|+||..-+|.++.+ .+
T Consensus 159 gntrevLhkftVdlPkkhgrggqSalrfarlR~ekRhnYVrkvae~a~q~fi~~~~~Nv~gLilaGsadfKtelsqSd~f 238 (431)
T KOG0688|consen 159 GNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAELAVQRFITNDKPNVAGLILAGSADFKTELSQSDMF 238 (431)
T ss_pred cchHhhhheeeecCccccCccchhHHhhhhhhhhhhccceeeecccceeEEecCCCcceeEEEEecccccccccchhhhc
Confidence 99999999999999999999 6776 777889999999999988883 678999999999988888875 56
Q ss_pred HHHHHhcccccccccCCcEEEEEcCCCccccHHHHhcCchhHHhhhhhhHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHH
Q 021563 208 LLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVLDAPNVMNMIKDTKAAQEVQALKDFFNMLTNDPTRACYGPKHVEV 287 (311)
Q Consensus 208 ~~~~~~~~~~~~~~~~~k~~~~~~s~~~~~gl~Evl~~~~v~~~l~d~k~~~e~~~le~f~~~l~~~~~~~~YG~~eV~~ 287 (311)
+++++.+. +.++++|+||.+|++++|.-. .++|++.++++|.+++.+||++++.|.++.|||++++..
T Consensus 239 d~rlqskv----------i~~vdvsyGGengfnQaIeL~--aevlsnvk~vqekkli~~yfdEisqdtgky~Fgv~dTl~ 306 (431)
T KOG0688|consen 239 DPRLQSKV----------LKTVDVSYGGENGFNQAIELS--AEVLSNVKFVQEKKLIGKYFDEISQDTGKYCFGVEDTLL 306 (431)
T ss_pred chHHhhhH----------HhhhcccccchhhHHHHHHHH--HhhhhcceeeehhhHHHHHhhhhhcccCcccccHHHHHH
Confidence 77765422 257999999999999999988 899999999999999999999999999999999999999
Q ss_pred HHhcCCccEEEEecCCc
Q 021563 288 AHERMAVQTLLITDDLF 304 (311)
Q Consensus 288 A~e~GAVetLLIsD~l~ 304 (311)
|+++|||+||++.+.|=
T Consensus 307 aLe~gavetli~~enLd 323 (431)
T KOG0688|consen 307 ALEMGAVETLIVWENLD 323 (431)
T ss_pred HHHcCCeeehhHhhhhh
Confidence 99999999999988764
No 11
>PF03465 eRF1_3: eRF1 domain 3; InterPro: IPR005142 This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known []. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site []. This domain is also found in other proteins which may also be involved in translation termination but this awaits experimental verification.; PDB: 3OBY_A 3E1Y_D 1DT9_A 2KTU_A 2KTV_A 3IR9_A 3E20_H 3OBW_A 3AGJ_F 3MCA_B ....
Probab=99.43 E-value=1.6e-13 Score=110.96 Aligned_cols=52 Identities=44% Similarity=0.603 Sum_probs=48.9
Q ss_pred HHHHHHHHHHHHHHHhcCCCcEEEcHHHHHHHHhcCCccEEEEecCCcccCC
Q 021563 257 AAQEVQALKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLFRLVC 308 (311)
Q Consensus 257 ~~~e~~~le~f~~~l~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l~r~~d 308 (311)
+++|.++|++||++++++|+++|||+++|.+|+++|||+||||+|+++|+.+
T Consensus 1 ~~~E~~~ve~f~~~l~k~~~~~~yG~~eV~~Al~~GaV~~LlI~d~l~~~~~ 52 (113)
T PF03465_consen 1 IIKEKKLVEEFFEELAKDPGLAVYGIEEVKKALEMGAVETLLISDDLFRSRD 52 (113)
T ss_dssp HHHHHHHHHHHHHHHHTTCSSEEESHHHHHHHHHTT-EEEEEEEHHHHTESC
T ss_pred CHHHHHHHHHHHHHHhhCCCcEEECHHHHHHHHHhCCCcEEEEecccccccc
Confidence 5789999999999999999999999999999999999999999999999865
No 12
>PF10116 Host_attach: Protein required for attachment to host cells; InterPro: IPR019291 Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells [, ].
Probab=95.49 E-value=0.049 Score=45.25 Aligned_cols=91 Identities=15% Similarity=0.136 Sum_probs=59.4
Q ss_pred EEEEEeCCeEEEEEEecceE---EE------------EEEEEEecCCCCCC--Cc--c------hhhHHHHHHHHHHHHH
Q 021563 124 AVVLMQEGLAHILLVGRSMT---IT------------RSRIETSIPRKHGP--AI--A------GYESALNKFFENVLQA 178 (311)
Q Consensus 124 ~~vvid~g~a~i~ll~~~~~---~~------------~~~i~~~ip~K~~~--~~--s------~~~~~~~~f~~~v~~~ 178 (311)
.+||.|.+.|.|+...+... .. -+.+..+-||.... |+ + ..+...++|.++|++.
T Consensus 2 wVvVaD~~~Ar~f~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~d~~Gr~~~~~g~~~~~~~~~~~~~~~~~~Fa~~vA~~ 81 (138)
T PF10116_consen 2 WVVVADGSRARIFENEGDESEPLLELEELDHPESRLKDRDLVSDRPGRFHDSAGQRGSMEERTDPKEEEEERFAREVADR 81 (138)
T ss_pred EEEEEecceeEEEEecCCCCCcchhhhhhcccccccchhhhccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 47888999999998887643 11 13344555554222 11 1 1567788999999999
Q ss_pred HHhcccccCccEEEEECCcccHHHHHHHHHHHHHhc
Q 021563 179 FLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAERR 214 (311)
Q Consensus 179 l~~~~~~~~~~~iIIaGPGf~k~~f~~~l~~~~~~~ 214 (311)
|.+.......+.+||++|--+--.+.+.|.....+.
T Consensus 82 L~~~~~~~~~~~LvlvA~p~~LG~LR~~L~~~~~~~ 117 (138)
T PF10116_consen 82 LEKARRAGKFDRLVLVAPPRFLGLLREHLSKAVRKR 117 (138)
T ss_pred HHHHHHhCCCCeEEEEECHHHHHHHHHHhCHHHHHH
Confidence 999888777777877777744345555555555443
No 13
>TIGR03677 rpl7ae 50S ribosomal protein L7Ae. Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs. Interacts with protein L15e.
Probab=71.15 E-value=9.4 Score=30.85 Aligned_cols=30 Identities=23% Similarity=0.338 Sum_probs=27.6
Q ss_pred CCCcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 274 DPTRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 274 ~~~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
..+..++|.++|.+|++.|-+.-++|+.+.
T Consensus 23 ragkl~~G~~~v~kaikkgka~LVilA~D~ 52 (117)
T TIGR03677 23 ETGKIKKGTNEVTKAVERGIAKLVVIAEDV 52 (117)
T ss_pred HcCCEeEcHHHHHHHHHcCCccEEEEeCCC
Confidence 448999999999999999999999999876
No 14
>PF01248 Ribosomal_L7Ae: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family; InterPro: IPR004038 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, ribosomal protein L30 from eukaryotes and archaebacteria, Gadd45 and MyD118 [].; PDB: 2CZW_A 3V7E_B 2QEX_F 1YJ9_F 1VQ8_F 1YJN_F 3I56_F 1VQ6_F 2OTJ_F 1YIJ_F ....
Probab=71.11 E-value=10 Score=28.94 Aligned_cols=38 Identities=16% Similarity=0.229 Sum_probs=30.1
Q ss_pred HHHHHHhcCCCcEEEcHHHHHHHHhcCCccEEEEecCCc
Q 021563 266 DFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLF 304 (311)
Q Consensus 266 ~f~~~l~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l~ 304 (311)
..+....+. ++.++|.++|.+|++.|-+.-++++.+.-
T Consensus 5 ~~l~~a~~~-~~lv~G~~~v~k~l~~~~~~lvilA~d~~ 42 (95)
T PF01248_consen 5 KLLKLARKA-GRLVKGIKEVLKALKKGKAKLVILAEDCS 42 (95)
T ss_dssp HHHHHHHHH-SEEEESHHHHHHHHHTTCESEEEEETTSS
T ss_pred HHHHHHHhc-CCEEEchHHHHHHHHcCCCcEEEEcCCCC
Confidence 344444433 78999999999999999999999987753
No 15
>PRK07283 hypothetical protein; Provisional
Probab=70.41 E-value=5.3 Score=31.21 Aligned_cols=32 Identities=16% Similarity=0.184 Sum_probs=28.2
Q ss_pred hcCCCcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 272 TNDPTRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 272 ~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
+...++++.|.+.|.+|+..|.+.-++++.+.
T Consensus 13 A~raGklv~G~~~v~~aik~gk~~lVi~A~Da 44 (98)
T PRK07283 13 AQRAGRIISGEELVVKAIQSGQAKLVFLANDA 44 (98)
T ss_pred HHHhCCeeEcHHHHHHHHHcCCccEEEEeCCC
Confidence 44559999999999999999999999998764
No 16
>PRK07714 hypothetical protein; Provisional
Probab=69.98 E-value=5.2 Score=31.29 Aligned_cols=36 Identities=14% Similarity=0.245 Sum_probs=29.3
Q ss_pred HHHHHhcCCCcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 267 FFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 267 f~~~l~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
++.... ..+++++|.+.|.+|+..|-+.-++++.+.
T Consensus 9 ~Lgla~-raGk~v~G~~~v~~al~~g~~~lViiA~D~ 44 (100)
T PRK07714 9 FLGLAN-RARKVISGEELVLKEVRSGKAKLVLLSEDA 44 (100)
T ss_pred HHHHHH-HhCCeeecHHHHHHHHHhCCceEEEEeCCC
Confidence 333334 449999999999999999999999998764
No 17
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=68.70 E-value=5.8 Score=31.42 Aligned_cols=32 Identities=22% Similarity=0.318 Sum_probs=28.3
Q ss_pred hcCCCcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 272 TNDPTRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 272 ~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
+...+++++|.+.|.+|+..|.+.-|+++++.
T Consensus 12 A~rAGklv~G~~~v~~aik~gk~~lVI~A~D~ 43 (104)
T PRK05583 12 TKKAGKLLEGYNKCEEAIKKKKVYLIIISNDI 43 (104)
T ss_pred HHHhCCeeecHHHHHHHHHcCCceEEEEeCCC
Confidence 44559999999999999999999999998775
No 18
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=64.58 E-value=18 Score=29.39 Aligned_cols=40 Identities=15% Similarity=0.145 Sum_probs=32.1
Q ss_pred HHHHHHHHhcCCCcEEEcHHHHHHHHhcCCccEEEEecCCc
Q 021563 264 LKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDLF 304 (311)
Q Consensus 264 le~f~~~l~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l~ 304 (311)
+-.++....+. +....|.++|.+|++.|-+.-++|+++.-
T Consensus 18 i~~lL~la~ra-gklv~G~~~v~kaikkgkakLVilA~D~s 57 (122)
T PRK04175 18 ALEAVEKARDT-GKIKKGTNETTKAVERGIAKLVVIAEDVD 57 (122)
T ss_pred HHHHHHHHHHc-CCEeEcHHHHHHHHHcCCccEEEEeCCCC
Confidence 33444444444 89999999999999999999999998863
No 19
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=64.53 E-value=15 Score=29.32 Aligned_cols=39 Identities=10% Similarity=0.186 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCCcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 264 LKDFFNMLTNDPTRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 264 le~f~~~l~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
++.++... ...++.+.|.++|.+|+..|-+.-++|+.+.
T Consensus 13 i~~~Lgla-~raGKlv~G~~~vlkalk~gkaklViiA~D~ 51 (108)
T PTZ00106 13 INSKLQLV-MKSGKYTLGTKSTLKALRNGKAKLVIISNNC 51 (108)
T ss_pred HHHHHHHH-HHhCCeeecHHHHHHHHHcCCeeEEEEeCCC
Confidence 34444444 4459999999999999999999999999875
No 20
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=63.26 E-value=15 Score=27.77 Aligned_cols=28 Identities=21% Similarity=0.337 Sum_probs=26.0
Q ss_pred CcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 276 TRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 276 ~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
++...|.++|.+|++.|-+.-++|..+.
T Consensus 10 gkl~~G~~~v~kai~~gkaklViiA~D~ 37 (82)
T PRK13602 10 KSIVIGTKQTVKALKRGSVKEVVVAEDA 37 (82)
T ss_pred CCEEEcHHHHHHHHHcCCeeEEEEECCC
Confidence 7899999999999999999999998764
No 21
>PRK09190 hypothetical protein; Provisional
Probab=62.21 E-value=33 Score=30.97 Aligned_cols=32 Identities=16% Similarity=0.156 Sum_probs=27.9
Q ss_pred hcCCCcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 272 TNDPTRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 272 ~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
++..++++.|.+.|..|+..|-+.-||++.+.
T Consensus 106 ArRAGklVsG~~~V~~alk~gk~~Lvi~A~Da 137 (220)
T PRK09190 106 ARKAGQVVSGFEKVDAALRSGEAAALIHASDG 137 (220)
T ss_pred HhhhCCEeecHHHHHHHHHcCCceEEEEeccC
Confidence 44559999999999999999999999988764
No 22
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=61.10 E-value=21 Score=27.89 Aligned_cols=29 Identities=10% Similarity=0.142 Sum_probs=27.0
Q ss_pred CCcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 275 PTRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 275 ~~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
.++.+.|.++|.+|++.|-+.-++|+++.
T Consensus 14 agkl~~G~~~v~kai~~gkaklViiA~D~ 42 (99)
T PRK01018 14 TGKVILGSKRTIKAIKLGKAKLVIVASNC 42 (99)
T ss_pred cCCEEEcHHHHHHHHHcCCceEEEEeCCC
Confidence 58999999999999999999999999874
No 23
>TIGR01175 pilM type IV pilus assembly protein PilM. This protein is required for the assembly of the type IV fimbria in Pseudomonas aeruginosa responsible for twitching motility, and for a similar pilus-like structure in Synechocystis. It is also found in species such as Deinococcus described as having natural transformation (for which a type IV pilus-like structure is proposed) but not fimbria.
Probab=60.63 E-value=1.1e+02 Score=28.68 Aligned_cols=89 Identities=12% Similarity=0.133 Sum_probs=56.3
Q ss_pred EEEEEEeCCeEEEEEEecceEEEEEEEEEe-------------cCC------CCCCCcc--hhhHHHHHHHHHHHHHHHh
Q 021563 123 LAVVLMQEGLAHILLVGRSMTITRSRIETS-------------IPR------KHGPAIA--GYESALNKFFENVLQAFLK 181 (311)
Q Consensus 123 ~~~vvid~g~a~i~ll~~~~~~~~~~i~~~-------------ip~------K~~~~~s--~~~~~~~~f~~~v~~~l~~ 181 (311)
.++|-+..+...++++.+........+... +|- |...+.. .....++.++++++..+.+
T Consensus 190 ~~lvdiG~~~t~l~i~~~g~~~~~r~i~~G~~~i~~~i~~~~~~~~~~Ae~~k~~~~~~~~~~~~~~~~~~~~l~~eI~~ 269 (348)
T TIGR01175 190 AALVDIGATSSTLNLLHPGRMLFTREVPFGTRQLTSELSRAYGLNPEEAGEAKQQGGLPLLYDPEVLRRFKGELVDEIRR 269 (348)
T ss_pred EEEEEECCCcEEEEEEECCeEEEEEEeechHHHHHHHHHHHcCCCHHHHHHHHhcCCCCCchhHHHHHHHHHHHHHHHHH
Confidence 778888889999999988877776666532 110 0000100 0122344555556555554
Q ss_pred ccc-------ccCccEEEEECCcccHHHHHHHHHHHH
Q 021563 182 HVD-------FNVVRCAVIASPGFTKDQFHRHLLLEA 211 (311)
Q Consensus 182 ~~~-------~~~~~~iIIaGPGf~k~~f~~~l~~~~ 211 (311)
.++ ...+..|+|+|-|.--..|.+++.+.+
T Consensus 270 ~l~~~~~~~~~~~i~~I~LtGgga~~~gl~~~l~~~l 306 (348)
T TIGR01175 270 SLQFFTAQSGTNSLDGLVLAGGGATLSGLDAAIYQRL 306 (348)
T ss_pred HHHhhcCCCCCcccceEEEECccccchhHHHHHHHHH
Confidence 443 235889999998888788888888876
No 24
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [, ]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose []. This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [, ]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes []. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; GO: 0008168 methyltransferase activity; PDB: 1GZ0_D 1IPA_A.
Probab=59.72 E-value=12 Score=26.93 Aligned_cols=24 Identities=25% Similarity=0.374 Sum_probs=22.8
Q ss_pred EEcHHHHHHHHhcCC-ccEEEEecC
Q 021563 279 CYGPKHVEVAHERMA-VQTLLITDD 302 (311)
Q Consensus 279 ~YG~~eV~~A~e~GA-VetLLIsD~ 302 (311)
.||...|.+|++.|. +..|+++++
T Consensus 2 ieG~~~V~eaL~~~~~i~~l~~~~~ 26 (76)
T PF08032_consen 2 IEGRHAVEEALKSGPRIKKLFVTEE 26 (76)
T ss_dssp EESHHHHHHHHHCTGGEEEEEEETT
T ss_pred EEEHHHHHHHHcCCCCccEEEEEcC
Confidence 699999999999987 999999998
No 25
>PF03485 Arg_tRNA_synt_N: Arginyl tRNA synthetase N terminal domain; InterPro: IPR005148 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found at the N terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA recognition [].; GO: 0000166 nucleotide binding, 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1F7V_A 1F7U_A 1BS2_A 2ZUE_A 2ZUF_A 1IQ0_A 3GDZ_B.
Probab=58.09 E-value=12 Score=28.09 Aligned_cols=29 Identities=14% Similarity=0.348 Sum_probs=21.2
Q ss_pred HHHHHHHHHHhccccc-CccEEEEECCccc
Q 021563 171 FFENVLQAFLKHVDFN-VVRCAVIASPGFT 199 (311)
Q Consensus 171 f~~~v~~~l~~~~~~~-~~~~iIIaGPGf~ 199 (311)
==.+|++.+.+.+... .++.+=++||||+
T Consensus 52 ~P~~iA~~i~~~l~~~~~i~~vev~gpGFi 81 (85)
T PF03485_consen 52 NPREIAEEIAEKLEKSPIIEKVEVAGPGFI 81 (85)
T ss_dssp -HHHHHHHHHHCHCTTTTEEEEEEETTTEE
T ss_pred CHHHHHHHHHHhcCCCCCEEEEEEcCCcEE
Confidence 3446777777777533 3889999999986
No 26
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=56.56 E-value=18 Score=27.43 Aligned_cols=29 Identities=24% Similarity=0.327 Sum_probs=26.5
Q ss_pred CCcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 275 PTRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 275 ~~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
+++.+.|.++|.+|++.|-++-++|..+.
T Consensus 6 ~GKlv~G~~~vlkaIk~gkakLViiA~Da 34 (82)
T PRK13601 6 PSKRVVGAKQTLKAITNCNVLQVYIAKDA 34 (82)
T ss_pred CccEEEchHHHHHHHHcCCeeEEEEeCCC
Confidence 47899999999999999999999998764
No 27
>PRK06683 hypothetical protein; Provisional
Probab=56.25 E-value=23 Score=26.69 Aligned_cols=30 Identities=20% Similarity=0.256 Sum_probs=27.1
Q ss_pred CCCcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 274 DPTRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 274 ~~~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
+.++.+.|.++|.+|++.|-++.++|..+.
T Consensus 8 ~agk~v~G~~~v~kaik~gkaklViiA~Da 37 (82)
T PRK06683 8 NAENVVVGHKRTLEAIKNGIVKEVVIAEDA 37 (82)
T ss_pred hCCCEEEcHHHHHHHHHcCCeeEEEEECCC
Confidence 448899999999999999999999998764
No 28
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=53.39 E-value=23 Score=27.01 Aligned_cols=27 Identities=26% Similarity=0.338 Sum_probs=24.1
Q ss_pred cEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 277 RACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 277 ~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
...+|.+++.+|++.|-+..++|..+.
T Consensus 13 ~~vvG~kqt~Kai~kg~~~~v~iA~Da 39 (84)
T PRK13600 13 HFVVGLKETLKALKKDQVTSLIIAEDV 39 (84)
T ss_pred CceeeHHHHHHHHhcCCceEEEEeCCC
Confidence 348999999999999999999998764
No 29
>PRK09557 fructokinase; Reviewed
Probab=48.58 E-value=64 Score=29.85 Aligned_cols=47 Identities=9% Similarity=0.099 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHh
Q 021563 167 ALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAER 213 (311)
Q Consensus 167 ~~~~f~~~v~~~l~~~~~~~~~~~iIIaGPGf~k~~f~~~l~~~~~~ 213 (311)
.++++.+.++.++.......++..|||+|.-...+.|.+.+.+...+
T Consensus 224 ~l~~~~~~La~~l~~l~~~ldP~~IvlgG~~~~~~~~~~~l~~~~~~ 270 (301)
T PRK09557 224 AFRRYEDRLAKSLAHVINILDPDVIVLGGGMSNVDRLYPTLPALLKQ 270 (301)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCEEEEcCcccchHHHHHHHHHHHHH
Confidence 35566666666777777778899999999866556676666555543
No 30
>PRK05082 N-acetylmannosamine kinase; Provisional
Probab=47.91 E-value=41 Score=30.94 Aligned_cols=46 Identities=7% Similarity=0.049 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHh
Q 021563 168 LNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAER 213 (311)
Q Consensus 168 ~~~f~~~v~~~l~~~~~~~~~~~iIIaGPGf~k~~f~~~l~~~~~~ 213 (311)
+++|.+.++..+.......++..|||+|+....+.|.+.+.+.+.+
T Consensus 214 ~~~~~~~la~~l~~l~~~~dpe~IvlgG~~~~~~~~~~~i~~~l~~ 259 (291)
T PRK05082 214 INRSAQAIARLIADLKATLDCQCVVLGGSVGLAEGYLELVQAYLAQ 259 (291)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCEEEEcCccccHHHHHHHHHHHHHh
Confidence 3455556666666666677899999999987777777766665543
No 31
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=46.12 E-value=1.7e+02 Score=29.76 Aligned_cols=130 Identities=13% Similarity=0.177 Sum_probs=69.4
Q ss_pred ecCCCCEEEEEEEEeecCccccc---ccEEEEEEccCCceEEEEccCChhhHHHHH-HhcCCCCCCcEEEEEEeCCeEEE
Q 021563 60 YDKEGSVLRIRGKNILENEHVKI---GAFHTLEIELHRAFVLRKDLWDSLALDTLH-QAADPTASADLAVVLMQEGLAHI 135 (311)
Q Consensus 60 f~~~~~~Lri~G~i~~~~e~v~~---G~~HTl~i~~~~~i~i~K~~wd~~~le~L~-ea~~~~~~~~~~~vvid~g~a~i 135 (311)
|++.+=++|++-=+ ++..|. |..+-..| -.+-+++.+++.+. +.++...+..=.++=|+...|++
T Consensus 146 Fd~~TMSvHLKeg~---~P~aK~GkpG~~k~v~l--------~d~pl~~~ele~ia~eIi~~a~~~~~sfIEi~r~GatV 214 (604)
T COG1855 146 FDEETMSVHLKEGV---PPMAKKGKPGEWKLVRL--------SDKPLTREELEEIAREIIERAKRDPDSFIEIDRPGATV 214 (604)
T ss_pred cCCcceEEeeccCC---CcccccCCCCcEEEEEc--------CCccCCHHHHHHHHHHHHHHHhhCcCceEEEccCCceE
Confidence 67766667765422 223333 44333332 22234444444433 22222222234799999999999
Q ss_pred EEEecceEEE-------EEEEEEecCCCCCCCcchhhHHHHHH--HHHHHHHHHhcccccCccEEEEEC-CcccHHHHHH
Q 021563 136 LLVGRSMTIT-------RSRIETSIPRKHGPAIAGYESALNKF--FENVLQAFLKHVDFNVVRCAVIAS-PGFTKDQFHR 205 (311)
Q Consensus 136 ~ll~~~~~~~-------~~~i~~~ip~K~~~~~s~~~~~~~~f--~~~v~~~l~~~~~~~~~~~iIIaG-PGf~k~~f~~ 205 (311)
.-++.+.+.+ ..+++..-|=-+- .++.| =..+.+.|.+ .-++|+||| ||-=|..|.+
T Consensus 215 vQlrn~RIvIarPPfSd~~EITavRPvvk~--------~ledY~L~dkl~eRL~e-----raeGILIAG~PGaGKsTFaq 281 (604)
T COG1855 215 VQLRNYRIVIARPPFSDRWEITAVRPVVKL--------SLEDYGLSDKLKERLEE-----RAEGILIAGAPGAGKSTFAQ 281 (604)
T ss_pred EEeccEEEEEecCCCCCceEEEEEeeeEEe--------chhhcCCCHHHHHHHHh-----hhcceEEecCCCCChhHHHH
Confidence 9999888776 3455555553211 11111 0112223333 356899988 6888999987
Q ss_pred HHHHHHHh
Q 021563 206 HLLLEAER 213 (311)
Q Consensus 206 ~l~~~~~~ 213 (311)
-|..-+.+
T Consensus 282 AlAefy~~ 289 (604)
T COG1855 282 ALAEFYAS 289 (604)
T ss_pred HHHHHHHh
Confidence 66555443
No 32
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=45.02 E-value=45 Score=27.02 Aligned_cols=30 Identities=23% Similarity=0.305 Sum_probs=26.7
Q ss_pred CCCcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 274 DPTRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 274 ~~~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
..+.+.+|.++|.+|++.|-..-++|+.+.
T Consensus 24 ~~~ki~~G~~e~~Kai~~g~a~LVviA~Dv 53 (116)
T COG1358 24 RAGKLKKGTNEVTKAIERGKAKLVVIAEDV 53 (116)
T ss_pred hcCCchhhHHHHHHHHHcCCCcEEEEecCC
Confidence 347899999999999999999999998764
No 33
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=43.66 E-value=90 Score=29.70 Aligned_cols=64 Identities=19% Similarity=0.252 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHHHHHHhcccccCccEEEEEC--CcccHHHHHHHHHHHHHhcccccccccCCcEEEEEcCCCccccHHHH
Q 021563 165 ESALNKFFENVLQAFLKHVDFNVVRCAVIAS--PGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREV 242 (311)
Q Consensus 165 ~~~~~~f~~~v~~~l~~~~~~~~~~~iIIaG--PGf~k~~f~~~l~~~~~~~~~~~~~~~~~k~~~~~~s~~~~~gl~Ev 242 (311)
+...+.|.+.+...+.. .+.+||+| |.-+..++|.-|-+.+++ .+..+++|+|. ..|.++
T Consensus 113 ~~~~~~~l~~~~~~l~~------~d~VvlsGSlP~g~~~d~y~~li~~~~~---------~g~~vilD~Sg---~~L~~~ 174 (310)
T COG1105 113 EAELEQFLEQLKALLES------DDIVVLSGSLPPGVPPDAYAELIRILRQ---------QGAKVILDTSG---EALLAA 174 (310)
T ss_pred HHHHHHHHHHHHHhccc------CCEEEEeCCCCCCCCHHHHHHHHHHHHh---------cCCeEEEECCh---HHHHHH
Confidence 45667777655444433 44699999 434444555545555543 24557888876 346677
Q ss_pred hcCc
Q 021563 243 LDAP 246 (311)
Q Consensus 243 l~~~ 246 (311)
|+-+
T Consensus 175 L~~~ 178 (310)
T COG1105 175 LEAK 178 (310)
T ss_pred HccC
Confidence 6654
No 34
>PRK13310 N-acetyl-D-glucosamine kinase; Provisional
Probab=35.59 E-value=1.2e+02 Score=27.95 Aligned_cols=47 Identities=9% Similarity=0.040 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHHHh
Q 021563 167 ALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEAER 213 (311)
Q Consensus 167 ~~~~f~~~v~~~l~~~~~~~~~~~iIIaGPGf~k~~f~~~l~~~~~~ 213 (311)
.+++|.+.++..+....+..++..|||+|+-...+.|.+.+.+.+.+
T Consensus 225 ~~~~~~~~la~~l~n~~~~ldP~~IvlgG~~~~~~~~~~~l~~~~~~ 271 (303)
T PRK13310 225 HVERYLDLLAICLGNILTIVDPHLVVLGGGLSNFDAIYEQLPKRLPR 271 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCEEEECCcccChHHHHHHHHHHHHH
Confidence 34455556666666666677899999999754445566656555543
No 35
>COG0018 ArgS Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=35.48 E-value=72 Score=33.04 Aligned_cols=27 Identities=22% Similarity=0.524 Sum_probs=20.2
Q ss_pred HHHHHHHHhccccc-CccEEEEECCccc
Q 021563 173 ENVLQAFLKHVDFN-VVRCAVIASPGFT 199 (311)
Q Consensus 173 ~~v~~~l~~~~~~~-~~~~iIIaGPGf~ 199 (311)
++||+.+...+..+ .+..|-+|||||.
T Consensus 57 ~eiA~~i~~~l~~~~~~~~veiaGpgfI 84 (577)
T COG0018 57 REIAEEIAEKLDTDEIIEKVEIAGPGFI 84 (577)
T ss_pred HHHHHHHHHhccccCcEeEEEEcCCCEE
Confidence 45777777766644 4788999999975
No 36
>COG4972 PilM Tfp pilus assembly protein, ATPase PilM [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=34.89 E-value=76 Score=30.54 Aligned_cols=47 Identities=11% Similarity=0.189 Sum_probs=39.1
Q ss_pred hHHHHHHHHHHHHHHHhccc-------ccCccEEEEECCcccHHHHHHHHHHHH
Q 021563 165 ESALNKFFENVLQAFLKHVD-------FNVVRCAVIASPGFTKDQFHRHLLLEA 211 (311)
Q Consensus 165 ~~~~~~f~~~v~~~l~~~~~-------~~~~~~iIIaGPGf~k~~f~~~l~~~~ 211 (311)
...+..|..++.+.+.+.+. ..++++|+++|||-.-..+.+++.+++
T Consensus 258 ~~vl~~f~~~l~~ei~Rslqfy~~~s~~~~id~i~LaGggA~l~gL~~~i~qrl 311 (354)
T COG4972 258 SEVLRPFLGELTQEIRRSLQFYLSQSEMVDIDQILLAGGGASLEGLAAAIQQRL 311 (354)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccceeeEEEEecCCcchhhHHHHHHHHh
Confidence 44567899999999977664 467999999999999999988888876
No 37
>COG1911 RPL30 Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]
Probab=32.35 E-value=75 Score=24.96 Aligned_cols=33 Identities=9% Similarity=0.085 Sum_probs=28.6
Q ss_pred hcCCCcEEEcHHHHHHHHhcCCccEEEEecCCc
Q 021563 272 TNDPTRACYGPKHVEVAHERMAVQTLLITDDLF 304 (311)
Q Consensus 272 ~~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l~ 304 (311)
+.+.|++..|.+...+++.+|..+-++|..+..
T Consensus 14 avkTGkvilG~k~tiK~lk~gkaKliiiAsN~P 46 (100)
T COG1911 14 AVKTGKVILGSKRTIKSLKLGKAKLIIIASNCP 46 (100)
T ss_pred HHhcCCEEEehHHHHHHHHcCCCcEEEEecCCC
Confidence 335589999999999999999999999987654
No 38
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=32.27 E-value=2.7e+02 Score=22.60 Aligned_cols=71 Identities=14% Similarity=0.098 Sum_probs=52.1
Q ss_pred hhHHHHHHhcCC-CCCCcEEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCCCCcchhhHHHHHHHHHHHHHHHhcc
Q 021563 106 LALDTLHQAADP-TASADLAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGPAIAGYESALNKFFENVLQAFLKHV 183 (311)
Q Consensus 106 ~~le~L~ea~~~-~~~~~~~~vvid~g~a~i~ll~~~~~~~~~~i~~~ip~K~~~~~s~~~~~~~~f~~~v~~~l~~~~ 183 (311)
-.|+.+++.+.. ....-++.|---++-...+.++..+++++--.... .....+..+..||++|.+.-.+.+
T Consensus 35 ~sLD~iee~~~~~~~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~~~-------~~~~~d~~ik~fF~~vh~~Y~~~~ 106 (132)
T PF04628_consen 35 SSLDVIEEKLWKSSSDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHDMS-------DNSIRDEDIKQFFKEVHELYVKAL 106 (132)
T ss_dssp HHHHHHHHCCHCSSSCSEEEEEEEETTEEEEEEETTT--EEEEEECGG-------G-S--HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhhcccccccCceehhhhHHHHhhhccCceeEEEEEecc-------cCCcchHHHHHHHHHHHHHHHHHc
Confidence 468889988777 66667888888899999999999998887655421 111257889999999999887766
No 39
>PTZ00288 glucokinase 1; Provisional
Probab=28.85 E-value=4.3e+02 Score=26.08 Aligned_cols=87 Identities=22% Similarity=0.224 Sum_probs=44.5
Q ss_pred ChhhHHHHHHhcCCCCC--CcEEEEEEeCCe--EEEEEEec--ceEEEEEEEEEecC-CCCCCCcchhhHHHHHHHHHHH
Q 021563 104 DSLALDTLHQAADPTAS--ADLAVVLMQEGL--AHILLVGR--SMTITRSRIETSIP-RKHGPAIAGYESALNKFFENVL 176 (311)
Q Consensus 104 d~~~le~L~ea~~~~~~--~~~~~vvid~g~--a~i~ll~~--~~~~~~~~i~~~ip-~K~~~~~s~~~~~~~~f~~~v~ 176 (311)
+..+++.|.+..+.+.+ ....+|.+|-|. +.+++... +............| ++. .-...-+||.++.
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~DiGgt~~R~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~ 78 (405)
T PTZ00288 5 DEIFLEQLAEELKTDASWSSGPIFVGCDVGGTNARVGFAREVQHDDSGVHIIYVRFNVTKT------DIRELLEFFDEVL 78 (405)
T ss_pred hHHHHHHHHHHhccCcccccCCeEEEEEecCCceEEEEEeccCCCCCceeEEEEecccccc------cHHHHHHHHHHHH
Confidence 34567888877765442 222355566665 44665543 11111222333344 221 1234668899999
Q ss_pred HHHHhccc-ccCcc--EEEEECC
Q 021563 177 QAFLKHVD-FNVVR--CAVIASP 196 (311)
Q Consensus 177 ~~l~~~~~-~~~~~--~iIIaGP 196 (311)
+.+.+... ...+. ||-||||
T Consensus 79 ~~l~~~~~~~~~~~~a~iAvAGP 101 (405)
T PTZ00288 79 QKLKKNLSFIQRVAAGAISVPGP 101 (405)
T ss_pred HHHHhcCccccCcCeEEEEEeCc
Confidence 98887542 12333 4555555
No 40
>PRK15080 ethanolamine utilization protein EutJ; Provisional
Probab=27.93 E-value=1.3e+02 Score=27.54 Aligned_cols=44 Identities=9% Similarity=0.092 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHhcccccCccEEEEECCcccHHHHHHHHHHHH
Q 021563 168 LNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKDQFHRHLLLEA 211 (311)
Q Consensus 168 ~~~f~~~v~~~l~~~~~~~~~~~iIIaGPGf~k~~f~~~l~~~~ 211 (311)
++.+++++++.+.+.+....+..|+++|-|---..+.+++.+.+
T Consensus 202 i~~~~~~i~~~i~~~l~~~~~~~IvLtGG~s~lpgl~e~l~~~l 245 (267)
T PRK15080 202 VKPVVEKMASIVARHIEGQDVEDIYLVGGTCCLPGFEEVFEKQT 245 (267)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCEEEEECCcccchhHHHHHHHHh
Confidence 44567777777777776667888888888766666666666665
No 41
>PF07116 DUF1372: Protein of unknown function (DUF1372); InterPro: IPR010779 This entry is represented by Streptococcus phage Sfi11, Gp93. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several Streptococcus bacteriophage sequences and related proteins from Streptococcus species. Members of this family are typically around 100 residues in length and their function is unknown.
Probab=27.76 E-value=89 Score=24.70 Aligned_cols=37 Identities=27% Similarity=0.399 Sum_probs=30.3
Q ss_pred EEEEEEEeecCcccccccEEEEEEccCCceEEEEccCChh
Q 021563 67 LRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSL 106 (311)
Q Consensus 67 Lri~G~i~~~~e~v~~G~~HTl~i~~~~~i~i~K~~wd~~ 106 (311)
--+.|++++-. ..|.++|+++..--.|-+.|+.+++.
T Consensus 56 ~ei~GkVt~K~---~ig~~yTvti~~YGkFlVtkeqY~~i 92 (104)
T PF07116_consen 56 AEIFGKVTEKE---IIGGLYTVTIGAYGKFLVTKEQYESI 92 (104)
T ss_pred cEEEEEEeece---eECCEEEEEecCceEEEEehhhccee
Confidence 56889998754 57999999999988999998777653
No 42
>KOG0283 consensus WD40 repeat-containing protein [Function unknown]
Probab=23.85 E-value=6e+02 Score=27.09 Aligned_cols=84 Identities=17% Similarity=0.179 Sum_probs=55.5
Q ss_pred EEEEeecCCCCEEEEEEEEeecCcccccccEEEEEEccCCceEEEEccCChhhHHHHHHhcCCCCCCcEEEEEEeCCeEE
Q 021563 55 VEVVDYDKEGSVLRIRGKNILENEHVKIGAFHTLEIELHRAFVLRKDLWDSLALDTLHQAADPTASADLAVVLMQEGLAH 134 (311)
Q Consensus 55 Ve~ief~~~~~~Lri~G~i~~~~e~v~~G~~HTl~i~~~~~i~i~K~~wd~~~le~L~ea~~~~~~~~~~~vvid~g~a~ 134 (311)
|+.|.|+|-+++..|+|-+ =|+-.-+.| +.+.+. .|...+ +.+-.+|- .+...+++|=.-.|.|.
T Consensus 412 VTcVaFnPvDDryFiSGSL--------D~KvRiWsI-~d~~Vv----~W~Dl~-~lITAvcy-~PdGk~avIGt~~G~C~ 476 (712)
T KOG0283|consen 412 VTCVAFNPVDDRYFISGSL--------DGKVRLWSI-SDKKVV----DWNDLR-DLITAVCY-SPDGKGAVIGTFNGYCR 476 (712)
T ss_pred eEEEEecccCCCcEeeccc--------ccceEEeec-CcCeeE----eehhhh-hhheeEEe-ccCCceEEEEEeccEEE
Confidence 7899999999999999943 144444444 233333 354332 33334433 33468899999999999
Q ss_pred EEEEecceEEEEEEEEEec
Q 021563 135 ILLVGRSMTITRSRIETSI 153 (311)
Q Consensus 135 i~ll~~~~~~~~~~i~~~i 153 (311)
||...+.....-..|...-
T Consensus 477 fY~t~~lk~~~~~~I~~~~ 495 (712)
T KOG0283|consen 477 FYDTEGLKLVSDFHIRLHN 495 (712)
T ss_pred EEEccCCeEEEeeeEeecc
Confidence 9998887777666665553
No 43
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=23.83 E-value=67 Score=25.20 Aligned_cols=21 Identities=38% Similarity=0.540 Sum_probs=18.5
Q ss_pred EEeecCCCCEEEEEEEEeecC
Q 021563 57 VVDYDKEGSVLRIRGKNILEN 77 (311)
Q Consensus 57 ~ief~~~~~~Lri~G~i~~~~ 77 (311)
.|.||+.+++|+|+|.-..++
T Consensus 2 ~V~Fd~~~g~l~i~GeSypEn 22 (99)
T PF09345_consen 2 EVDFDFDTGRLEISGESYPEN 22 (99)
T ss_pred eEEEEccCCEEEEecccCccC
Confidence 488999999999999887766
No 44
>COG1940 NagC Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]
Probab=22.51 E-value=2e+02 Score=26.66 Aligned_cols=46 Identities=9% Similarity=0.061 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHhcccccCccEEEEEC--CcccHHHHHHHHHHHHHh
Q 021563 168 LNKFFENVLQAFLKHVDFNVVRCAVIAS--PGFTKDQFHRHLLLEAER 213 (311)
Q Consensus 168 ~~~f~~~v~~~l~~~~~~~~~~~iIIaG--PGf~k~~f~~~l~~~~~~ 213 (311)
++++.+.++..+....+..++..|||+| +....+.|.+.+......
T Consensus 228 ~~~~~~~la~~ianl~~~~~P~~IvigG~g~~~~~~~~~~~l~~~~~~ 275 (314)
T COG1940 228 IERAADYLARGLANLINLLDPEVIVIGGGGVSALGDLLLPRLRKLLAK 275 (314)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCeEEEECcccccchhHHHHHHHHHHHH
Confidence 4455556666666666677888999987 665667777777766554
No 45
>PF14213 DUF4325: Domain of unknown function (DUF4325)
Probab=22.45 E-value=92 Score=22.63 Aligned_cols=68 Identities=12% Similarity=0.161 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHhccc-ccCccEEEEECCcccHHHHHHHHHHHHHhcccccccccCCcEEEEEcCCCccccHHHHh
Q 021563 169 NKFFENVLQAFLKHVD-FNVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTSSGYKHSLREVL 243 (311)
Q Consensus 169 ~~f~~~v~~~l~~~~~-~~~~~~iIIaGPGf~k~~f~~~l~~~~~~~~~~~~~~~~~k~~~~~~s~~~~~gl~Evl 243 (311)
+++|+.+..++..--. .-+..+|-..||+|+-+-|-..+....... ...++.+.+.+.....-|+.++
T Consensus 4 ~~~~~~i~~~l~~~~~V~lDF~gv~~~~ssFl~eafg~l~~~~~~~~-------~~~~l~~~~~~~~~~~~I~~vi 72 (74)
T PF14213_consen 4 ERLRDEIEPALKEGEKVVLDFEGVESITSSFLNEAFGQLVREFGEEE-------IKKRLKFKNANESIKEMIKRVI 72 (74)
T ss_pred HHHHHHHHHHHhcCCeEEEECCCcccccHHHHHHHHHHHHHHcCHHH-------HhheeEEecCCHHHHHHHHHHH
Confidence 5678887777763210 123455677899999999887665543221 1234555665554444444433
No 46
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=22.18 E-value=85 Score=23.98 Aligned_cols=19 Identities=37% Similarity=0.394 Sum_probs=15.3
Q ss_pred hhhhHhhhcCCCCEEEEEe
Q 021563 11 DLWFAYNLIAPGDSVMAVT 29 (311)
Q Consensus 11 Dlw~lynli~~GD~V~~~T 29 (311)
|.-.++..+++||+|+|.-
T Consensus 53 d~~~~~~~f~~GDiV~AkV 71 (92)
T cd05791 53 DKVEMYKCFRPGDIVRAKV 71 (92)
T ss_pred chHHHHhhcCCCCEEEEEE
Confidence 3334888899999999974
No 47
>PTZ00222 60S ribosomal protein L7a; Provisional
Probab=21.24 E-value=2.8e+02 Score=25.77 Aligned_cols=31 Identities=19% Similarity=0.348 Sum_probs=27.1
Q ss_pred cCCCcEEEcHHHHHHHHhcCCccEEEEecCC
Q 021563 273 NDPTRACYGPKHVEVAHERMAVQTLLITDDL 303 (311)
Q Consensus 273 ~~~~~~~YG~~eV~~A~e~GAVetLLIsD~l 303 (311)
+.|-.+.+|.++|.++++.|-+.-++|..+.
T Consensus 128 kkp~~LvsG~n~VtkaIekkKAkLVIIA~DV 158 (263)
T PTZ00222 128 KAPLAVVTGLQEVTRAIEKKQARMVVIANNV 158 (263)
T ss_pred CCCCeeccCHHHHHHHHHcCCceEEEEeCCC
Confidence 4455689999999999999999999999875
No 48
>PF11215 DUF3010: Protein of unknown function (DUF3010); InterPro: IPR021378 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=21.11 E-value=5e+02 Score=21.74 Aligned_cols=61 Identities=16% Similarity=0.071 Sum_probs=37.6
Q ss_pred EEEEEEeCCeEEEEEEecceEEEEEEEEEecCCCCCC----CcchhhHHHHHHHHHHHHHHHhcccccCccEEEE
Q 021563 123 LAVVLMQEGLAHILLVGRSMTITRSRIETSIPRKHGP----AIAGYESALNKFFENVLQAFLKHVDFNVVRCAVI 193 (311)
Q Consensus 123 ~~~vvid~g~a~i~ll~~~~~~~~~~i~~~ip~K~~~----~~s~~~~~~~~f~~~v~~~l~~~~~~~~~~~iII 193 (311)
++-|=+..++|.||+|+...-. .++|.-+.. ..+.....+.+|...+++-+.++ +++.|+|
T Consensus 3 vCGVELkgneaii~ll~~~~~~------~~~pdcr~~k~~l~~~~~~~~vr~Fq~~f~kl~~dy----~Vd~VvI 67 (138)
T PF11215_consen 3 VCGVELKGNEAIICLLSLDDGL------FQLPDCRVRKFSLSDDNSTEEVRKFQFTFAKLMEDY----KVDKVVI 67 (138)
T ss_pred EEEEEEecCeEEEEEEecCCCc------eECCccceeEEEcCCCccHHHHHHHHHHHHHHHHHc----CCCEEEE
Confidence 3456678899999998854322 233321111 11123457888998888777775 6778887
No 49
>TIGR00744 ROK_glcA_fam ROK family protein (putative glucokinase). This alignment models one branch of the ROK superfamily of proteins. The three members of the seed alignment for this model all have experimental evidence for activity as glucokinase, but the set of related proteins is crowded with paralogs of different or unknown function. Proteins scoring above the trusted_cutoff will show strong similarity to at least one known glucokinase and may be designated as putative glucokinases. However, definitive identification of glucokinases should be done only with extreme caution.
Probab=20.94 E-value=3e+02 Score=25.33 Aligned_cols=47 Identities=6% Similarity=-0.075 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHhcccccCccEEEEECCccc-HHHHHHHHHHHHHh
Q 021563 167 ALNKFFENVLQAFLKHVDFNVVRCAVIASPGFT-KDQFHRHLLLEAER 213 (311)
Q Consensus 167 ~~~~f~~~v~~~l~~~~~~~~~~~iIIaGPGf~-k~~f~~~l~~~~~~ 213 (311)
.++++.+.++..+....+..++..|||+|+-+. .+.|.+.+.+...+
T Consensus 231 i~~~~~~~L~~~i~~~~~~~dP~~IvlgG~~~~~~~~~~~~i~~~~~~ 278 (318)
T TIGR00744 231 SYREVARWAGAGLADLASLFNPSAIVLGGGLSDAGDLLLDPIRKSYKR 278 (318)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCEEEECChhhhCcHHHHHHHHHHHHH
Confidence 344455555555555656668899999997543 24566666555543
No 50
>PF12984 DUF3868: Domain of unknown function, B. Theta Gene description (DUF3868); InterPro: IPR024480 This domain of unknown function is found in a number of bacterial proteins. The function of the proteins is not known, but the Bacteroides thetaiotaomicron gene appears to be upregulated in the presence of host or other bacterial species compared to pure culture [, ].
Probab=20.59 E-value=2e+02 Score=22.98 Aligned_cols=39 Identities=26% Similarity=0.324 Sum_probs=22.5
Q ss_pred EEEEEEEeecCCCCEEEEEEEEeecCcccccccEEEEEEcc
Q 021563 52 EIKVEVVDYDKEGSVLRIRGKNILENEHVKIGAFHTLEIEL 92 (311)
Q Consensus 52 ~i~Ve~ief~~~~~~Lri~G~i~~~~e~v~~G~~HTl~i~~ 92 (311)
+|.|+..++...++.|.|.=.+--.+ +++++-|++.+.|
T Consensus 29 ~i~v~~~~~~~~gd~L~V~m~idl~~--l~v~s~~~l~ltP 67 (115)
T PF12984_consen 29 QIKVTNVSVEKQGDSLHVDMDIDLSG--LKVKSNRSLILTP 67 (115)
T ss_pred cEEEEeeEEEEECCEEEEEEEEEecc--cccCCCCEEEEEe
Confidence 35666666666677777776654433 3445555555543
No 51
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=20.37 E-value=77 Score=22.11 Aligned_cols=19 Identities=26% Similarity=0.303 Sum_probs=11.7
Q ss_pred ccccEEEEEEccCCceEEE
Q 021563 81 KIGAFHTLEIELHRAFVLR 99 (311)
Q Consensus 81 ~~G~~HTl~i~~~~~i~i~ 99 (311)
+.|.+||+.++||..|..-
T Consensus 17 ~Kgr~~Ti~L~~G~~fhTh 35 (54)
T PF14801_consen 17 PKGRKHTITLEPGGEFHTH 35 (54)
T ss_dssp TT--EEEEE--TT-EEEET
T ss_pred CCCCeeeEEECCCCeEEcC
Confidence 4799999999999998764
No 52
>PRK09698 D-allose kinase; Provisional
Probab=20.23 E-value=3.4e+02 Score=24.89 Aligned_cols=47 Identities=9% Similarity=0.135 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHhcccccCccEEEEECCcccHH-HHHHHHHHHHHh
Q 021563 167 ALNKFFENVLQAFLKHVDFNVVRCAVIASPGFTKD-QFHRHLLLEAER 213 (311)
Q Consensus 167 ~~~~f~~~v~~~l~~~~~~~~~~~iIIaGPGf~k~-~f~~~l~~~~~~ 213 (311)
.+++|.+.++..+...++..++..|||+|...-.. .|.++|.+.+.+
T Consensus 216 ~~~~~~~~la~~l~~li~~ldP~~IvlgG~~~~~~~~~~~~l~~~~~~ 263 (302)
T PRK09698 216 FIQSLLENLARAIATSINLFDPDAIILGGGVMDMPAFPRETLIAMIQK 263 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCEEEEcCccccCchhHHHHHHHHHHH
Confidence 45566677777777777777899999999754332 344555555543
Done!