Query psy17307
Match_columns 342
No_of_seqs 191 out of 728
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 18:39:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17307.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17307hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2869|consensus 100.0 2E-76 4.3E-81 555.4 20.0 278 1-342 1-328 (379)
2 TIGR00111 pelota probable tran 100.0 9E-69 2E-73 524.4 31.6 266 1-332 1-304 (351)
3 COG1537 PelA Predicted RNA-bin 100.0 2.3E-66 5E-71 495.8 28.7 274 1-341 1-308 (352)
4 PF03463 eRF1_1: eRF1 domain 1 100.0 5.7E-35 1.2E-39 249.2 6.4 131 1-195 1-132 (132)
5 TIGR00108 eRF peptide chain re 100.0 7.1E-33 1.5E-37 276.0 19.8 187 139-332 80-319 (409)
6 TIGR03676 aRF1/eRF1 peptide ch 100.0 3.4E-31 7.3E-36 263.3 19.7 183 140-331 77-314 (403)
7 PRK04011 peptide chain release 100.0 9.5E-31 2.1E-35 260.9 20.4 186 140-333 84-324 (411)
8 COG1503 eRF1 Peptide chain rel 99.8 2.5E-21 5.4E-26 190.0 9.9 186 140-332 84-322 (411)
9 KOG0688|consensus 99.7 2.1E-18 4.6E-23 163.1 6.9 183 140-332 85-323 (431)
10 PF03464 eRF1_2: eRF1 domain 2 99.7 4E-17 8.6E-22 139.3 10.2 98 200-297 1-133 (133)
11 COG1537 PelA Predicted RNA-bin 99.1 1.8E-10 3.9E-15 111.5 6.1 93 60-155 56-159 (352)
12 PF03465 eRF1_3: eRF1 domain 3 98.8 2.4E-09 5.2E-14 89.1 1.6 37 301-337 17-53 (113)
13 TIGR00111 pelota probable tran 98.4 3.7E-07 8E-12 90.1 5.8 89 63-154 60-160 (351)
14 PF03463 eRF1_1: eRF1 domain 1 98.0 1.1E-06 2.4E-11 75.0 -0.9 75 68-155 1-78 (132)
15 KOG2869|consensus 98.0 5.3E-06 1.2E-10 79.8 3.6 45 79-123 15-59 (379)
16 COG1096 Predicted RNA-binding 66.7 56 0.0012 29.7 9.4 77 13-108 46-130 (188)
17 CHL00121 rpl27 ribosomal prote 58.3 9 0.0002 30.3 2.5 52 125-176 17-69 (86)
18 TIGR00108 eRF peptide chain re 57.3 0.12 2.7E-06 52.2 -10.4 117 31-152 28-160 (409)
19 PRK05435 rpmA 50S ribosomal pr 56.2 11 0.00024 29.6 2.6 53 125-177 17-70 (82)
20 COG0211 RpmA Ribosomal protein 55.4 10 0.00022 29.9 2.3 49 127-175 19-68 (87)
21 PF08032 SpoU_sub_bind: RNA 2' 54.0 15 0.00034 27.2 3.1 24 307-330 2-26 (76)
22 TIGR00062 L27 ribosomal protei 52.4 13 0.00028 29.3 2.4 53 125-177 17-70 (83)
23 PRK07714 hypothetical protein; 52.0 20 0.00043 28.8 3.7 31 301-331 14-44 (100)
24 PRK07283 hypothetical protein; 50.4 23 0.00049 28.5 3.7 31 301-331 14-44 (98)
25 KOG4600|consensus 49.1 13 0.00027 32.0 2.1 46 127-172 46-93 (144)
26 PF04076 BOF: Bacterial OB fol 46.8 45 0.00098 27.2 5.0 36 70-106 49-84 (103)
27 PRK05583 ribosomal protein L7A 46.5 27 0.00059 28.5 3.7 32 301-332 13-44 (104)
28 PF01248 Ribosomal_L7Ae: Ribos 41.6 45 0.00097 26.0 4.1 31 302-332 12-42 (95)
29 PRK13601 putative L7Ae-like ri 40.8 42 0.00091 26.3 3.8 29 303-331 6-34 (82)
30 PRK04175 rpl7ae 50S ribosomal 40.3 42 0.00091 28.2 3.9 32 301-332 26-57 (122)
31 PTZ00106 60S ribosomal protein 38.5 41 0.00089 27.6 3.6 31 301-331 21-51 (108)
32 PF10664 NdhM: Cyanobacterial 38.4 79 0.0017 25.9 5.0 48 145-197 8-59 (108)
33 PRK13602 putative ribosomal pr 38.2 47 0.001 25.8 3.7 30 302-331 8-37 (82)
34 PRK01018 50S ribosomal protein 38.2 47 0.001 26.7 3.8 30 302-331 13-42 (99)
35 TIGR03677 rpl7ae 50S ribosomal 37.1 50 0.0011 27.4 3.9 31 301-331 22-52 (117)
36 PRK06683 hypothetical protein; 37.0 51 0.0011 25.7 3.7 31 301-331 7-37 (82)
37 PRK13600 putative ribosomal pr 36.5 44 0.00096 26.3 3.3 26 306-331 14-39 (84)
38 cd05791 S1_CSL4 S1_CSL4: CSL4, 34.0 91 0.002 24.6 4.8 63 34-107 4-71 (92)
39 PF10447 EXOSC1: Exosome compo 32.8 1.8E+02 0.004 22.7 6.2 32 76-107 44-79 (82)
40 TIGR00156 conserved hypothetic 31.4 44 0.00095 28.4 2.7 35 71-106 73-107 (126)
41 PRK09190 hypothetical protein; 27.0 82 0.0018 29.3 3.9 52 280-331 85-137 (220)
42 PRK09521 exosome complex RNA-b 25.4 2.8E+02 0.006 24.7 7.0 72 16-107 49-129 (189)
43 PRK10053 hypothetical protein; 24.6 66 0.0014 27.5 2.6 37 69-106 75-111 (130)
44 COG1358 RPL8A Ribosomal protei 24.2 74 0.0016 26.6 2.8 31 301-331 23-53 (116)
45 COG0186 RpsQ Ribosomal protein 22.5 4E+02 0.0087 21.2 7.3 56 56-111 14-70 (87)
46 PF14801 GCD14_N: tRNA methylt 21.0 84 0.0018 22.8 2.1 20 159-178 17-36 (54)
No 1
>KOG2869|consensus
Probab=100.00 E-value=2e-76 Score=555.41 Aligned_cols=278 Identities=63% Similarity=0.926 Sum_probs=260.4
Q ss_pred CeeeeecccCCCCceeEEEeeCCCcchhhhhhcccCCCEEEEEEEEEEeeccCCCCccceEEEEEEEEEEEEEeecccce
Q psy17307 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQAC 80 (342)
Q Consensus 1 Mk~~~~~~~~~~~~~~v~l~~e~~dDlw~lynli~~gD~v~~~t~Rkv~~~~~~g~~~~~~~~~~l~i~v~~~~f~~~~~ 80 (342)
||++++.+ .++++|.|+++||++|||||+||+|++||.|++.|.|||+.+.++|+++++|+.
T Consensus 1 MKli~K~~-~rng~G~vtmvpEe~eDmw~~ynli~~gD~v~a~T~rkvq~e~a~G~~~s~rv~----------------- 62 (379)
T KOG2869|consen 1 MKLIRKDI-ERNGSGSVTMVPEESEDLWHLYNLIQVGDSVIASTIRKVQKEEATGKTKSSRVL----------------- 62 (379)
T ss_pred Cccchhhh-hcCCCceEEECcCchhHHHHHHhhccCCceeEEEEEEEeeeccccCcccceEEE-----------------
Confidence 99999998 999999999999999999999999999999999999999999888865544444
Q ss_pred EEEEeecCceeeeeeccCCCCeEEEEEeeeeeeccCCCCcccceeeeEEEEEEEEEeeeccccEEEEeceeeeccccccc
Q psy17307 81 VLRLKESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQACVLRLKGRNIQENQYVKM 160 (342)
Q Consensus 81 ~l~~~~~dd~~~~~~li~~Gd~v~~~t~Rkv~~e~~~~~~~~~r~~~~l~i~Ve~~ef~~~~~~lri~G~~~~~~e~v~~ 160 (342)
++|+|.||.++||..+..||++|+++++|++|++
T Consensus 63 ----------------------------------------------~~L~i~VesidfD~~~~~L~~KGrti~eNe~Vk~ 96 (379)
T KOG2869|consen 63 ----------------------------------------------LKLKIKVESIDFDTKACVLRLKGRTIEENEYVKM 96 (379)
T ss_pred ----------------------------------------------EEEEEEEEEeeccccccEEEEeeeeeeecccccc
Confidence 7888888888888888999999999999999999
Q ss_pred cceEEEEeecCceeEEEecCCChhhHHHHHHHhcccCCCcEEEEEEeCCeEEEEEEeCCeEEEEEEEEeecCCcccCcc-
Q psy17307 161 GAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDNK- 239 (342)
Q Consensus 161 G~~HTl~i~~~~~~~i~K~~W~~~~le~L~ea~~~~~~~~~~~Vv~deg~A~i~ll~~~~~~~~~~i~~~ip~K~~~~~- 239 (342)
|+|||++|+++++|+|+|++||++.+++|++||++.+.+++|+|+|+||.|+||+++.+++..+++|+.++|+||+++.
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 9999999999999999999999999999999999999999999999999999999999999999999999999987521
Q ss_pred -----------------------ccccee--eCCcc---------hHHHHhhccHHHHhcCCcEEEEecCCcchhHHHHH
Q psy17307 240 -----------------------DLLKEL--LSPIT---------TVEAVKMDNKVLLENKSKFLLVHSSSAFKHSLKEI 285 (342)
Q Consensus 240 -----------------------~~~k~V--agPG~---------~k~~~~~~~~~~~~~k~k~v~~~~S~g~~~gL~Ev 285 (342)
+++||+ ||||| ++++.+.+++.+++|++||+.+|+|+|+.++|+|+
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 568887 99995 45566778899999999999999999999999999
Q ss_pred hcChhhhhhhhcccc---------------CCCCeEEEcHHHHHHHHHcCCccEEEEecCCCCCCCchhhcC
Q psy17307 286 LADPTVTSKMQDTKA---------------LDPSRAFYGYRHVSAANESQAIDTLLIADCLFRNSDLNERKK 342 (342)
Q Consensus 286 L~~~~v~~~l~d~k~---------------~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l~r~~d~~~Rk~ 342 (342)
|.+|.+.+.|+|+|+ ++|++||||++||.+|+|+|||++|||||++||+.|+++|++
T Consensus 257 L~dp~v~~~l~dtK~~~EvkalddF~~~l~~~~drA~yG~khV~~A~e~~AI~tLLitD~lfr~~DV~tRkk 328 (379)
T KOG2869|consen 257 LKDPAVASKLQDTKAAKEVKALDDFYVMLSKDPDRACYGPKHVEKANEYGAIETLLITDELFRSQDVATRKK 328 (379)
T ss_pred hcChHHHHHhhchhhHHHHHHHHHHHHHhccCccccccCHHHHHHHHhhcchhheehhhhhcccccHHHHHH
Confidence 999999999999997 899999999999999999999999999999999999999985
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=9e-69 Score=524.39 Aligned_cols=266 Identities=30% Similarity=0.424 Sum_probs=236.5
Q ss_pred CeeeeecccCCCCceeEEEeeCCCcchhhhhhcccCCCEEEEEEEEEEeeccCCCCccceEEEEEEEEEEEEEeecccce
Q psy17307 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQAC 80 (342)
Q Consensus 1 Mk~~~~~~~~~~~~~~v~l~~e~~dDlw~lynli~~gD~v~~~t~Rkv~~~~~~g~~~~~~~~~~l~i~v~~~~f~~~~~ 80 (342)
||++++++ ++++|+|+|+||++||||||||||++||.|+|+|.|+|+++..+|+.+
T Consensus 1 Mki~~~~~--~~~~g~v~l~pe~~dDlw~l~nli~~GD~V~~~T~Rkv~~~~~~g~~~---------------------- 56 (351)
T TIGR00111 1 MSIVEESF--NKGGAVIKLLPETLDDLWHLYQIIEKGDVEFAFTKRRTQDLDKIRSDK---------------------- 56 (351)
T ss_pred Cceeeeec--CCCcEEEEEEeCChHHHHHHHHhCCCCCEEEEEEEEEEeccccCCCcc----------------------
Confidence 99999997 667789999999999999999999999999999999998876555443
Q ss_pred EEEEeecCceeeeeeccCCCCeEEEEEeeeeeeccCCCCcccceeeeEEEEEEEEEeeeccccEEEEeceeeecc-cccc
Q psy17307 81 VLRLKESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQACVLRLKGRNIQEN-QYVK 159 (342)
Q Consensus 81 ~l~~~~~dd~~~~~~li~~Gd~v~~~t~Rkv~~e~~~~~~~~~r~~~~l~i~Ve~~ef~~~~~~lri~G~~~~~~-e~v~ 159 (342)
+|++++|+|+||+++||+++++||++|+++.+| ++|+
T Consensus 57 ------------------------------------------er~~~~l~i~Ve~ief~~~~~~Lri~G~i~~~~e~~v~ 94 (351)
T TIGR00111 57 ------------------------------------------SKDTVKLGIEVESVEFDMKTERLRYKGVIVTGPEDDVP 94 (351)
T ss_pred ------------------------------------------eEEEEEEEEEEEEEEecCCCCEEEEEEEEecCCccccc
Confidence 445578888888888899999999999999976 8999
Q ss_pred ccceEEEEeecCceeEEEecCCChhhHHHHHHHhcccCCCcEEEEEEeCCeEEEEEEeCCeEEEEEEEEeecCCcccC--
Q psy17307 160 MGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRD-- 237 (342)
Q Consensus 160 ~G~~HTl~i~~~~~~~i~K~~W~~~~le~L~ea~~~~~~~~~~~Vv~deg~A~i~ll~~~~~~~~~~i~~~ip~K~~~-- 237 (342)
+|+|||++|+||++|+|+|++|++|++++|++|++++.++.+++|+||+|+|+||+|+++++++++++++++|+|+++
T Consensus 95 ~G~~HTl~ie~~~~i~i~K~~w~~~~le~L~ea~~~~~~~~~~~vv~d~g~A~i~ll~~~~~~~~~~i~~~iP~K~~~~~ 174 (351)
T TIGR00111 95 VGSYHTLEIKYVYPLSIIKQNWKKWQLKRLREAVEISKRPKTAAVVMEEGIAHVGLVRQYSVEEIQKIEYHMPGKKRTLK 174 (351)
T ss_pred ccceEEEEEcCCCcEEEEEecCCHHHHHHHHHHhccccCCcEEEEEEeCCcEEEEEEcCCEEEEEEEEEEeCCCCcccch
Confidence 999999999999999999999999999999999999988999999999999999999999999999999999999842
Q ss_pred -------cc----------ccccee--eCCcchHHHHhhccHHHHhc-CCcEEEEecCCcchhHHHHHhcChhhhhhhhc
Q psy17307 238 -------NK----------DLLKEL--LSPITTVEAVKMDNKVLLEN-KSKFLLVHSSSAFKHSLKEILADPTVTSKMQD 297 (342)
Q Consensus 238 -------~~----------~~~k~V--agPG~~k~~~~~~~~~~~~~-k~k~v~~~~S~g~~~gL~EvL~~~~v~~~l~d 297 (342)
|. +.+++| |||||+++.|.+.....+.. ..+.++.++|+||.+||+|+|++|.++++|++
T Consensus 175 ~e~~~~~Ff~~v~~~l~~~~~v~~iIiaGPGf~k~~f~~~l~~~~~~~~~k~ii~~~s~g~~~gl~EvL~~~~v~~~l~d 254 (351)
T TIGR00111 175 FGELRKEFYKEIAKKLLNFDDLKTIIVAGPGFYKNDFYDFIFERYPEEANKAVLENCSTGGRAGINEVLKRGLVARILQE 254 (351)
T ss_pred hHHHHHHHHHHHHHHHhhhcccCEEEEECCHHHHHHHHHHHHHHhhhhhCCcEEEecCCCchhHHHHHHhChHHHHHHhh
Confidence 11 135665 99999999886554333322 23566789999999999999999999999999
Q ss_pred ccc---------------CCCCeEEEcHHHHHHHHHcCCccEEEEecCCC
Q psy17307 298 TKA---------------LDPSRAFYGYRHVSAANESQAIDTLLIADCLF 332 (342)
Q Consensus 298 ~k~---------------~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l~ 332 (342)
+++ +|+++||||+++|.+|+++|||++|||||++|
T Consensus 255 ~k~~~E~~~l~~f~~~l~kd~~~~~YG~~eV~~Ale~GAVetLLIsD~l~ 304 (351)
T TIGR00111 255 TRYAKEIMVIDEFLEHLAKDGDKAVYGEDEVVKAAEYGAIEYLLVTDKVL 304 (351)
T ss_pred hhHHHHHHHHHHHHHHHhcCCCeEEECHHHHHHHHHcCCceEEEEecchh
Confidence 986 78899999999999999999999999999997
No 3
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=100.00 E-value=2.3e-66 Score=495.84 Aligned_cols=274 Identities=31% Similarity=0.507 Sum_probs=240.0
Q ss_pred CeeeeecccCCCCceeEEEeeCCCcchhhhhhcccCCCEEEEEEEEEEeeccCCCCccceEEEEEEEEEEEEEeecccce
Q psy17307 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQAC 80 (342)
Q Consensus 1 Mk~~~~~~~~~~~~~~v~l~~e~~dDlw~lynli~~gD~v~~~t~Rkv~~~~~~g~~~~~~~~~~l~i~v~~~~f~~~~~ 80 (342)
|+++.++. ++|.|+|+||++||||||||+|++||.|+|+|.|+.++....++
T Consensus 1 M~ile~~~----k~g~I~l~pE~lDDLw~L~~Ii~~GD~v~a~T~Rr~~~~d~~r~------------------------ 52 (352)
T COG1537 1 MRILEEDK----KRGVIKLVPETLDDLWHLYNIIEKGDKVFAKTTRRDESSDVIRS------------------------ 52 (352)
T ss_pred Ccceeccc----cCceEEEecCChHHHHHHHHhcCCCCEEEEEEEEeccccccccc------------------------
Confidence 89999987 69999999999999999999999999999999999322111112
Q ss_pred EEEEeecCceeeeeeccCCCCeEEEEEeeeeeeccCCCCcccceeeeEEEEEEEEEeeeccccEEEEeceeeeccccccc
Q psy17307 81 VLRLKESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQACVLRLKGRNIQENQYVKM 160 (342)
Q Consensus 81 ~l~~~~~dd~~~~~~li~~Gd~v~~~t~Rkv~~e~~~~~~~~~r~~~~l~i~Ve~~ef~~~~~~lri~G~~~~~~e~v~~ 160 (342)
.+.+|+||+|+|+||++|||.|+++||++|++++.++.+++
T Consensus 53 ---------------------------------------~~~eri~m~L~IkVe~ieF~~f~nrLRi~G~i~~~~e~~~~ 93 (352)
T COG1537 53 ---------------------------------------KKGERIPMTLGIKVEKIEFDKFANRLRIKGPIVEGPEEVVK 93 (352)
T ss_pred ---------------------------------------CcceEEEEEEEEEEEEEEeeecccEEEEEEEEEEcCccccc
Confidence 23456668888888888888899999999999998888889
Q ss_pred cceEEEEeecCceeEEEecCCChhhHHHHHHHhcccCCCcEEEEEEeCCeEEEEEEeCCeEEEEEEEEeecCCcccCcc-
Q psy17307 161 GAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRRDNK- 239 (342)
Q Consensus 161 G~~HTl~i~~~~~~~i~K~~W~~~~le~L~ea~~~~~~~~~~~Vv~deg~A~i~ll~~~~~~~~~~i~~~ip~K~~~~~- 239 (342)
|+|||++|++|++|+|+|++|+.+++++|++|++++.++.+++|+||+|+|+||++++|++.++++++.+.|+|+.+..
T Consensus 94 G~yHTi~v~~g~~i~I~K~~W~~~~lerLkeA~~~~~~~~~~~v~~degea~i~iv~~ygi~~~~~i~~~~~gK~~~~~~ 173 (352)
T COG1537 94 GSYHTINVTIGTEIEIEKEEWNKDQLERLKEAVEASKRPEVAIVVVDEGEAAIAIVRDYGIIILGKIRSGIPGKREGDIR 173 (352)
T ss_pred ccceEEEeccCceEEEEEccCCHHHHHHHHHHhhcccCCceEEEEEecCceEEEEEeccceEEEEEEeccCCCCcccchh
Confidence 9999999999999999998899999999999999999999999999999999999999999999999999999876421
Q ss_pred --------------cc--cc-ee-eCCcchHHHHhhccHHHHhcCCcEEEEecCCcchhHHHHHhcChhhhhhhhcccc-
Q psy17307 240 --------------DL--LK-EL-LSPITTVEAVKMDNKVLLENKSKFLLVHSSSAFKHSLKEILADPTVTSKMQDTKA- 300 (342)
Q Consensus 240 --------------~~--~k-~V-agPG~~k~~~~~~~~~~~~~k~k~v~~~~S~g~~~gL~EvL~~~~v~~~l~d~k~- 300 (342)
+. .+ .| |||||+|+.+.........+...|+++++|++|.+||+|+|+++.+.++++++++
T Consensus 174 ~~~k~~~~i~~~~~~~~~~~~iIvaGPGF~k~~~~~~~~~~~p~~~~~~~~~~s~~g~~gi~EvLkr~~v~ki~~e~ria 253 (352)
T COG1537 174 AERKFFDEIAKALKEYANLDIIIVAGPGFAKEDFYDFLRERYPELANIVIEDTSTGGRAGINEVLKRGAVDKILSETRIA 253 (352)
T ss_pred hHHHHHHHHHHHHHHhhCCCeEEEeCCchHHHHHHHHHHHhcccccceEEEeccCcchHHHHHHHhhhhHHhHhhhhHHH
Confidence 11 22 23 9999999887655444443333489999999999999999999999999999985
Q ss_pred --------------CCCCeEEEcHHHHHHHHHcCCccEEEEecCCCCCCCchhhc
Q psy17307 301 --------------LDPSRAFYGYRHVSAANESQAIDTLLIADCLFRNSDLNERK 341 (342)
Q Consensus 301 --------------~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l~r~~d~~~Rk 341 (342)
+++++||||++||.+|++||||++|||+|++||+.+.+.|.
T Consensus 254 ~e~~~~e~fl~~iak~~~~v~YG~~eV~~A~e~GAve~LLv~De~lr~~~~~~re 308 (352)
T COG1537 254 EEIELVEEFLERLAKDDDKVAYGLEEVEKAAEYGAVETLLVTDELLRSDDVEERE 308 (352)
T ss_pred HHHHHHHHHHHHHhcCCCceeEcHHHHHHHHhcCcceeEEeehhhhcccchhhHH
Confidence 88999999999999999999999999999999999998875
No 4
>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=5.7e-35 Score=249.16 Aligned_cols=131 Identities=46% Similarity=0.795 Sum_probs=117.1
Q ss_pred CeeeeecccCCCCceeEEEeeCCCcchhhhhhcccCCCEEEEEEEEEEeec-cCCCCccceEEEEEEEEEEEEEeecccc
Q psy17307 1 MKLVHKNINDKDKSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQSE-SNTGSSTSSRVRTMLTISVESIDFDTQA 79 (342)
Q Consensus 1 Mk~~~~~~~~~~~~~~v~l~~e~~dDlw~lynli~~gD~v~~~t~Rkv~~~-~~~g~~~~~~~~~~l~i~v~~~~f~~~~ 79 (342)
|||+++.+ ..+++|.|+++||++||||||||||.+||.|++.|.|+|+.+ +.+|
T Consensus 1 Mki~~~~~-~~~~~~~i~ll~e~~dDlw~L~~li~~gD~v~~~t~Rkv~~~~~~~~------------------------ 55 (132)
T PF03463_consen 1 MKIISKDI-EKNGKGLIKLLPEEKDDLWHLYNLIIPGDEVISKTTRKVQEASNIKG------------------------ 55 (132)
T ss_dssp -EEEEECH-CHHHHHEEEEETTSHHHHHHHHHHEETTTEEEECCHCHHHHCTCESS------------------------
T ss_pred Cccchhhh-ccccCceEEEcccccCCcEEEEEEEECCCEEEEEEEEeeeecccccC------------------------
Confidence 99999999 577899999999999999999999999999999999999432 2222
Q ss_pred eEEEEeecCceeeeeeccCCCCeEEEEEeeeeeeccCCCCcccceeeeEEEEEEEEEeeeccccEEEEeceeeecccccc
Q psy17307 80 CVLRLKESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQACVLRLKGRNIQENQYVK 159 (342)
Q Consensus 80 ~~l~~~~~dd~~~~~~li~~Gd~v~~~t~Rkv~~e~~~~~~~~~r~~~~l~i~Ve~~ef~~~~~~lri~G~~~~~~e~v~ 159 (342)
+..+++++++|+++|++++|+|+++.||++|+++.+|++++
T Consensus 56 ---------------------------------------~~~~~~v~~~L~i~ve~v~~~~~~~~Lri~G~i~~~~~~~~ 96 (132)
T PF03463_consen 56 ---------------------------------------SKTRERVQIALTIKVEKVEFDPENGLLRISGKIVEENEDVK 96 (132)
T ss_dssp ---------------------------------------HHHHHCEEEEEEEEEEEEEEETTTTEEEEEEEEEEGSCGGG
T ss_pred ---------------------------------------CcceEEEEEEEEEEEEEeEecCCCCEEEEEeEEccCCCCCC
Confidence 23356677899999999999999999999999999999999
Q ss_pred ccceEEEEeecCceeEEEecCCChhhHHHHHHHhcc
Q psy17307 160 MGAYHTLDLELNRKFELSKPEWDSIALERIEVACNI 195 (342)
Q Consensus 160 ~G~~HTl~i~~~~~~~i~K~~W~~~~le~L~ea~~~ 195 (342)
+|+|||++|+||+||+|+|++||++++++|++|+++
T Consensus 97 ~G~~hT~~i~~~~~~ti~K~~wd~~~~~~l~ea~~e 132 (132)
T PF03463_consen 97 LGKYHTLDIEPGRPFTIIKYRWDSYFLDRLKEAMDE 132 (132)
T ss_dssp TTSEEEEEEETSSEEEEEEEEEEHHHHHHHHHHTSH
T ss_pred cceEEEEEEeCCCceEEEEecCCHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999863
No 5
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=100.00 E-value=7.1e-33 Score=276.01 Aligned_cols=187 Identities=18% Similarity=0.183 Sum_probs=157.1
Q ss_pred eccccEEEEeceeeeccccccccceEEEEeecCceeEEEec-CCChhhHHHHHHHhcccCCCcEEEEEEeCCeEEEEEEe
Q psy17307 139 DTQACVLRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKP-EWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLIT 217 (342)
Q Consensus 139 ~~~~~~lri~G~~~~~~e~v~~G~~HTl~i~~~~~~~i~K~-~W~~~~le~L~ea~~~~~~~~~~~Vv~deg~A~i~ll~ 217 (342)
-|..+.++..|.+..++. .|+|||++|+|++||+++|+ ||++|++++|++|++.. +.+++|+||+|.|+||+++
T Consensus 80 ~p~nglv~~~G~v~~~~~---~~~~~t~~iep~~pi~~~~y~~d~~f~le~L~e~~~~~--~~~g~VvvD~~~A~i~~l~ 154 (409)
T TIGR00108 80 PPENGLVIFCGMVPREGP---TEKMETYVIEPPEPIKTYIYHCDSKFYLEPLSEMLEEK--DKYGLIVLDRQEATIGLVK 154 (409)
T ss_pred CCCCcEEEEEeEeccCCC---cccEEEEEEeCCCceEEEEEccCChhHHHHHHHHhcCC--CCEEEEEEecCCEEEEEEc
Confidence 355678999999887764 38999999999999999998 78899999999999974 5999999999999999999
Q ss_pred CCeEEEEEEEEeecCCccc-Ccc---------------------c----c--------ccee--eCCcchHHHHhhccHH
Q psy17307 218 ASMSLVRTKIETNIPRKRR-DNK---------------------D----L--------LKEL--LSPITTVEAVKMDNKV 261 (342)
Q Consensus 218 ~~~~~~~~~i~~~ip~K~~-~~~---------------------~----~--------~k~V--agPG~~k~~~~~~~~~ 261 (342)
++++++++++++++|+|++ |++ + . +++| ||||++++.|.+....
T Consensus 155 g~~~~~~~~i~~~vp~K~~~GGqS~~Rf~r~~e~~~~~f~~~Vae~~~~~f~~~~~~~v~~IIlaGpg~~K~~f~~~~~l 234 (409)
T TIGR00108 155 GKRITVLKKLTSGVPGKHKAGGQSARRFERLRELAAHEFLKKVGEVANEAFLPNDDVKLKGIILGGPGHTKEEFAEGEYL 234 (409)
T ss_pred CCEEEEEEEEeeeCCCcccCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHhhhcccccceEEEEeccHHHHHHhhhhhhH
Confidence 9999999999999999985 332 1 1 3444 9999999988763211
Q ss_pred HHhcCCcEE-EEecCCcchhHHHHHhcChhhhhhhhcccc---------------CCCCeEEEcHHHHHHHHHcCCccEE
Q psy17307 262 LLENKSKFL-LVHSSSAFKHSLKEILADPTVTSKMQDTKA---------------LDPSRAFYGYRHVSAANESQAIDTL 325 (342)
Q Consensus 262 ~~~~k~k~v-~~~~S~g~~~gL~EvL~~~~v~~~l~d~k~---------------~d~~~a~YG~~eV~~A~e~GAVetL 325 (342)
..+.+.+++ ++++|+||.+|++|+|++. +++|+++++ +|+|+||||+++|.+|+++|||+||
T Consensus 235 ~~~l~~kvi~~vdvs~gg~~gl~E~l~~~--~~~L~~~k~~~E~~lle~F~~ei~~d~G~avyG~~eV~~ALe~GAVetL 312 (409)
T TIGR00108 235 HHELKKKVISTVDVSYTGEFGIRELIEKS--ADVLAEVDYMREKKLVQRFLKELIQEDGLACYGEDEVLKALDLGAVETL 312 (409)
T ss_pred HHHhhhhEEEEEEcCCCcccCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhcCCCcEEeCHHHHHHHHHhCCCcEE
Confidence 112223553 7899999999999999975 488888774 6789999999999999999999999
Q ss_pred EEecCCC
Q psy17307 326 LIADCLF 332 (342)
Q Consensus 326 LIsD~l~ 332 (342)
||+|+|.
T Consensus 313 LV~d~l~ 319 (409)
T TIGR00108 313 IVSEDLE 319 (409)
T ss_pred EEecccc
Confidence 9999993
No 6
>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=99.97 E-value=3.4e-31 Score=263.30 Aligned_cols=183 Identities=21% Similarity=0.182 Sum_probs=154.1
Q ss_pred ccccEEEEeceeeeccccccccceEEEEeecCceeEEEec-CCChhhHHHHHHHhcccCCCcEEEEEEeCCeEEEEEEeC
Q psy17307 140 TQACVLRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKP-EWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLITA 218 (342)
Q Consensus 140 ~~~~~lri~G~~~~~~e~v~~G~~HTl~i~~~~~~~i~K~-~W~~~~le~L~ea~~~~~~~~~~~Vv~deg~A~i~ll~~ 218 (342)
|.++.+-..|.+..+. ...+|||++|+|++||+++|+ ||++|++++|++|++. ++.+++|+||+++|.||++++
T Consensus 77 p~nGlv~f~g~~~~~~---~~~~~~t~~iep~~pi~~~~y~cd~~f~lepL~e~l~~--~~~~g~VvvD~~~A~i~~l~g 151 (403)
T TIGR03676 77 PENGLVLFAGMVPTGG---GTEKMETYVIEPPEPINTYLYRCDSKFYLEPLEEMLEE--KDVYGLIVLDRREATIGLLKG 151 (403)
T ss_pred CCCeEEEEEeeecCCC---CceeEEEEEEeCCCceEEEEecCCChHHHHHHHHHhcC--CCCEEEEEEecCceEEEEEcC
Confidence 5555666667776543 236999999999999999998 6889999999999997 569999999999999999999
Q ss_pred CeEEEEEEEEeecCCccc-Ccc-------------------------c--------cccee--eCCcchHHHHhh--ccH
Q psy17307 219 SMSLVRTKIETNIPRKRR-DNK-------------------------D--------LLKEL--LSPITTVEAVKM--DNK 260 (342)
Q Consensus 219 ~~~~~~~~i~~~ip~K~~-~~~-------------------------~--------~~k~V--agPG~~k~~~~~--~~~ 260 (342)
+++++++++++++|+|++ +++ + .+++| ||||++++.|.+ .+.
T Consensus 152 ~~~e~~~~i~~~vp~K~~~GGqS~~Rf~R~~e~~~~~f~~~Vae~~~~~f~~~~~~~v~~lILaGpg~~K~~f~~~~~L~ 231 (403)
T TIGR03676 152 KRIEVLKELTSGVPGKHRAGGQSARRFERLIEIAAHEFYKRVGEAANEAFLPLKDKKLKGILIGGPGPTKEEFAEGDYLH 231 (403)
T ss_pred CEEEEEEEEEeeCCCCccCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccEEEEeCCHHHHHHHhhhhhhh
Confidence 999999999999999986 432 1 03444 999999998876 333
Q ss_pred HHHhcCCcE-EEEecCCcchhHHHHHhcChhhhhhhhcccc---------------CCCCeEEEcHHHHHHHHHcCCccE
Q psy17307 261 VLLENKSKF-LLVHSSSAFKHSLKEILADPTVTSKMQDTKA---------------LDPSRAFYGYRHVSAANESQAIDT 324 (342)
Q Consensus 261 ~~~~~k~k~-v~~~~S~g~~~gL~EvL~~~~v~~~l~d~k~---------------~d~~~a~YG~~eV~~A~e~GAVet 324 (342)
..+. .++ .++++|+++.+|++|+|++. +++|++.++ +|++++|||+++|.+|++||||+|
T Consensus 232 ~~l~--~kvi~~vd~s~~~~~Gl~Evl~~~--~~~L~~~k~~~E~~lle~f~~el~~d~g~avyG~~eV~~ALe~GAVet 307 (403)
T TIGR03676 232 HELK--KKILGLFDVSYTGESGLRELVEKA--EDLLKDLELMKEKKLMERFFKELVKDGGLAAYGEEEVRKALEMGAVDT 307 (403)
T ss_pred HHHH--hhEEEEEecCCCCccCHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHHHHHhCCCcE
Confidence 3333 356 58899999999999999984 588888874 688999999999999999999999
Q ss_pred EEEecCC
Q psy17307 325 LLIADCL 331 (342)
Q Consensus 325 LLIsD~l 331 (342)
|||+|+|
T Consensus 308 LLV~d~l 314 (403)
T TIGR03676 308 LLISEDL 314 (403)
T ss_pred EEEEccc
Confidence 9999999
No 7
>PRK04011 peptide chain release factor 1; Provisional
Probab=99.97 E-value=9.5e-31 Score=260.92 Aligned_cols=186 Identities=20% Similarity=0.165 Sum_probs=154.8
Q ss_pred ccccEEEEeceeeeccccccccceEEEEeecCceeEEEec-CCChhhHHHHHHHhcccCCCcEEEEEEeCCeEEEEEEeC
Q psy17307 140 TQACVLRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKP-EWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLITA 218 (342)
Q Consensus 140 ~~~~~lri~G~~~~~~e~v~~G~~HTl~i~~~~~~~i~K~-~W~~~~le~L~ea~~~~~~~~~~~Vv~deg~A~i~ll~~ 218 (342)
|..+.+-..|.+..+++ ..|.|||++|+||+||+++|+ ||+.|++++|++|+++ ++.+++|+||+|+|+||++++
T Consensus 84 p~nGl~~f~g~~~~~~~--~~~~~~t~~i~p~~~i~~~~y~~d~~f~le~L~e~~~~--~~~~~~VvvD~~~A~i~~l~g 159 (411)
T PRK04011 84 PENGLVIFCGAVPIGGP--GTEDMETYVIEPPEPVPTFFYRCDSEFHTEPLEDMLED--KEVYGLIVVDRREATIGLLKG 159 (411)
T ss_pred CCCeEEEEEeecccCCC--CCceEEEEEEcCCCccEEEEecCCcHHHHHHHHHHhcC--CCCEEEEEEecCceEEEEEeC
Confidence 34556666666655432 248999999999999999998 5777999999999987 669999999999999999999
Q ss_pred CeEEEEEEEEeecCCccc-Ccc---------------------c------------cccee--eCCcchHHHHhh--ccH
Q psy17307 219 SMSLVRTKIETNIPRKRR-DNK---------------------D------------LLKEL--LSPITTVEAVKM--DNK 260 (342)
Q Consensus 219 ~~~~~~~~i~~~ip~K~~-~~~---------------------~------------~~k~V--agPG~~k~~~~~--~~~ 260 (342)
+++++++++++++|+|++ +++ + .+++| ||||++++.|.+ .+.
T Consensus 160 ~~~~~~~~i~~~vp~K~~~GG~S~~Rf~r~~e~~~~~f~k~Vae~~~~~f~~~~~~~v~~IvlaGpg~~K~~f~~~~~L~ 239 (411)
T PRK04011 160 KRIEVLKELTSFVPGKHRKGGQSARRFERLIEQAAHEFYKRVGEKANEAFLPLLEGKLKGILIGGPGPTKEEFLEGDYLH 239 (411)
T ss_pred CEEEEEEEEEeeCCCCccCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccEEEEECChhHHHHHhhhhhhh
Confidence 999999999999999976 332 0 13444 999999998876 333
Q ss_pred HHHhcCCcEE-EEecCCcchhHHHHHhcChhhhhhhhcccc---------------CCCCeEEEcHHHHHHHHHcCCccE
Q psy17307 261 VLLENKSKFL-LVHSSSAFKHSLKEILADPTVTSKMQDTKA---------------LDPSRAFYGYRHVSAANESQAIDT 324 (342)
Q Consensus 261 ~~~~~k~k~v-~~~~S~g~~~gL~EvL~~~~v~~~l~d~k~---------------~d~~~a~YG~~eV~~A~e~GAVet 324 (342)
..+. .+++ ++++|+++.+|++|+|++ ++++|+++++ ++++++|||+++|.+|+++|||++
T Consensus 240 ~~l~--~~vv~~~~~s~~~~~Gl~E~l~~--~~~~L~~~k~~~e~~lle~f~~~l~~d~g~avyG~~~V~~Ale~GAVet 315 (411)
T PRK04011 240 YELK--KKILGLFDVSYTGESGLRELVDK--ASDLLKEQELVKEKKLMEEFFKELAKDGGLAVYGEEEVRKALEMGAVDT 315 (411)
T ss_pred HHHH--hheEEEEecCCCCccCHHHHHHH--HHHHHHHhHHHHHHHHHHHHHHHHhcCCCcEEEcHHHHHHHHHcCCceE
Confidence 3333 3453 889999999999999998 4588888875 588999999999999999999999
Q ss_pred EEEecCCCC
Q psy17307 325 LLIADCLFR 333 (342)
Q Consensus 325 LLIsD~l~r 333 (342)
|||+|++++
T Consensus 316 LLV~d~l~~ 324 (411)
T PRK04011 316 LLISEDLRK 324 (411)
T ss_pred EEEeccccc
Confidence 999999987
No 8
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=2.5e-21 Score=189.96 Aligned_cols=186 Identities=22% Similarity=0.200 Sum_probs=152.5
Q ss_pred ccccEEEEeceeeeccccccccceEEEEeecCceeEEEec-CCChhhHHHHHHHhcccCCCcEEEEEEeCCeEEEEEEeC
Q psy17307 140 TQACVLRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKP-EWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLITA 218 (342)
Q Consensus 140 ~~~~~lri~G~~~~~~e~v~~G~~HTl~i~~~~~~~i~K~-~W~~~~le~L~ea~~~~~~~~~~~Vv~deg~A~i~ll~~ 218 (342)
|..+.....|.+..... ....-|..++|+.|++.+.+ |++.|++++|+++.... ..+++++|+.++|+|++|.+
T Consensus 84 P~nGlv~f~g~v~~~~~---~t~~~~~~~~PP~Pi~~~ly~cDs~F~~e~L~~~l~~~--~~ygliv~dr~ea~ig~l~g 158 (411)
T COG1503 84 PENGLVLFVGDVLGGGG---KTKKVTVVIEPPEPINTFLYRCDSKFYLEPLEEMLEDK--DLYGLIVLDRIEATIGLLKG 158 (411)
T ss_pred CCCCeEEEEeeeccCCC---ccceeeecccCCCCcceeeeccccHHHHHHHHHHhhhc--ccccEEEEecccceeeeecc
Confidence 34566777777665321 13456777899999998887 89999999999999884 48999999999999999999
Q ss_pred CeEEEEEEEEeecCCccc-Ccc-----------------------------c----cccee--eCCcchHHHHhhccHHH
Q psy17307 219 SMSLVRTKIETNIPRKRR-DNK-----------------------------D----LLKEL--LSPITTVEAVKMDNKVL 262 (342)
Q Consensus 219 ~~~~~~~~i~~~ip~K~~-~~~-----------------------------~----~~k~V--agPG~~k~~~~~~~~~~ 262 (342)
..+.+++++++.+|+||+ |+| . -++.| +|||.+++.+.++....
T Consensus 159 ~r~evl~~~~s~vpgKh~~Ggqsa~rferl~ee~~h~f~k~vge~A~e~f~~~~~~~~kgIilgGp~~tk~ef~e~~yL~ 238 (411)
T COG1503 159 KRIEVLKELTSDVPGKHRAGGQSARRFERLIEEAAHEFYKKVGEAASEAFLPIAKKELKGIILGGPGPTKEEFVEGDYLH 238 (411)
T ss_pred ceeeHhhhhcccCcchhhcccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhhhhcceEeeCCcccchhhhcccccc
Confidence 999999999999999997 544 0 02334 99999998887764444
Q ss_pred HhcCCcEE-EEecCCcchhHHHHHhcChhhhhhhhcccc---------------CCCCeEEEcHHHHHHHHHcCCccEEE
Q psy17307 263 LENKSKFL-LVHSSSAFKHSLKEILADPTVTSKMQDTKA---------------LDPSRAFYGYRHVSAANESQAIDTLL 326 (342)
Q Consensus 263 ~~~k~k~v-~~~~S~g~~~gL~EvL~~~~v~~~l~d~k~---------------~d~~~a~YG~~eV~~A~e~GAVetLL 326 (342)
.+.+.+++ ++++|+++.+||+|++.... +.|+++++ +++|+++||.++|.+|++||||++||
T Consensus 239 ~~lk~kv~~lvDv~y~~esg~~eli~~A~--d~L~~~~~~~eK~l~e~f~~e~~~~~Gla~yG~~~vr~aL~~gaVd~ll 316 (411)
T COG1503 239 HELKKKVLGLVDVSYTGESGLRELIEKAE--DALKDVDYVREKKLMEEFFKELAKDSGLAVYGEEEVREALEMGAVDTLL 316 (411)
T ss_pred hHHHHHHHhhccccccccccHHHHHHHhH--HHHHhhhhhcchhHHHHHHHHhccCcceeecchHHHHHHHHhcccceEE
Confidence 44455664 89999999999999999988 77766654 78899999999999999999999999
Q ss_pred EecCCC
Q psy17307 327 IADCLF 332 (342)
Q Consensus 327 IsD~l~ 332 (342)
|+.++-
T Consensus 317 v~Edl~ 322 (411)
T COG1503 317 VSEDLE 322 (411)
T ss_pred eecccc
Confidence 999876
No 9
>KOG0688|consensus
Probab=99.74 E-value=2.1e-18 Score=163.10 Aligned_cols=183 Identities=14% Similarity=0.139 Sum_probs=147.6
Q ss_pred ccccEEEEeceeeeccccccccceEEEEeecCceeE--EEecCCChhhHHHHHHHhcccCCCcEEEEEEeCCeEEEEEEe
Q psy17307 140 TQACVLRLKGRNIQENQYVKMGAYHTLDLELNRKFE--LSKPEWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLIT 217 (342)
Q Consensus 140 ~~~~~lri~G~~~~~~e~v~~G~~HTl~i~~~~~~~--i~K~~W~~~~le~L~ea~~~~~~~~~~~Vv~deg~A~i~ll~ 217 (342)
|..+.+-..|.++.+.- .-+.-+++++|-+||. +|- |++.||++.|.+.+.... .+++++||...+.++.+.
T Consensus 85 Ppnglvly~gti~tedg---kekkv~idfepfkpintslyL-cdNkfhte~l~~Ll~sd~--kfgfivmDg~~tlfgtl~ 158 (431)
T KOG0688|consen 85 PPNGLVLYTGTIVTEDG---KEKKVNIDFEPFKPINTSLYL-CDNKFHTEALKELLESDN--KFGFIVMDGNGTLFGTLQ 158 (431)
T ss_pred CCCceEEEeeeeEccCC---ceeeeecccccccccccceEe-cCCccchHHHHHHHhhcc--cccEEEEcCCceeEEEec
Confidence 45566777788876541 3567799999999995 555 999999999999998866 799999999999999999
Q ss_pred CCeEEEEEEEEeecCCccc-Ccc----------------------------------ccccee-eCCcchHHHHhhc--c
Q psy17307 218 ASMSLVRTKIETNIPRKRR-DNK----------------------------------DLLKEL-LSPITTVEAVKMD--N 259 (342)
Q Consensus 218 ~~~~~~~~~i~~~ip~K~~-~~~----------------------------------~~~k~V-agPG~~k~~~~~~--~ 259 (342)
++..++++++.+.+|+||. |++ ++.-.| ||...+|..+.+. +
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 9999999999999999986 554 001123 7777776655432 2
Q ss_pred HHHHhcCCcE-EEEecCCcchhHHHHHhcChhhhhhhhcccc---------------CCCCeEEEcHHHHHHHHHcCCcc
Q psy17307 260 KVLLENKSKF-LLVHSSSAFKHSLKEILADPTVTSKMQDTKA---------------LDPSRAFYGYRHVSAANESQAID 323 (342)
Q Consensus 260 ~~~~~~k~k~-v~~~~S~g~~~gL~EvL~~~~v~~~l~d~k~---------------~d~~~a~YG~~eV~~A~e~GAVe 323 (342)
.+.+ ++++ .++++||||+.|++++|+-.+ ++|++.|+ .|.|+.|||+++..+|++||||+
T Consensus 239 d~rl--qskvi~~vdvsyGGengfnQaIeL~a--evlsnvk~vqekkli~~yfdEisqdtgky~Fgv~dTl~aLe~gave 314 (431)
T KOG0688|consen 239 DPRL--QSKVLKTVDVSYGGENGFNQAIELSA--EVLSNVKFVQEKKLIGKYFDEISQDTGKYCFGVEDTLLALEMGAVE 314 (431)
T ss_pred chHH--hhhHHhhhcccccchhhHHHHHHHHH--hhhhcceeeehhhHHHHHhhhhhcccCcccccHHHHHHHHHcCCee
Confidence 2222 2344 489999999999999999887 88888886 78999999999999999999999
Q ss_pred EEEEecCCC
Q psy17307 324 TLLIADCLF 332 (342)
Q Consensus 324 tLLIsD~l~ 332 (342)
||++.+.|-
T Consensus 315 tli~~enLd 323 (431)
T KOG0688|consen 315 TLIVWENLD 323 (431)
T ss_pred ehhHhhhhh
Confidence 999988764
No 10
>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=99.71 E-value=4e-17 Score=139.31 Aligned_cols=98 Identities=31% Similarity=0.394 Sum_probs=80.0
Q ss_pred cEEEEEEeCCeEEEEEEeCCeEEEEEEEEeecCCccc-Ccc-----------------------cc-------ccee--e
Q psy17307 200 DVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRR-DNK-----------------------DL-------LKEL--L 246 (342)
Q Consensus 200 ~~~~Vv~deg~A~i~ll~~~~~~~~~~i~~~ip~K~~-~~~-----------------------~~-------~k~V--a 246 (342)
++++|+||+|+|+||+|+++++++++++++++|+|+. |++ +. +++| |
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 4899999999999999999999999999999999986 321 11 3555 9
Q ss_pred CCcchHHHHhhccHHHHhc--CCcEEEEecCCcchhHHHHHhcChhhhhhhhc
Q psy17307 247 SPITTVEAVKMDNKVLLEN--KSKFLLVHSSSAFKHSLKEILADPTVTSKMQD 297 (342)
Q Consensus 247 gPG~~k~~~~~~~~~~~~~--k~k~v~~~~S~g~~~gL~EvL~~~~v~~~l~d 297 (342)
||||+++.|.+..+..... +.+++++++|+||++||+|+|++|+++++|+|
T Consensus 81 GPGf~k~~f~~~l~~~~~~~~~~~i~~~~~s~~~~~gl~Evl~~~~v~~~l~d 133 (133)
T PF03464_consen 81 GPGFTKEEFYKYLKAEARRKDKKKIVVVDTSSGGESGLNEVLKRPEVQKILKD 133 (133)
T ss_dssp ESTTHHHHHHHHHHHHHHHHTCCEEEEEE-SSSCHHHHHHHHHSHHHHHHHCT
T ss_pred CCHHHHHHHHHHHHHhhHhhcCCEEEEEECCCCCHHHHHHHHHhhhHHHHhcC
Confidence 9999999887655444332 25788999999999999999999999999875
No 11
>COG1537 PelA Predicted RNA-binding proteins [General function prediction only]
Probab=99.06 E-value=1.8e-10 Score=111.53 Aligned_cols=93 Identities=27% Similarity=0.335 Sum_probs=86.3
Q ss_pred eEEEEEEEEEEEEEeecccceEEEEee-----cCc----eeeeeeccCCCCeEEE-EE-eeeeeeccCCCCcccceeeeE
Q psy17307 60 SRVRTMLTISVESIDFDTQACVLRLKE-----SED----MWHAYNLITEGDSVRA-ST-IRKVQSESNTGSSTSSRVRTM 128 (342)
Q Consensus 60 ~~~~~~l~i~v~~~~f~~~~~~l~~~~-----~dd----~~~~~~li~~Gd~v~~-~t-~Rkv~~e~~~~~~~~~r~~~~ 128 (342)
+|+||+|+|+|+++|||+|+++|||.| ||+ +|||+| |.+|+++++ +. |.+.+++++++|.++++.|.+
T Consensus 56 eri~m~L~IkVe~ieF~~f~nrLRi~G~i~~~~e~~~~G~yHTi~-v~~g~~i~I~K~~W~~~~lerLkeA~~~~~~~~~ 134 (352)
T COG1537 56 ERIPMTLGIKVEKIEFDKFANRLRIKGPIVEGPEEVVKGSYHTIN-VTIGTEIEIEKEEWNKDQLERLKEAVEASKRPEV 134 (352)
T ss_pred eEEEEEEEEEEEEEEeeecccEEEEEEEEEEcCcccccccceEEE-eccCceEEEEEccCCHHHHHHHHHHhhcccCCce
Confidence 799999999999999999999999998 555 799999 999999999 54 999999999999999999999
Q ss_pred EEEEEEEEeeeccccEEEEeceeeecc
Q psy17307 129 LTISVESIDFDTQACVLRLKGRNIQEN 155 (342)
Q Consensus 129 l~i~Ve~~ef~~~~~~lri~G~~~~~~ 155 (342)
+.+.+++.+++. +.+|-+|+++...
T Consensus 135 ~~v~~degea~i--~iv~~ygi~~~~~ 159 (352)
T COG1537 135 AIVVVDEGEAAI--AIVRDYGIIILGK 159 (352)
T ss_pred EEEEEecCceEE--EEEeccceEEEEE
Confidence 999999999998 6899999998743
No 12
>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=98.76 E-value=2.4e-09 Score=89.11 Aligned_cols=37 Identities=49% Similarity=0.697 Sum_probs=34.8
Q ss_pred CCCCeEEEcHHHHHHHHHcCCccEEEEecCCCCCCCc
Q psy17307 301 LDPSRAFYGYRHVSAANESQAIDTLLIADCLFRNSDL 337 (342)
Q Consensus 301 ~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l~r~~d~ 337 (342)
++++++|||+++|.+|+++|||++|||+|+++|+.+.
T Consensus 17 k~~~~~~yG~~eV~~Al~~GaV~~LlI~d~l~~~~~~ 53 (113)
T PF03465_consen 17 KDPGLAVYGIEEVKKALEMGAVETLLISDDLFRSRDV 53 (113)
T ss_dssp TTCSSEEESHHHHHHHHHTT-EEEEEEEHHHHTESCH
T ss_pred hCCCcEEECHHHHHHHHHhCCCcEEEEecccccccce
Confidence 7889999999999999999999999999999999887
No 13
>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=98.40 E-value=3.7e-07 Score=90.05 Aligned_cols=89 Identities=21% Similarity=0.183 Sum_probs=78.8
Q ss_pred EEEEEEEEEEEeecccceEEEEee-----cCc-----eeeeeeccCCCCeEEEE--EeeeeeeccCCCCcccceeeeEEE
Q psy17307 63 RTMLTISVESIDFDTQACVLRLKE-----SED-----MWHAYNLITEGDSVRAS--TIRKVQSESNTGSSTSSRVRTMLT 130 (342)
Q Consensus 63 ~~~l~i~v~~~~f~~~~~~l~~~~-----~dd-----~~~~~~li~~Gd~v~~~--t~Rkv~~e~~~~~~~~~r~~~~l~ 130 (342)
+|+|+|+|++++||+++++|||+| +|+ .|||++ |+||+.+++. .|.+++.+++..+.+.++.+....
T Consensus 60 ~~~l~i~Ve~ief~~~~~~Lri~G~i~~~~e~~v~~G~~HTl~-ie~~~~i~i~K~~w~~~~le~L~ea~~~~~~~~~~~ 138 (351)
T TIGR00111 60 TVKLGIEVESVEFDMKTERLRYKGVIVTGPEDDVPVGSYHTLE-IKYVYPLSIIKQNWKKWQLKRLREAVEISKRPKTAA 138 (351)
T ss_pred EEEEEEEEEEEEecCCCCEEEEEEEEecCCcccccccceEEEE-EcCCCcEEEEEecCCHHHHHHHHHHhccccCCcEEE
Confidence 489999999999999999999998 334 799999 9999999994 599999999999887777788899
Q ss_pred EEEEEEeeeccccEEEEeceeeec
Q psy17307 131 ISVESIDFDTQACVLRLKGRNIQE 154 (342)
Q Consensus 131 i~Ve~~ef~~~~~~lri~G~~~~~ 154 (342)
|.++..++.. +.|+-+|+.+..
T Consensus 139 vv~d~g~A~i--~ll~~~~~~~~~ 160 (351)
T TIGR00111 139 VVMEEGIAHV--GLVRQYSVEEIQ 160 (351)
T ss_pred EEEeCCcEEE--EEEcCCEEEEEE
Confidence 9999999987 678888888764
No 14
>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=97.97 E-value=1.1e-06 Score=75.02 Aligned_cols=75 Identities=31% Similarity=0.523 Sum_probs=53.0
Q ss_pred EEEEEEeec---ccceEEEEeecCceeeeeeccCCCCeEEEEEeeeeeeccCCCCcccceeeeEEEEEEEEEeeeccccE
Q psy17307 68 ISVESIDFD---TQACVLRLKESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQACV 144 (342)
Q Consensus 68 i~v~~~~f~---~~~~~l~~~~~dd~~~~~~li~~Gd~v~~~t~Rkv~~e~~~~~~~~~r~~~~l~i~Ve~~ef~~~~~~ 144 (342)
|++.+-++. ....+|.++.+||+||+||||.|||.|.++|.|+++ + ..+..+......+.+.+ +
T Consensus 1 Mki~~~~~~~~~~~~i~ll~e~~dDlw~L~~li~~gD~v~~~t~Rkv~-~--~~~~~~~~~~~~v~~~L----------~ 67 (132)
T PF03463_consen 1 MKIISKDIEKNGKGLIKLLPEEKDDLWHLYNLIIPGDEVISKTTRKVQ-E--ASNIKGSKTRERVQIAL----------T 67 (132)
T ss_dssp -EEEEECHCHHHHHEEEEETTSHHHHHHHHHHEETTTEEEECCHCHHH-H--CTCESSHHHHHCEEEEE----------E
T ss_pred CccchhhhccccCceEEEcccccCCcEEEEEEEECCCEEEEEEEEeee-e--cccccCCcceEEEEEEE----------E
Confidence 455555555 667788888899999999999999999999999993 3 22223334455555555 6
Q ss_pred EEEeceeeecc
Q psy17307 145 LRLKGRNIQEN 155 (342)
Q Consensus 145 lri~G~~~~~~ 155 (342)
+++..+...+.
T Consensus 68 i~ve~v~~~~~ 78 (132)
T PF03463_consen 68 IKVEKVEFDPE 78 (132)
T ss_dssp EEEEEEEEETT
T ss_pred EEEEEeEecCC
Confidence 77777777643
No 15
>KOG2869|consensus
Probab=97.97 E-value=5.3e-06 Score=79.80 Aligned_cols=45 Identities=60% Similarity=0.835 Sum_probs=39.0
Q ss_pred ceEEEEeecCceeeeeeccCCCCeEEEEEeeeeeeccCCCCcccc
Q psy17307 79 ACVLRLKESEDMWHAYNLITEGDSVRASTIRKVQSESNTGSSTSS 123 (342)
Q Consensus 79 ~~~l~~~~~dd~~~~~~li~~Gd~v~~~t~Rkv~~e~~~~~~~~~ 123 (342)
..++-++.+||+||+||||++||.|++.|.||++.+..+|++.++
T Consensus 15 ~vtmvpEe~eDmw~~ynli~~gD~v~a~T~rkvq~e~a~G~~~s~ 59 (379)
T KOG2869|consen 15 SVTMVPEESEDLWHLYNLIQVGDSVIASTIRKVQKEEATGKTKSS 59 (379)
T ss_pred eEEECcCchhHHHHHHhhccCCceeEEEEEEEeeeccccCcccce
Confidence 456777889999999999999999999999999999888865433
No 16
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=66.66 E-value=56 Score=29.66 Aligned_cols=77 Identities=21% Similarity=0.255 Sum_probs=52.8
Q ss_pred CceeEEEeeCCCcchhhhhhcccCCCEEEEEEEEEEeeccCCCCccceEEEEEEEEEEEEEeecc------cceEEEEee
Q psy17307 13 KSGVVALVPEESEDMWHAYNLIAEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDT------QACVLRLKE 86 (342)
Q Consensus 13 ~~~~v~l~~e~~dDlw~lynli~~gD~v~~~t~Rkv~~~~~~g~~~~~~~~~~l~i~v~~~~f~~------~~~~l~~~~ 86 (342)
++..+.+.|... ..++..+||+|.+.-++.= .++ -.++|..++-.+ +...++|+.
T Consensus 46 ~n~~~~V~p~~~-----~~~~~K~GdiV~grV~~v~----------~~~----a~V~i~~ve~~~r~~~~~~~~~ihvs~ 106 (188)
T COG1096 46 KNRVISVKPGKK-----TPPLPKGGDIVYGRVTDVR----------EQR----ALVRIVGVEGKERELATSGAADIHVSQ 106 (188)
T ss_pred cceEEEeccCCC-----CCCCCCCCCEEEEEEeecc----------ceE----EEEEEEEEecccccCCCCceeeEEEEe
Confidence 444677888776 7899999999999864321 111 235555666544 778888887
Q ss_pred cCc--eeeeeeccCCCCeEEEEEe
Q psy17307 87 SED--MWHAYNLITEGDSVRASTI 108 (342)
Q Consensus 87 ~dd--~~~~~~li~~Gd~v~~~t~ 108 (342)
..| .-.+-+-+++||.|+++-.
T Consensus 107 ~~~~~~~~~~d~f~~GDivrA~Vi 130 (188)
T COG1096 107 VRDGYVEKLSDAFRIGDIVRARVI 130 (188)
T ss_pred cccccccccccccccccEEEEEEE
Confidence 533 3455577999999999644
No 17
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=58.34 E-value=9 Score=30.34 Aligned_cols=52 Identities=13% Similarity=0.098 Sum_probs=40.2
Q ss_pred eeeEEEEEEEEEeeeccccE-EEEeceeeeccccccccceEEEEeecCceeEE
Q psy17307 125 VRTMLTISVESIDFDTQACV-LRLKGRNIQENQYVKMGAYHTLDLELNRKFEL 176 (342)
Q Consensus 125 ~~~~l~i~Ve~~ef~~~~~~-lri~G~~~~~~e~v~~G~~HTl~i~~~~~~~i 176 (342)
.+.+|.++.-..+|-..++- +|++|..+.|-+.|.+|+=|||-=-..=.+..
T Consensus 17 ~~KrLGvK~~~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~TlfAl~~G~V~f 69 (86)
T CHL00121 17 NAKRLGVKRFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDFTLYALIDGFVKF 69 (86)
T ss_pred CcccceeEEcCCEEEcCCcEEEEcCCCeECCCCcccccCCceEEEccceEEEE
Confidence 45689999999999554444 99999999999999999999986443333443
No 18
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=57.27 E-value=0.12 Score=52.18 Aligned_cols=117 Identities=12% Similarity=0.073 Sum_probs=69.1
Q ss_pred hhcccCCCEE--EEEEEEEEeeccCCCCccceEEEEEEEEEEEEEeeccc-----ceEEEEee--c-Cc---eeeeeecc
Q psy17307 31 YNLIAEGDSV--RASTIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQ-----ACVLRLKE--S-ED---MWHAYNLI 97 (342)
Q Consensus 31 ynli~~gD~v--~~~t~Rkv~~~~~~g~~~~~~~~~~l~i~v~~~~f~~~-----~~~l~~~~--~-dd---~~~~~~li 97 (342)
+.+|.|||.| .+.+.|+--...++=..++.|.+|...|+.....|+.| .+-++..| + ++ .|||++ |
T Consensus 28 sl~ipp~~~i~~~~~~l~~e~~~a~niks~~~r~~v~~ai~~~~~~lk~~~~~p~nglv~~~G~v~~~~~~~~~~t~~-i 106 (409)
T TIGR00108 28 SLYIPPDRQISDVAKHLREELSQASNIKSKQTRKNVLSAIEAILQRLKLFNKPPENGLVIFCGMVPREGPTEKMETYV-I 106 (409)
T ss_pred EEEeCCCCcHHHHHHHHHHHHhhhhcccccchhhhHHHHHHHHHHHhhccCCCCCCcEEEEEeEeccCCCcccEEEEE-E
Confidence 3456677777 55555552111111011245666666666665566555 23344444 2 32 799999 8
Q ss_pred CCCCeEEEE---EeeeeeeccCCCCcccceeeeEEEEEEEEEeeeccccEEEEeceee
Q psy17307 98 TEGDSVRAS---TIRKVQSESNTGSSTSSRVRTMLTISVESIDFDTQACVLRLKGRNI 152 (342)
Q Consensus 98 ~~Gd~v~~~---t~Rkv~~e~~~~~~~~~r~~~~l~i~Ve~~ef~~~~~~lri~G~~~ 152 (342)
+|++.|.+. -|.+.+.+.+..+.+.. +....|.|+..+++. +.++-+++.+
T Consensus 107 ep~~pi~~~~y~~d~~f~le~L~e~~~~~--~~~g~VvvD~~~A~i--~~l~g~~~~~ 160 (409)
T TIGR00108 107 EPPEPIKTYIYHCDSKFYLEPLSEMLEEK--DKYGLIVLDRQEATI--GLVKGKRITV 160 (409)
T ss_pred eCCCceEEEEEccCChhHHHHHHHHhcCC--CCEEEEEEecCCEEE--EEEcCCEEEE
Confidence 999999994 36688888887654433 467777787777776 3344444443
No 19
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=56.23 E-value=11 Score=29.63 Aligned_cols=53 Identities=17% Similarity=0.165 Sum_probs=40.9
Q ss_pred eeeEEEEEEEEEeeeccccE-EEEeceeeeccccccccceEEEEeecCceeEEE
Q psy17307 125 VRTMLTISVESIDFDTQACV-LRLKGRNIQENQYVKMGAYHTLDLELNRKFELS 177 (342)
Q Consensus 125 ~~~~l~i~Ve~~ef~~~~~~-lri~G~~~~~~e~v~~G~~HTl~i~~~~~~~i~ 177 (342)
.+..|.++.-..+|-..++- +|++|..+.|-+.|.+|.=|||-=-..=.+..+
T Consensus 17 ~~krLGvK~~~g~~V~~G~IivRQRGtk~~PG~nVg~GrD~TlfA~~~G~V~f~ 70 (82)
T PRK05435 17 ESKRLGVKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVKFE 70 (82)
T ss_pred CcccceeEecCCEEEcCCcEEEEeCCCeECCCCCEeecCCceEEEecceEEEEE
Confidence 45689999999998554444 999999999999999999999874444444443
No 20
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=55.45 E-value=10 Score=29.87 Aligned_cols=49 Identities=18% Similarity=0.192 Sum_probs=37.7
Q ss_pred eEEEEEEEEEeeeccccE-EEEeceeeeccccccccceEEEEeecCceeE
Q psy17307 127 TMLTISVESIDFDTQACV-LRLKGRNIQENQYVKMGAYHTLDLELNRKFE 175 (342)
Q Consensus 127 ~~l~i~Ve~~ef~~~~~~-lri~G~~~~~~e~v~~G~~HTl~i~~~~~~~ 175 (342)
.+|.++.-..+|-..++. +|++|..+.|-..|.+|+-|||=--..=-+.
T Consensus 19 krLGvK~~~Gq~v~aG~IivRQRGTk~hpG~NVG~GkDhTlFAl~dG~Vk 68 (87)
T COG0211 19 KRLGVKKFGGQFVKAGSIIVRQRGTKFHPGVNVGRGKDHTLFALVDGVVK 68 (87)
T ss_pred cccceeeeCCeEEecccEEEEeccccccCCcccccCCCceEEEeeccEEE
Confidence 578888888888665554 9999999999999999999998633333333
No 21
>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=53.98 E-value=15 Score=27.17 Aligned_cols=24 Identities=25% Similarity=0.315 Sum_probs=22.5
Q ss_pred EEcHHHHHHHHHcCC-ccEEEEecC
Q psy17307 307 FYGYRHVSAANESQA-IDTLLIADC 330 (342)
Q Consensus 307 ~YG~~eV~~A~e~GA-VetLLIsD~ 330 (342)
.||..-|..|++.|. +..|+++++
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 22
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=52.44 E-value=13 Score=29.33 Aligned_cols=53 Identities=19% Similarity=0.224 Sum_probs=40.4
Q ss_pred eeeEEEEEEEEEeeeccccE-EEEeceeeeccccccccceEEEEeecCceeEEE
Q psy17307 125 VRTMLTISVESIDFDTQACV-LRLKGRNIQENQYVKMGAYHTLDLELNRKFELS 177 (342)
Q Consensus 125 ~~~~l~i~Ve~~ef~~~~~~-lri~G~~~~~~e~v~~G~~HTl~i~~~~~~~i~ 177 (342)
.+..|.+++-..+|-..++- +|++|..+.|-+.|.+|+=|||-=-..=.+..+
T Consensus 17 ~~krLGvK~~~gq~V~~G~IivRQRGtk~hPG~nVg~GrD~TlfAl~~G~V~f~ 70 (83)
T TIGR00062 17 EAKRLGVKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGKDHTLFALSDGVVKFE 70 (83)
T ss_pred CCccceeEecCCEEEcCCcEEEEcCCceECCCCcccccCCCeEEEecceEEEEE
Confidence 45689999999998554444 999999999999999999999864433334333
No 23
>PRK07714 hypothetical protein; Provisional
Probab=52.05 E-value=20 Score=28.82 Aligned_cols=31 Identities=13% Similarity=0.082 Sum_probs=27.6
Q ss_pred CCCCeEEEcHHHHHHHHHcCCccEEEEecCC
Q psy17307 301 LDPSRAFYGYRHVSAANESQAIDTLLIADCL 331 (342)
Q Consensus 301 ~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l 331 (342)
...+++.+|.++|.+|+..|-+.-++++.+.
T Consensus 14 ~raGk~v~G~~~v~~al~~g~~~lViiA~D~ 44 (100)
T PRK07714 14 NRARKVISGEELVLKEVRSGKAKLVLLSEDA 44 (100)
T ss_pred HHhCCeeecHHHHHHHHHhCCceEEEEeCCC
Confidence 4568999999999999999999999998764
No 24
>PRK07283 hypothetical protein; Provisional
Probab=50.42 E-value=23 Score=28.46 Aligned_cols=31 Identities=19% Similarity=0.149 Sum_probs=27.8
Q ss_pred CCCCeEEEcHHHHHHHHHcCCccEEEEecCC
Q psy17307 301 LDPSRAFYGYRHVSAANESQAIDTLLIADCL 331 (342)
Q Consensus 301 ~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l 331 (342)
...+++..|.+.|.+|+..|.+.-++++.+.
T Consensus 14 ~raGklv~G~~~v~~aik~gk~~lVi~A~Da 44 (98)
T PRK07283 14 QRAGRIISGEELVVKAIQSGQAKLVFLANDA 44 (98)
T ss_pred HHhCCeeEcHHHHHHHHHcCCccEEEEeCCC
Confidence 4568999999999999999999999998764
No 25
>KOG4600|consensus
Probab=49.06 E-value=13 Score=32.02 Aligned_cols=46 Identities=22% Similarity=0.241 Sum_probs=36.8
Q ss_pred eEEEEEEEEEeeecccc-EEEEeceeeeccccccccceEEEE-eecCc
Q psy17307 127 TMLTISVESIDFDTQAC-VLRLKGRNIQENQYVKMGAYHTLD-LELNR 172 (342)
Q Consensus 127 ~~l~i~Ve~~ef~~~~~-~lri~G~~~~~~e~v~~G~~HTl~-i~~~~ 172 (342)
.+|.|+--+.+|-..++ .+|++|....|-++|.+|+-|||- |++|.
T Consensus 46 rrlGvKk~egq~V~~G~IIvrQRgtkfHPG~nVGiGKDhtifaL~eG~ 93 (144)
T KOG4600|consen 46 RRLGVKKYEGQSVIPGNIIVRQRGTKFHPGDNVGIGKDHTIFALEEGR 93 (144)
T ss_pred ccccceecCCeeeecccEEEEecccccCCCcccccCCcceEEEeeccE
Confidence 47888887777754444 499999999999999999999975 66664
No 26
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=46.75 E-value=45 Score=27.25 Aligned_cols=36 Identities=22% Similarity=0.418 Sum_probs=26.6
Q ss_pred EEEEeecccceEEEEeecCceeeeeeccCCCCeEEEE
Q psy17307 70 VESIDFDTQACVLRLKESEDMWHAYNLITEGDSVRAS 106 (342)
Q Consensus 70 v~~~~f~~~~~~l~~~~~dd~~~~~~li~~Gd~v~~~ 106 (342)
=++-.|...++.++|+=+++.|+-.+ |.|+|.|++.
T Consensus 49 ~d~Y~F~D~TG~I~VeId~~~w~g~~-vt~~~~Vri~ 84 (103)
T PF04076_consen 49 DDKYLFRDATGEIEVEIDDDVWRGQT-VTPDDKVRIS 84 (103)
T ss_dssp TTEEEEEETTEEEEEE--GGGSTT-----TTSEEEEE
T ss_pred CCEEEEECCCCcEEEEEChhhcCCcc-cCCCCEEEEE
Confidence 35678999999999999999999988 9999999994
No 27
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=46.53 E-value=27 Score=28.46 Aligned_cols=32 Identities=13% Similarity=0.273 Sum_probs=28.2
Q ss_pred CCCCeEEEcHHHHHHHHHcCCccEEEEecCCC
Q psy17307 301 LDPSRAFYGYRHVSAANESQAIDTLLIADCLF 332 (342)
Q Consensus 301 ~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l~ 332 (342)
...+++.+|.+.|.+|+..|.+.-+|++++.-
T Consensus 13 ~rAGklv~G~~~v~~aik~gk~~lVI~A~D~s 44 (104)
T PRK05583 13 KKAGKLLEGYNKCEEAIKKKKVYLIIISNDIS 44 (104)
T ss_pred HHhCCeeecHHHHHHHHHcCCceEEEEeCCCC
Confidence 45689999999999999999999999988653
No 28
>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=41.62 E-value=45 Score=26.01 Aligned_cols=31 Identities=16% Similarity=0.166 Sum_probs=27.3
Q ss_pred CCCeEEEcHHHHHHHHHcCCccEEEEecCCC
Q psy17307 302 DPSRAFYGYRHVSAANESQAIDTLLIADCLF 332 (342)
Q Consensus 302 d~~~a~YG~~eV~~A~e~GAVetLLIsD~l~ 332 (342)
..++..+|.++|.+|++.|=+.-++++.+.-
T Consensus 12 ~~~~lv~G~~~v~k~l~~~~~~lvilA~d~~ 42 (95)
T PF01248_consen 12 KAGRLVKGIKEVLKALKKGKAKLVILAEDCS 42 (95)
T ss_dssp HHSEEEESHHHHHHHHHTTCESEEEEETTSS
T ss_pred hcCCEEEchHHHHHHHHcCCCcEEEEcCCCC
Confidence 4578999999999999999999999988653
No 29
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=40.84 E-value=42 Score=26.25 Aligned_cols=29 Identities=21% Similarity=0.206 Sum_probs=26.5
Q ss_pred CCeEEEcHHHHHHHHHcCCccEEEEecCC
Q psy17307 303 PSRAFYGYRHVSAANESQAIDTLLIADCL 331 (342)
Q Consensus 303 ~~~a~YG~~eV~~A~e~GAVetLLIsD~l 331 (342)
.|+...|.++|.+|++.|-+.-++|+.+.
T Consensus 6 ~GKlv~G~~~vlkaIk~gkakLViiA~Da 34 (82)
T PRK13601 6 PSKRVVGAKQTLKAITNCNVLQVYIAKDA 34 (82)
T ss_pred CccEEEchHHHHHHHHcCCeeEEEEeCCC
Confidence 57899999999999999999999999764
No 30
>PRK04175 rpl7ae 50S ribosomal protein L7Ae; Validated
Probab=40.25 E-value=42 Score=28.16 Aligned_cols=32 Identities=19% Similarity=0.137 Sum_probs=28.9
Q ss_pred CCCCeEEEcHHHHHHHHHcCCccEEEEecCCC
Q psy17307 301 LDPSRAFYGYRHVSAANESQAIDTLLIADCLF 332 (342)
Q Consensus 301 ~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l~ 332 (342)
...+....|.++|.+|++.|-+.-++|+++.-
T Consensus 26 ~ragklv~G~~~v~kaikkgkakLVilA~D~s 57 (122)
T PRK04175 26 RDTGKIKKGTNETTKAVERGIAKLVVIAEDVD 57 (122)
T ss_pred HHcCCEeEcHHHHHHHHHcCCccEEEEeCCCC
Confidence 45689999999999999999999999998764
No 31
>PTZ00106 60S ribosomal protein L30; Provisional
Probab=38.51 E-value=41 Score=27.65 Aligned_cols=31 Identities=10% Similarity=0.146 Sum_probs=28.2
Q ss_pred CCCCeEEEcHHHHHHHHHcCCccEEEEecCC
Q psy17307 301 LDPSRAFYGYRHVSAANESQAIDTLLIADCL 331 (342)
Q Consensus 301 ~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l 331 (342)
...|+..+|.++|.+|++.|-+.-++|+.+.
T Consensus 21 ~raGKlv~G~~~vlkalk~gkaklViiA~D~ 51 (108)
T PTZ00106 21 MKSGKYTLGTKSTLKALRNGKAKLVIISNNC 51 (108)
T ss_pred HHhCCeeecHHHHHHHHHcCCeeEEEEeCCC
Confidence 4669999999999999999999999999865
No 32
>PF10664 NdhM: Cyanobacterial and plastid NDH-1 subunit M; InterPro: IPR018922 The NADH dehydrogenase I complex shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in plants is believed to be plastoquinone. The NADH dehydrogenase I complex couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. This entry represents subunit M of the NADH dehydrogenase I complex in cyanobacteria and plant chloroplasts []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=38.41 E-value=79 Score=25.88 Aligned_cols=48 Identities=23% Similarity=0.447 Sum_probs=36.6
Q ss_pred EEEeceeeeccccccccceEEEEeecCceeEEEecCCChhhHHHH----HHHhcccC
Q psy17307 145 LRLKGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERI----EVACNIEK 197 (342)
Q Consensus 145 lri~G~~~~~~e~v~~G~~HTl~i~~~~~~~i~K~~W~~~~le~L----~ea~~~~~ 197 (342)
+||+--.+++|+.++--..-|+++.|..+|. |+...++.. .+.++...
T Consensus 8 vrIftA~v~~~~lv~~~~~LTLdlDPdNEF~-----W~~~~l~kVy~~F~eLVe~~~ 59 (108)
T PF10664_consen 8 VRIFTAEVENNELVPSDDKLTLDLDPDNEFN-----WNEEALQKVYRKFDELVESYA 59 (108)
T ss_pred EEEEEEEEecCceecCCCeeEEecCCCcccc-----cCHHHHHHHHHHHHHHHHhhc
Confidence 7777777887877777788999999999984 988888764 44554433
No 33
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=38.21 E-value=47 Score=25.79 Aligned_cols=30 Identities=10% Similarity=0.205 Sum_probs=26.9
Q ss_pred CCCeEEEcHHHHHHHHHcCCccEEEEecCC
Q psy17307 302 DPSRAFYGYRHVSAANESQAIDTLLIADCL 331 (342)
Q Consensus 302 d~~~a~YG~~eV~~A~e~GAVetLLIsD~l 331 (342)
..++...|.++|.+|++.|-+.-++|+.+.
T Consensus 8 ragkl~~G~~~v~kai~~gkaklViiA~D~ 37 (82)
T PRK13602 8 QAKSIVIGTKQTVKALKRGSVKEVVVAEDA 37 (82)
T ss_pred hcCCEEEcHHHHHHHHHcCCeeEEEEECCC
Confidence 457899999999999999999999998764
No 34
>PRK01018 50S ribosomal protein L30e; Reviewed
Probab=38.17 E-value=47 Score=26.69 Aligned_cols=30 Identities=13% Similarity=0.200 Sum_probs=27.5
Q ss_pred CCCeEEEcHHHHHHHHHcCCccEEEEecCC
Q psy17307 302 DPSRAFYGYRHVSAANESQAIDTLLIADCL 331 (342)
Q Consensus 302 d~~~a~YG~~eV~~A~e~GAVetLLIsD~l 331 (342)
..++...|.++|.+|++.|-+.-++|+++.
T Consensus 13 ragkl~~G~~~v~kai~~gkaklViiA~D~ 42 (99)
T PRK01018 13 DTGKVILGSKRTIKAIKLGKAKLVIVASNC 42 (99)
T ss_pred HcCCEEEcHHHHHHHHHcCCceEEEEeCCC
Confidence 468999999999999999999999999874
No 35
>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=37.14 E-value=50 Score=27.43 Aligned_cols=31 Identities=19% Similarity=0.205 Sum_probs=28.3
Q ss_pred CCCCeEEEcHHHHHHHHHcCCccEEEEecCC
Q psy17307 301 LDPSRAFYGYRHVSAANESQAIDTLLIADCL 331 (342)
Q Consensus 301 ~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l 331 (342)
...+...+|.++|.+|++.|-+.-++|+++.
T Consensus 22 ~ragkl~~G~~~v~kaikkgka~LVilA~D~ 52 (117)
T TIGR03677 22 RETGKIKKGTNEVTKAVERGIAKLVVIAEDV 52 (117)
T ss_pred HHcCCEeEcHHHHHHHHHcCCccEEEEeCCC
Confidence 4568899999999999999999999999876
No 36
>PRK06683 hypothetical protein; Provisional
Probab=37.02 E-value=51 Score=25.66 Aligned_cols=31 Identities=13% Similarity=0.188 Sum_probs=27.7
Q ss_pred CCCCeEEEcHHHHHHHHHcCCccEEEEecCC
Q psy17307 301 LDPSRAFYGYRHVSAANESQAIDTLLIADCL 331 (342)
Q Consensus 301 ~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l 331 (342)
.+.++...|.++|.+|++.|-++-++|..+.
T Consensus 7 ~~agk~v~G~~~v~kaik~gkaklViiA~Da 37 (82)
T PRK06683 7 SNAENVVVGHKRTLEAIKNGIVKEVVIAEDA 37 (82)
T ss_pred HhCCCEEEcHHHHHHHHHcCCeeEEEEECCC
Confidence 3568899999999999999999999999764
No 37
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=36.46 E-value=44 Score=26.33 Aligned_cols=26 Identities=19% Similarity=0.314 Sum_probs=23.7
Q ss_pred EEEcHHHHHHHHHcCCccEEEEecCC
Q psy17307 306 AFYGYRHVSAANESQAIDTLLIADCL 331 (342)
Q Consensus 306 a~YG~~eV~~A~e~GAVetLLIsD~l 331 (342)
..+|.+++.+|++.|-+..++|..+.
T Consensus 14 ~vvG~kqt~Kai~kg~~~~v~iA~Da 39 (84)
T PRK13600 14 FVVGLKETLKALKKDQVTSLIIAEDV 39 (84)
T ss_pred ceeeHHHHHHHHhcCCceEEEEeCCC
Confidence 48999999999999999999998764
No 38
>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=34.04 E-value=91 Score=24.60 Aligned_cols=63 Identities=22% Similarity=0.303 Sum_probs=36.2
Q ss_pred ccCCCEEEEEEEEEEeeccCCCCccceEEEEEEEEEEEEEee-cccceEEEEee----cCceeeeeeccCCCCeEEEEE
Q psy17307 34 IAEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESIDF-DTQACVLRLKE----SEDMWHAYNLITEGDSVRAST 107 (342)
Q Consensus 34 i~~gD~v~~~t~Rkv~~~~~~g~~~~~~~~~~l~i~v~~~~f-~~~~~~l~~~~----~dd~~~~~~li~~Gd~v~~~t 107 (342)
-++||+|.+.-.+ +.. ..-.+.+ +.++.... .++.+-||+++ +-|.--++..+++||.|+++-
T Consensus 4 P~~GDiVig~V~~-v~~---------~~~~v~I-~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkV 71 (92)
T cd05791 4 PKVGSIVIARVTR-INP---------RFAKVDI-LCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKV 71 (92)
T ss_pred CCCCCEEEEEEEE-EcC---------CEEEEEE-EEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEE
Confidence 4899999998653 321 1111111 12233333 35677788775 222333667789999999963
No 39
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=32.75 E-value=1.8e+02 Score=22.68 Aligned_cols=32 Identities=25% Similarity=0.431 Sum_probs=18.0
Q ss_pred cccceEEEEee----cCceeeeeeccCCCCeEEEEE
Q psy17307 76 DTQACVLRLKE----SEDMWHAYNLITEGDSVRAST 107 (342)
Q Consensus 76 ~~~~~~l~~~~----~dd~~~~~~li~~Gd~v~~~t 107 (342)
+.|.+-||.++ +-|.=-.+.-.+|||.|+++-
T Consensus 44 ~~f~GiIR~~DVR~te~Dkv~~~~~FrpGDIVrA~V 79 (82)
T PF10447_consen 44 EPFQGIIRKQDVRATEKDKVKMYDCFRPGDIVRARV 79 (82)
T ss_dssp -SS-S-EEEEGGGT-SS----GGGT--SSSEEEEEE
T ss_pred cccEEEEEeeeecccccchhhHHhccCCCCEEEEEE
Confidence 47888999986 455444566678999999963
No 40
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=31.45 E-value=44 Score=28.42 Aligned_cols=35 Identities=14% Similarity=0.301 Sum_probs=32.0
Q ss_pred EEEeecccceEEEEeecCceeeeeeccCCCCeEEEE
Q psy17307 71 ESIDFDTQACVLRLKESEDMWHAYNLITEGDSVRAS 106 (342)
Q Consensus 71 ~~~~f~~~~~~l~~~~~dd~~~~~~li~~Gd~v~~~ 106 (342)
+.-.|...++.+.|+=+++.|+-.+ +.|+|.|++.
T Consensus 73 d~Y~F~D~TG~I~VeId~~~w~G~~-v~p~d~V~I~ 107 (126)
T TIGR00156 73 DRYVFRDKSGEINVVIPAAVWNGRE-VQPKDMVNIS 107 (126)
T ss_pred ceEEEECCCCCEEEEECHHHcCCCc-CCCCCEEEEE
Confidence 6688999999999999999999999 9999999994
No 41
>PRK09190 hypothetical protein; Provisional
Probab=27.03 E-value=82 Score=29.30 Aligned_cols=52 Identities=15% Similarity=0.154 Sum_probs=36.8
Q ss_pred hHHHHHhcChhhhhhhhcccc-CCCCeEEEcHHHHHHHHHcCCccEEEEecCC
Q psy17307 280 HSLKEILADPTVTSKMQDTKA-LDPSRAFYGYRHVSAANESQAIDTLLIADCL 331 (342)
Q Consensus 280 ~gL~EvL~~~~v~~~l~d~k~-~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l 331 (342)
..|.+.|..--.+++++=..+ ...+.+++|.+.|..|+..|-+.-||++.+.
T Consensus 85 ~~l~~~l~~~l~~ril~lLGLArRAGklVsG~~~V~~alk~gk~~Lvi~A~Da 137 (220)
T PRK09190 85 PDLADLVEALLARRALDALGLARKAGQVVSGFEKVDAALRSGEAAALIHASDG 137 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhCCEeecHHHHHHHHHcCCceEEEEeccC
Confidence 445555443333334433333 6779999999999999999999999988764
No 42
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=25.38 E-value=2.8e+02 Score=24.73 Aligned_cols=72 Identities=18% Similarity=0.293 Sum_probs=40.8
Q ss_pred eEEEeeCCCcchhhh-hhcccCCCEEEEEEEEEEeeccCCCCccceEEEEEEEEEEEEEe------ecccceEEEEeecC
Q psy17307 16 VVALVPEESEDMWHA-YNLIAEGDSVRASTIRKVQSESNTGSSTSSRVRTMLTISVESID------FDTQACVLRLKESE 88 (342)
Q Consensus 16 ~v~l~~e~~dDlw~l-ynli~~gD~v~~~t~Rkv~~~~~~g~~~~~~~~~~l~i~v~~~~------f~~~~~~l~~~~~d 88 (342)
.|.|.| |.- -...++||+|.+.-.+-.. ..+.+.+..++ -..+.+-|+++...
T Consensus 49 ~Isv~P------~~~~~~~~~~GdiV~GkV~~i~~--------------~g~~V~I~~~~~~~~~l~~~~~G~l~~s~i~ 108 (189)
T PRK09521 49 KISVIP------FKKTPPLLKKGDIVYGRVVDVKE--------------QRALVRIVSIEGSERELATSKLAYIHISQVS 108 (189)
T ss_pred EEEEec------CcCCCCCCCCCCEEEEEEEEEcC--------------CeEEEEEEEecccccccCCCceeeEEhhHcC
Confidence 466644 554 3566899999997644321 12233333332 13456667776532
Q ss_pred ce--eeeeeccCCCCeEEEEE
Q psy17307 89 DM--WHAYNLITEGDSVRAST 107 (342)
Q Consensus 89 d~--~~~~~li~~Gd~v~~~t 107 (342)
+. =.....+.+||.|.++-
T Consensus 109 ~~~~~~~~~~~~~GD~V~akV 129 (189)
T PRK09521 109 DGYVESLTDAFKIGDIVRAKV 129 (189)
T ss_pred hhhhhhHHhccCCCCEEEEEE
Confidence 21 12355689999999963
No 43
>PRK10053 hypothetical protein; Provisional
Probab=24.64 E-value=66 Score=27.49 Aligned_cols=37 Identities=3% Similarity=0.118 Sum_probs=32.9
Q ss_pred EEEEEeecccceEEEEeecCceeeeeeccCCCCeEEEE
Q psy17307 69 SVESIDFDTQACVLRLKESEDMWHAYNLITEGDSVRAS 106 (342)
Q Consensus 69 ~v~~~~f~~~~~~l~~~~~dd~~~~~~li~~Gd~v~~~ 106 (342)
.=+.-.|...++.+.|+=+++.|.-.+ |.|.|.|++.
T Consensus 75 g~d~Y~F~D~tG~I~VeID~~~w~G~~-v~p~~kV~I~ 111 (130)
T PRK10053 75 GDDRYVFRDKSGEINVIIPAAVFDGRE-VQPDQMININ 111 (130)
T ss_pred CCceEEEECCCCcEEEEeCHHHcCCCc-CCCCCEEEEE
Confidence 336788999999999999999999998 9999999994
No 44
>COG1358 RPL8A Ribosomal protein HS6-type (S12/L30/L7a) [Translation, ribosomal structure and biogenesis]
Probab=24.20 E-value=74 Score=26.59 Aligned_cols=31 Identities=19% Similarity=0.170 Sum_probs=27.9
Q ss_pred CCCCeEEEcHHHHHHHHHcCCccEEEEecCC
Q psy17307 301 LDPSRAFYGYRHVSAANESQAIDTLLIADCL 331 (342)
Q Consensus 301 ~d~~~a~YG~~eV~~A~e~GAVetLLIsD~l 331 (342)
...+...+|.+++-+|++.|=..-++|+.+.
T Consensus 23 ~~~~ki~~G~~e~~Kai~~g~a~LVviA~Dv 53 (116)
T COG1358 23 SRAGKLKKGTNEVTKAIERGKAKLVVIAEDV 53 (116)
T ss_pred HhcCCchhhHHHHHHHHHcCCCcEEEEecCC
Confidence 4667999999999999999999999999864
No 45
>COG0186 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=22.49 E-value=4e+02 Score=21.20 Aligned_cols=56 Identities=18% Similarity=0.190 Sum_probs=38.9
Q ss_pred CccceEEEEEEEEEEEEEeecccceEEEEeecCceee-eeeccCCCCeEEEEEeeee
Q psy17307 56 SSTSSRVRTMLTISVESIDFDTQACVLRLKESEDMWH-AYNLITEGDSVRASTIRKV 111 (342)
Q Consensus 56 ~~~~~~~~~~l~i~v~~~~f~~~~~~l~~~~~dd~~~-~~~li~~Gd~v~~~t~Rkv 111 (342)
.+.|.+..=++.+++|..-||+-+++.--..--=.=| =-|-..+||.|+|...|..
T Consensus 14 ~VvS~Km~KTvvV~ve~~~~hp~Y~K~v~r~kK~~aHde~~~~k~GD~V~I~EtRPL 70 (87)
T COG0186 14 VVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAHDECNEAKVGDIVRIAETRPL 70 (87)
T ss_pred EEEEccCceeEEEEEEEEEecccceEEEEEEeeeEeecccccCCCCCEEEEEEcccc
Confidence 3345566668899999999999988876654211111 1234799999999877777
No 46
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=20.97 E-value=84 Score=22.80 Aligned_cols=20 Identities=30% Similarity=0.463 Sum_probs=11.9
Q ss_pred cccceEEEEeecCceeEEEe
Q psy17307 159 KMGAYHTLDLELNRKFELSK 178 (342)
Q Consensus 159 ~~G~~HTl~i~~~~~~~i~K 178 (342)
+.|.+||+.|+||..|.-.+
T Consensus 17 ~Kgr~~Ti~L~~G~~fhThr 36 (54)
T PF14801_consen 17 PKGRKHTITLEPGGEFHTHR 36 (54)
T ss_dssp TT--EEEEE--TT-EEEETT
T ss_pred CCCCeeeEEECCCCeEEcCc
Confidence 35999999999999998543
Done!