Query 024440
Match_columns 267
No_of_seqs 140 out of 937
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 04:37:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024440.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024440hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0094 RplE Ribosomal protein 100.0 2.3E-70 5E-75 473.9 18.4 179 61-239 1-179 (180)
2 PRK00010 rplE 50S ribosomal pr 100.0 2E-69 4.3E-74 471.6 18.9 179 61-239 1-179 (179)
3 CHL00078 rpl5 ribosomal protei 100.0 9.8E-69 2.1E-73 468.0 19.2 179 61-239 2-180 (181)
4 KOG0398 Mitochondrial/chloropl 100.0 1.7E-60 3.8E-65 426.0 11.9 236 1-241 28-277 (278)
5 PTZ00156 60S ribosomal protein 100.0 7.3E-48 1.6E-52 333.4 13.7 129 83-221 5-133 (172)
6 PRK04219 rpl5p 50S ribosomal p 100.0 1.5E-47 3.2E-52 333.4 13.0 137 81-226 7-143 (177)
7 PF00673 Ribosomal_L5_C: ribos 100.0 4.5E-38 9.8E-43 249.2 9.5 95 144-238 1-95 (95)
8 KOG0397 60S ribosomal protein 100.0 7.3E-29 1.6E-33 209.5 6.2 135 82-226 6-140 (176)
9 PF00281 Ribosomal_L5: Ribosom 99.8 1.7E-20 3.6E-25 136.1 7.1 56 84-140 1-56 (56)
10 KOG0641 WD40 repeat protein [G 27.0 53 0.0011 31.2 2.6 42 17-59 207-253 (350)
11 PF05258 DUF721: Protein of un 22.0 2.1E+02 0.0046 20.7 4.7 44 40-87 43-86 (89)
No 1
>COG0094 RplE Ribosomal protein L5 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-70 Score=473.94 Aligned_cols=179 Identities=58% Similarity=0.987 Sum_probs=177.2
Q ss_pred hhhHHHHHHhhhhHHHHhhcCCCCccCCceeeeEEEEecCchhhhChhhHHHHHHHHHHHhCCCcEEEeeecccCCCCcc
Q 024440 61 TGRLKTTYLEKIVPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIR 140 (267)
Q Consensus 61 ~~rLk~~Y~~~I~~dL~~k~~y~N~m~vPkL~KIvLn~gvg~a~~d~k~L~~a~~~Le~ITGQkPv~tkAKksIa~FKiR 140 (267)
|+||+.+|.+.|.+.|+++|+|+|+|++|+|+|||||||+|++..|.+.|+.|..+|+.||||||++|+||+||++||||
T Consensus 1 ~~rlk~~y~~~i~~~l~~~~~y~n~M~~P~i~KVvvNmGvGEa~~d~~~l~~A~~~L~~ItGQKPv~tkAkksia~FkiR 80 (180)
T COG0094 1 MNRLKEKYKDEIVPALIKKFGYSNPMQVPRIEKVVVNMGVGEAAADGKRLEKAAKDLELITGQKPVITKAKKSIAGFKIR 80 (180)
T ss_pred CchhhHHHHHHHhHHHHHhhccCCccccceeEEEEEEccchhhhhchHHHHHHHHHHHHHhCCCceeeehhccccccccc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeeeEEEEchhhHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCcceeeccccccccCcccccCCCCCCCeeEEEEeec
Q 024440 141 EGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTA 220 (267)
Q Consensus 141 kG~piG~KVTLRG~~My~FLdKLi~~vLPRirdF~Gi~~~sfD~~GN~sfGIkd~~~FPEIeyD~~~~i~GmdItivTta 220 (267)
+||||||||||||++||+||++|++++|||+|||+|++.+|||++|||+|||+||++||||+||+.++++||||+|+|+|
T Consensus 81 ~g~pIG~KVTLRg~rm~eFL~rl~~i~lPrvrdfrGls~~sFDg~GN~sfGI~E~i~FPei~yD~~~~i~GMdi~ivtta 160 (180)
T COG0094 81 EGMPIGVKVTLRGERMYEFLDRLLNIALPRVRDFRGLSPKSFDGRGNYSFGIKEQIIFPEIDYDPIIGIRGMDITIVTTA 160 (180)
T ss_pred CCCeeeEEEEEchHHHHHHHHHHHHhhccccccccCCCccccCCCCceEecchheeecCccccCccCCccCceEEEEecC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHhcCCcccc
Q 024440 221 KTDKEGQRLLALMGMPFRE 239 (267)
Q Consensus 221 kt~~ea~~LLs~~g~PF~~ 239 (267)
++|.|++.||+.++|||..
T Consensus 161 ~~d~e~R~ll~~~~~Pf~~ 179 (180)
T COG0094 161 KGDVEARALLSAFGIPFRK 179 (180)
T ss_pred CChHHHHHHHHhcCCCCCC
Confidence 9999999999999999975
No 2
>PRK00010 rplE 50S ribosomal protein L5; Validated
Probab=100.00 E-value=2e-69 Score=471.56 Aligned_cols=179 Identities=59% Similarity=1.007 Sum_probs=176.8
Q ss_pred hhhHHHHHHhhhhHHHHhhcCCCCccCCceeeeEEEEecCchhhhChhhHHHHHHHHHHHhCCCcEEEeeecccCCCCcc
Q 024440 61 TGRLKTTYLEKIVPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIR 140 (267)
Q Consensus 61 ~~rLk~~Y~~~I~~dL~~k~~y~N~m~vPkL~KIvLn~gvg~a~~d~k~L~~a~~~Le~ITGQkPv~tkAKksIa~FKiR 140 (267)
|++|++||+++|++||+++++|+|+|++|+|+||+||+|+|++.+|++.|..|..+|++||||+|++|+||++|++||||
T Consensus 1 ~~~l~~~Y~~~v~~~L~~~~~y~n~m~iPki~KIvin~gvg~~~~~~~~l~~a~~~L~~ITGQkP~~t~aKksi~~fkiR 80 (179)
T PRK00010 1 MPRLKEKYKEEIVPALMKEFGYKNVMQVPKLEKIVLNMGVGEAVADKKLLENAVEDLTLITGQKPVVTKAKKSIAGFKLR 80 (179)
T ss_pred CchHHHHHHHHHHHHHHHHhCCCCcccCCceeEEEEEccCcchhhchHHHHHHHHHHHHHhCCceEEEeccccccccCCC
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeeeEEEEchhhHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCcceeeccccccccCcccccCCCCCCCeeEEEEeec
Q 024440 141 EGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTA 220 (267)
Q Consensus 141 kG~piG~KVTLRG~~My~FLdKLi~~vLPRirdF~Gi~~~sfD~~GN~sfGIkd~~~FPEIeyD~~~~i~GmdItivTta 220 (267)
+|+||||||||||++||+||+||+++||||+|||+|++.++||++|||+|||+|+++||||+||++++++||||||+|+|
T Consensus 81 kg~piG~kVTLRg~~my~FL~kli~~vlPrirdf~Gi~~~sfD~~Gn~sfGi~e~~~FPei~yd~~~~i~G~~Itivtta 160 (179)
T PRK00010 81 EGMPIGCKVTLRGERMYEFLDRLINIALPRVRDFRGLSPKSFDGRGNYTLGIKEQIIFPEIDYDKIDKIRGMDITIVTTA 160 (179)
T ss_pred CCCEEEEEEEECcHHHHHHHHHHHHHhcccccccccccccccCCCceEEECcchhhcCCCcccCccCCcCCceEEEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHhcCCcccc
Q 024440 221 KTDKEGQRLLALMGMPFRE 239 (267)
Q Consensus 221 kt~~ea~~LLs~~g~PF~~ 239 (267)
+||+||++||++|||||++
T Consensus 161 ~t~~ea~~LLs~~g~Pf~~ 179 (179)
T PRK00010 161 KTDEEARALLKAFGFPFRK 179 (179)
T ss_pred CCHHHHHHHHHHcCCCCCC
Confidence 9999999999999999973
No 3
>CHL00078 rpl5 ribosomal protein L5
Probab=100.00 E-value=9.8e-69 Score=467.95 Aligned_cols=179 Identities=61% Similarity=1.040 Sum_probs=176.9
Q ss_pred hhhHHHHHHhhhhHHHHhhcCCCCccCCceeeeEEEEecCchhhhChhhHHHHHHHHHHHhCCCcEEEeeecccCCCCcc
Q 024440 61 TGRLKTTYLEKIVPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIR 140 (267)
Q Consensus 61 ~~rLk~~Y~~~I~~dL~~k~~y~N~m~vPkL~KIvLn~gvg~a~~d~k~L~~a~~~Le~ITGQkPv~tkAKksIa~FKiR 140 (267)
.+||++||+++|+|||+++++|+|+|++|+|+||+||+|+|++.+|++.|+.|..+|+.||||+|++|+||++|++||+|
T Consensus 2 ~~~~~~~Y~~~v~~~L~~~~~~~n~m~iP~i~KIvin~gvg~~~~~~k~l~~a~~~L~~ITGQkP~~t~AKksia~FkiR 81 (181)
T CHL00078 2 VQRLKSLYKEKIVPKLIEKFLYKNIHQVPKLKKIVINRGLGEASQNSKILESSIKELTIITGQKPIITRAKKAIAGFKIR 81 (181)
T ss_pred chHHHHHHHHHHHHHHHHHhCCCCcccCCceeEEEEecCchhhhhchHHHHHHHHHHHHHhCCceEEEeecccchhcCcc
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeeeEEEEchhhHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCcceeeccccccccCcccccCCCCCCCeeEEEEeec
Q 024440 141 EGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTA 220 (267)
Q Consensus 141 kG~piG~KVTLRG~~My~FLdKLi~~vLPRirdF~Gi~~~sfD~~GN~sfGIkd~~~FPEIeyD~~~~i~GmdItivTta 220 (267)
+|+||||||||||++||+||+||+++||||+|||+|++.++||++|||+|||+|+++||||+||++++++||||||+|+|
T Consensus 82 kg~piG~kVTLRg~~my~FL~kli~~vlPrirdf~Gi~~~sfd~~Gn~sfGi~e~~~FPEi~~d~~~~i~G~~Itivtta 161 (181)
T CHL00078 82 EKMPVGVSVTLRGDKMYAFLDRLINLALPRIRDFQGLSPKSFDGHGNYNLGLKEQLMFPEIDYDKIDQIRGMDISIVTTA 161 (181)
T ss_pred CCCEEEEEEEECcHhHHHHHHHHHHHhcccccccccccccccCCCceEEECcchhccCCCcccCccCCcCCCeEEEEEee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CChHHHHHHHHhcCCcccc
Q 024440 221 KTDKEGQRLLALMGMPFRE 239 (267)
Q Consensus 221 kt~~ea~~LLs~~g~PF~~ 239 (267)
+|++||++||++|||||.+
T Consensus 162 ~t~~ea~~Ll~~~g~Pf~~ 180 (181)
T CHL00078 162 KTDQEGLALLKELGMPFKD 180 (181)
T ss_pred CCHHHHHHHHHHcCCCcCC
Confidence 9999999999999999976
No 4
>KOG0398 consensus Mitochondrial/chloroplast ribosomal protein L5/L7 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-60 Score=425.98 Aligned_cols=236 Identities=63% Similarity=0.980 Sum_probs=220.1
Q ss_pred CCCcchhhccccccccccCCCCCCcc---cCCCCCCCCCCCceEEEeeccceeEEeeCCchhh-------hhhHHHHHHh
Q 024440 1 MACPSLLHSSASSFHGRFPALSSSSY---VRPTYPNPINVNGVVSVKAAAGGIVLVEKSEAEK-------TGRLKTTYLE 70 (267)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~rLk~~Y~~ 70 (267)
|+.|+|+++++++|+++|.+...+.+ .+.+ +|.-.+ | ++++.++-++|+++++|. .++.+-.|.+
T Consensus 28 ~~~P~l~~d~~~~~s~~F~P~~t~~~RLn~h~l--~t~l~d-v--l~vsysh~v~v~ks~~e~aWsGDsPy~~nrpp~~~ 102 (278)
T KOG0398|consen 28 MASPSLLQDSASSFSGRFSPLATPSSRLNAHML--STPLRD-V--LKVSYSHTVLVEKSEAEKAWSGDSPYQRNRPPYLE 102 (278)
T ss_pred cCCCccccCcccccCCCcCCCCchhhHHHHHhh--ccchhh-h--hhhhcccchhhhhhhhhhhccCCChhhccCCcccc
Confidence 78999999999999999998854433 4432 233234 6 788999999999999997 5778889999
Q ss_pred hhhHHHHhhcCCCCccCCceeeeEEEEecCchhhhChhhHHHHHHHHHHHhCCCcEEEeeecccCCCCccCCceeeeEEE
Q 024440 71 KIVPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIREGEPLGIAVT 150 (267)
Q Consensus 71 ~I~~dL~~k~~y~N~m~vPkL~KIvLn~gvg~a~~d~k~L~~a~~~Le~ITGQkPv~tkAKksIa~FKiRkG~piG~KVT 150 (267)
...+.|..++.|-|+.++|+|+||||||+++|+.+|.+.++.|++++++||||+|..++||++|++||||+|+|+|+|||
T Consensus 103 Rg~kallp~~~~vn~~nvP~v~kVVvnc~~~eA~~n~~~l~~am~~~~~ITG~kP~~~~ar~dV~twKlR~g~p~G~kVt 182 (278)
T KOG0398|consen 103 RGIKALLPEFKYVNIHNVPKVQKVVVNCGIGEAAQNDKGLEAAMKDIALITGQKPIKTRARADVATWKLREGQPLGIKVT 182 (278)
T ss_pred cccccccccccccChhhCCceeeeeeecccHHhhhhHHHHHHHHHHHHHHhCCCcceeeecccCCceeeccCCcceeEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EchhhHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCcceeeccc--cccccCccc--ccCCCCCCCeeEEEEeecCChHHH
Q 024440 151 LRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVK--EQSVFPEIR--YDALGKPKGIDVCITTTAKTDKEG 226 (267)
Q Consensus 151 LRG~~My~FLdKLi~~vLPRirdF~Gi~~~sfD~~GN~sfGIk--d~~~FPEIe--yD~~~~i~GmdItivTtakt~~ea 226 (267)
|||+.||.||++|+++||||+|||+|+++.|+|++|||+||++ |+-+||||+ ||.+...+||||+|.|+|+.|.||
T Consensus 183 L~G~~My~FLs~L~elvLPr~rdfkGvSp~Sgd~~GniSfGl~aEd~~~FPeI~An~d~~pkt~Gm~vnI~T~ak~d~~a 262 (278)
T KOG0398|consen 183 LRGDVMYSFLSRLIELVLPRTRDFKGVSPSSGDGNGNISFGLKAEDQGVFPEIRANFDAVPKTRGMDVNISTTAKSDQEA 262 (278)
T ss_pred EechHHHHHHHHHHHHhccccccccCcCCCCcCCCCCEEeccchhhcccCchhhhhhhccccccceeEeecccccchHHH
Confidence 9999999999999999999999999999999999999999999 889999999 999999999999999999999999
Q ss_pred HHHHHhcCCccccCC
Q 024440 227 QRLLALMGMPFREGG 241 (267)
Q Consensus 227 ~~LLs~~g~PF~~~~ 241 (267)
|.||++|||||.+++
T Consensus 263 r~lls~~~~PF~~g~ 277 (278)
T KOG0398|consen 263 RKLLSLMGMPFREGG 277 (278)
T ss_pred HHHHHhcCCcccCCC
Confidence 999999999999865
No 5
>PTZ00156 60S ribosomal protein L11; Provisional
Probab=100.00 E-value=7.3e-48 Score=333.39 Aligned_cols=129 Identities=29% Similarity=0.533 Sum_probs=125.5
Q ss_pred CCccCCceeeeEEEEecCchhhhChhhHHHHHHHHHHHhCCCcEEEeeecccCCCCccCCceeeeEEEEchhhHHHHHHH
Q 024440 83 TNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIREGEPLGIAVTLRGNMMYSFLDR 162 (267)
Q Consensus 83 ~N~m~vPkL~KIvLn~gvg~a~~d~k~L~~a~~~Le~ITGQkPv~tkAKksIa~FKiRkG~piG~KVTLRG~~My~FLdK 162 (267)
+|+|++|+|+|||||+|+|++.+ .|+.|..+|+.||||+|++|+||+||++||||+||||||+|||||++||+||||
T Consensus 5 ~n~m~~PkI~KIvvN~gvGe~~~---~L~~a~~~L~~ITGQkPv~tkAKksia~FkiRkG~pIG~kVTLRg~~m~eFLdr 81 (172)
T PTZ00156 5 ENPMRKIRIEKLVLNICVGESGD---RLTRAAKVLEQLTGQKPVFSKARYTVRSFGIRRNEKIACHVTVRGDKAEEILER 81 (172)
T ss_pred CCCccCceeEEEEEEcCcCchHH---HHHHHHHHHHHHcCCceEEEEhhcccccccccCCCEEEEEEEEchHHHHHHHHH
Confidence 79999999999999999999876 499999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCCCCCCCCCCCCCCCCCcceeeccccccccCcccccCCCCCCCeeEEEEeecC
Q 024440 163 LINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTAK 221 (267)
Q Consensus 163 Li~~vLPRirdF~Gi~~~sfD~~GN~sfGIkd~~~FPEIeyD~~~~i~GmdItivTtak 221 (267)
|+ ++|||+ ++.++||++|||+|||+||++| |++||+..+++||||+|++..+
T Consensus 82 li-----rirDf~-l~~~sFD~~GN~sfGI~e~i~f-ei~yD~~~~i~GmdI~ivl~rp 133 (172)
T PTZ00156 82 GL-----KVKEFE-LKKRNFSDTGNFGFGIQEHIDL-GIKYDPSTGIYGMDFYVVLGRP 133 (172)
T ss_pred HH-----hhhccc-ccCcccCCCcccccCCchheee-ceecCcccCcccCceEEEEeCC
Confidence 99 889999 9999999999999999999999 9999999999999999999866
No 6
>PRK04219 rpl5p 50S ribosomal protein L5P; Reviewed
Probab=100.00 E-value=1.5e-47 Score=333.41 Aligned_cols=137 Identities=39% Similarity=0.626 Sum_probs=128.4
Q ss_pred CCCCccCCceeeeEEEEecCchhhhChhhHHHHHHHHHHHhCCCcEEEeeecccCCCCccCCceeeeEEEEchhhHHHHH
Q 024440 81 SYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIREGEPLGIAVTLRGNMMYSFL 160 (267)
Q Consensus 81 ~y~N~m~vPkL~KIvLn~gvg~a~~d~k~L~~a~~~Le~ITGQkPv~tkAKksIa~FKiRkG~piG~KVTLRG~~My~FL 160 (267)
--+|+|++|+|+||+||+|+|++.+. |..|..+|++||||+|++|+||++|++||||+|+||||+|||||++||+||
T Consensus 7 ~~~N~m~iPkI~KIvin~gvgea~~~---L~~a~~~L~~ITGQkP~~tkAKksIa~FkiRkG~pIG~kVTLRg~~m~~FL 83 (177)
T PRK04219 7 WEMNPMRKPRIEKVVVNIGVGESGER---LTKAEKLLEELTGQKPVRTRAKKTIPDFGIRKGEPIGVKVTLRGEKAEEFL 83 (177)
T ss_pred ccCCCccCceeeEEEEEcCcHHHHHH---HHHHHHHHHHHhCCCceeeeccccccccCccCCCEEEEEEEEccHHHHHHH
Confidence 35799999999999999999999863 999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhcCCCCCCCCCCCCCCCCCcceeeccccccccCcccccCCCCCCCeeEEEEeecCChHHH
Q 024440 161 DRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTAKTDKEG 226 (267)
Q Consensus 161 dKLi~~vLPRirdF~Gi~~~sfD~~GN~sfGIkd~~~FPEIeyD~~~~i~GmdItivTtakt~~ea 226 (267)
+||+++| || |++.++||++|||+|||+||++|||++||+..+++||||+|+|+.+-..-+
T Consensus 84 ~rli~iv-----d~-~l~~~sfD~~GN~sfGI~e~~~fpei~yd~~~~i~GmdI~ivt~rpg~rv~ 143 (177)
T PRK04219 84 KTALEAV-----GN-RLKASSFDETGNVSFGIEEHIDFPGVKYDPEIGIFGMDVCVTLERPGYRVA 143 (177)
T ss_pred HHHHHhh-----cC-CCCCcccCCCceEeeCchhhhccCccccCcccccccccEEEEEcCCccchh
Confidence 9999997 56 689999999999999999999999999999999999999999998754433
No 7
>PF00673 Ribosomal_L5_C: ribosomal L5P family C-terminus; InterPro: IPR002132 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 [, ]. Ribosomal protein L5, ~180 amino acids in length, is one of the proteins from the large ribosomal subunit. In Escherichia coli, L5 is known to be involved in binding 5S RNA to the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , , ], groups: Eubacterial L5. Algal chloroplast L5. Cyanelle L5. Archaebacterial L5. Mammalian L11. Tetrahymena thermophila L21. Dictyostelium discoideum (Slime mold) L5 Saccharomyces cerevisiae (Baker's yeast) L16 (39A). Plant mitochondrial L5. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1IQ4_B 2ZJR_D 2ZJP_D 3PIO_D 3CF5_D 2ZJQ_D 3DLL_D 3PIP_D 2WDL_G 3UZN_G ....
Probab=100.00 E-value=4.5e-38 Score=249.16 Aligned_cols=95 Identities=53% Similarity=0.927 Sum_probs=93.8
Q ss_pred eeeeEEEEchhhHHHHHHHHHHhhcCCCCCCCCCCCCCCCCCcceeeccccccccCcccccCCCCCCCeeEEEEeecCCh
Q 024440 144 PLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTAKTD 223 (267)
Q Consensus 144 piG~KVTLRG~~My~FLdKLi~~vLPRirdF~Gi~~~sfD~~GN~sfGIkd~~~FPEIeyD~~~~i~GmdItivTtakt~ 223 (267)
||||||||||++||+||+||+++||||+|||+|++.++||++|||+|||+|+++||||+||++++++||||+|+|+|+++
T Consensus 1 PiG~kvTLRg~~m~~FL~kli~~vlPrik~f~g~~~~~fd~~Gn~sfGi~e~~~Fpei~yd~~~~i~G~~i~i~t~ak~~ 80 (95)
T PF00673_consen 1 PIGCKVTLRGKKMYEFLDKLITIVLPRIKDFKGLKASSFDNSGNFSFGIKEHILFPEIEYDPFPGIFGMDITIVTTAKTP 80 (95)
T ss_dssp EEEEEEEEEHHHHHHHHHHHHHTTTTTSSSTSSBSSTTBSSSSEEEEEESSSSSSSSSSSTSSSSSSCEEEEEEESCSSH
T ss_pred CeEEEEEEccHHHHHHHHHHHHHhhhhcccccccCccccCCCceEEEEeeeeeecCCccccCCCCccceEEEEEEecCCc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCccc
Q 024440 224 KEGQRLLALMGMPFR 238 (267)
Q Consensus 224 ~ea~~LLs~~g~PF~ 238 (267)
+|+++||+++||||.
T Consensus 81 ~~~~~ll~~~~ipf~ 95 (95)
T PF00673_consen 81 KEARLLLKSFGIPFY 95 (95)
T ss_dssp HHHHHHHHHHHHHBH
T ss_pred HHHHHHHHHhCCccC
Confidence 999999999999984
No 8
>KOG0397 consensus 60S ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=7.3e-29 Score=209.53 Aligned_cols=135 Identities=27% Similarity=0.479 Sum_probs=127.8
Q ss_pred CCCccCCceeeeEEEEecCchhhhChhhHHHHHHHHHHHhCCCcEEEeeecccCCCCccCCceeeeEEEEchhhHHHHHH
Q 024440 82 YTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIREGEPLGIAVTLRGNMMYSFLD 161 (267)
Q Consensus 82 y~N~m~vPkL~KIvLn~gvg~a~~d~k~L~~a~~~Le~ITGQkPv~tkAKksIa~FKiRkG~piG~KVTLRG~~My~FLd 161 (267)
-.|+|+..+|+|++||+++|++++. |..|..+||++|||+|+..+|+.+|.+|+||.++.|+|.||+||.++++.|+
T Consensus 6 ~~npMrel~i~KL~lnIcvgESGdr---LtRAaKvLEQLtGQ~pvfskaryTvR~fGirRNEKIAvh~tVrG~KAeeiLe 82 (176)
T KOG0397|consen 6 AQNPMRELKIQKLVLNICVGESGDR---LTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKIAVHVTVRGPKAEEILE 82 (176)
T ss_pred ccCchHhhhhheeeEEEeecccchH---HHHHHHHHHHhcCCCccchhhhhhHHhhccccCceEEEEEEeeCccHHHHHH
Confidence 4699999999999999999999998 9999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcCCCCCCCCCCCCCCCCCcceeeccccccccCcccccCCCCCCCeeEEEEeecCChHHH
Q 024440 162 RLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTAKTDKEG 226 (267)
Q Consensus 162 KLi~~vLPRirdF~Gi~~~sfD~~GN~sfGIkd~~~FPEIeyD~~~~i~GmdItivTtakt~~ea 226 (267)
+-+ ++++|+ +..++|+.+|||.|||.||++. +|.||+..+++|||+.+++..+...-+
T Consensus 83 ~gL-----kVkeYe-L~~~nFS~tgnFGFGiqEHIDL-GikYDPsiGIyGmDFyVvl~RpG~rv~ 140 (176)
T KOG0397|consen 83 RGL-----KVKEYE-LRKRNFSDTGNFGFGIQEHIDL-GIKYDPSIGIYGMDFYVVLGRPGYRVA 140 (176)
T ss_pred hcc-----chhhhh-hhhhcccccCCcccchhhheec-cceeCCCcceeeeeEEEEecCCcchhh
Confidence 998 679986 8889999999999999999999 999999999999999999988765443
No 9
>PF00281 Ribosomal_L5: Ribosomal protein L5; InterPro: IPR002132 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 [, ]. Ribosomal protein L5, ~180 amino acids in length, is one of the proteins from the large ribosomal subunit. In Escherichia coli, L5 is known to be involved in binding 5S RNA to the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , , ], groups: Eubacterial L5. Algal chloroplast L5. Cyanelle L5. Archaebacterial L5. Mammalian L11. Tetrahymena thermophila L21. Dictyostelium discoideum (Slime mold) L5 Saccharomyces cerevisiae (Baker's yeast) L16 (39A). Plant mitochondrial L5. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1IQ4_B 4A1A_D 4A1C_D 4A17_D 4A1E_D 3BBO_H 3O5H_K 1S1I_J 3O58_K 3IZS_E ....
Probab=99.82 E-value=1.7e-20 Score=136.05 Aligned_cols=56 Identities=61% Similarity=0.904 Sum_probs=53.1
Q ss_pred CccCCceeeeEEEEecCchhhhChhhHHHHHHHHHHHhCCCcEEEeeecccCCCCcc
Q 024440 84 NIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIR 140 (267)
Q Consensus 84 N~m~vPkL~KIvLn~gvg~a~~d~k~L~~a~~~Le~ITGQkPv~tkAKksIa~FKiR 140 (267)
|+|++|+|+|||||+|+|++.+| +.|+.|..+|+.||||+|++|+||++|++||||
T Consensus 1 N~m~vPki~KIvin~gvg~~~~~-k~l~~a~~~L~~ItGQkp~~t~aKksia~FkiR 56 (56)
T PF00281_consen 1 NVMQVPKIEKIVINIGVGEAGDD-KVLEKAKKELEQITGQKPVITKAKKSIANFKIR 56 (56)
T ss_dssp STTTSSEEEEEEEEEESSTTSST-HHHHHHHHHHHHHHSS--EEEEESSSBSSSTBS
T ss_pred CCccccEEEEEEEECCCCccccc-hHHHHHHHHHHHHhCCceeEEEeeccccccccC
Confidence 89999999999999999999999 999999999999999999999999999999998
No 10
>KOG0641 consensus WD40 repeat protein [General function prediction only]
Probab=26.98 E-value=53 Score=31.20 Aligned_cols=42 Identities=26% Similarity=0.329 Sum_probs=30.9
Q ss_pred ccCCCCCCcccCCCCCCCCCCCc-----eEEEeeccceeEEeeCCchh
Q 024440 17 RFPALSSSSYVRPTYPNPINVNG-----VVSVKAAAGGIVLVEKSEAE 59 (267)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~ 59 (267)
+|-.++-+.+++. ++|..|+-| |.+|.+||+|++|+.+-+..
T Consensus 207 rfwdlrv~~~v~~-l~~~~~~~glessavaav~vdpsgrll~sg~~ds 253 (350)
T KOG0641|consen 207 RFWDLRVNSCVNT-LDNDFHDGGLESSAVAAVAVDPSGRLLASGHADS 253 (350)
T ss_pred EEEeeeccceeee-ccCcccCCCcccceeEEEEECCCcceeeeccCCC
Confidence 4555665555554 678787765 78899999999999887643
No 11
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=22.00 E-value=2.1e+02 Score=20.72 Aligned_cols=44 Identities=23% Similarity=0.332 Sum_probs=31.1
Q ss_pred eEEEeeccceeEEeeCCchhhhhhHHHHHHhhhhHHHHhhcCCCCccC
Q 024440 40 VVSVKAAAGGIVLVEKSEAEKTGRLKTTYLEKIVPLLREEFSYTNIHQ 87 (267)
Q Consensus 40 ~~~~~~~~~~~~~~~~~~~~~~~rLk~~Y~~~I~~dL~~k~~y~N~m~ 87 (267)
+++++ .|.++|.-......+.| .++...|...+...+++..+.+
T Consensus 43 ~~~i~---~g~L~i~v~~~~~~~~L-~~~~~~il~~l~~~~g~~~i~~ 86 (89)
T PF05258_consen 43 PVSIK---DGTLVIEVDSSAWAQEL-RYMKPQILKKLNEFLGFPAIKD 86 (89)
T ss_pred EEEEE---CCEEEEEECCHHHHHHH-HHHHHHHHHHHHHHcCCCCccE
Confidence 44554 56677666665667788 5678899999999998866543
Done!