Query 028582
Match_columns 207
No_of_seqs 133 out of 1149
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 13:46:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028582.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028582hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05592 rplO 50S ribosomal pr 100.0 1.3E-46 2.9E-51 306.7 11.4 115 74-198 1-115 (146)
2 TIGR01071 rplO_bact ribosomal 100.0 8.3E-45 1.8E-49 294.5 10.8 117 75-199 1-117 (145)
3 COG0200 RplO Ribosomal protein 100.0 5.7E-37 1.2E-41 252.9 8.4 117 74-198 1-119 (152)
4 KOG0846 Mitochondrial/chloropl 100.0 2.5E-34 5.4E-39 253.9 6.5 121 70-198 18-142 (274)
5 PF00828 Ribosomal_L18e: Ribos 99.8 3.2E-22 6.9E-27 157.6 -2.7 91 100-198 3-98 (129)
6 PRK06419 rpl15p 50S ribosomal 98.3 3.2E-06 6.8E-11 69.7 8.4 56 133-199 54-115 (148)
7 PTZ00160 60S ribosomal protein 97.0 0.00069 1.5E-08 56.3 3.8 67 87-161 5-80 (147)
8 PRK04005 50S ribosomal protein 96.6 0.00059 1.3E-08 54.4 0.0 36 128-171 18-54 (111)
9 PF09494 Slx4: Slx4 endonuclea 19.6 51 0.0011 23.3 0.8 27 150-176 21-51 (64)
10 PRK10590 ATP-dependent RNA hel 15.5 2.7E+02 0.0059 26.1 4.8 11 72-82 369-379 (456)
No 1
>PRK05592 rplO 50S ribosomal protein L15; Reviewed
Probab=100.00 E-value=1.3e-46 Score=306.70 Aligned_cols=115 Identities=55% Similarity=0.849 Sum_probs=107.7
Q ss_pred eecCCCCCCCCCCccccccccCCCCCCCCccccCCCCCCCCCCCCCCCcccCCCCCeEEecccccCCCCCCCCCCCeeee
Q 028582 74 FRLNNLGPQPGSRKRGKRKGRGIAAGQGNSCGFGMRGQKSRSGPGVRKGFEGGQMPLYRRIPKLRGIAGGMHAGLPKYVP 153 (207)
Q Consensus 74 m~L~nL~p~pGark~rKRvGRG~GSG~GKTsGRGhKGQksRsG~~~r~GFEGGQtPLyRRlPK~RGF~ng~~~~~~~y~~ 153 (207)
|+||||+|++||++++||+|||+|||+|||||||||||+||+|+.+++||||||||||||||| +||+|. ++++|.+
T Consensus 1 m~L~~l~~~~ga~~~~kRvGRG~gsG~GkT~GrG~KGqksR~g~~~~~gFEGGQ~Pl~rrlPk-~Gf~~~---~~~~y~~ 76 (146)
T PRK05592 1 MKLNELKPAPGSRKARKRVGRGIGSGLGKTAGRGHKGQKARSGGGVRPGFEGGQMPLYRRLPK-RGFTNI---FRKEYAV 76 (146)
T ss_pred CccccCcCCCCCcCCCccEecCCCCCCCCcCCCCCCcccCCCCCCCCCccccCCCceEEEccc-CCcCCC---CcceEEE
Confidence 789999999999999999999999999999999999999999988999999999999999999 699873 5789999
Q ss_pred eechhhhhhCCCCCCccCHHHHHHCCCCCCCCCCCCCCeEEeecC
Q 028582 154 VNLKDIEAAGFLEGDEVSLETLKKKGLINPSGRERKLPLKVQIMT 198 (207)
Q Consensus 154 VNL~~L~~~r~d~~~~It~e~L~~~glv~~~g~~~~~~VKILa~~ 198 (207)
|||++|++ ++++++||+++|++.+||+.+ .++||||+.|
T Consensus 77 VNL~~L~~--~~~~~~I~~~~L~~~gli~~~----~~~vKvLg~G 115 (146)
T PRK05592 77 VNLGDLNK--FEEGTEVTLEALKAAGLIRKN----IKGVKVLGNG 115 (146)
T ss_pred EeHHHhhc--cCCCCeECHHHHHHCCcccCC----CcceEEEecC
Confidence 99999984 888999999999999999765 5689999988
No 2
>TIGR01071 rplO_bact ribosomal protein L15, bacterial/organelle.
Probab=100.00 E-value=8.3e-45 Score=294.51 Aligned_cols=117 Identities=50% Similarity=0.771 Sum_probs=106.1
Q ss_pred ecCCCCCCCCCCccccccccCCCCCCCCccccCCCCCCCCCCCCCCCcccCCCCCeEEecccccCCCCCCCCCCCeeeee
Q 028582 75 RLNNLGPQPGSRKRGKRKGRGIAAGQGNSCGFGMRGQKSRSGPGVRKGFEGGQMPLYRRIPKLRGIAGGMHAGLPKYVPV 154 (207)
Q Consensus 75 ~L~nL~p~pGark~rKRvGRG~GSG~GKTsGRGhKGQksRsG~~~r~GFEGGQtPLyRRlPK~RGF~ng~~~~~~~y~~V 154 (207)
+||||+|+|||++++||+|||+|||+|||||||||||+||+|+++++||||||||||||||| +||+|.+ ++.+|.+|
T Consensus 1 ~l~~l~~~~g~~~~~kR~GRG~gsg~Gkt~GrG~kGqk~R~g~~~~~gfEGGQ~Pl~rrlPK-~GF~~~~--~~~~~~~V 77 (145)
T TIGR01071 1 KLNELKPAKGAKKRRKRVGRGIGSGLGKTSGRGHKGQKARSGGKVRRGFEGGQMPLYRRLPK-RGFSNKR--FKKEYAEV 77 (145)
T ss_pred CcccCcCCCCCcCCCcceeCCCCCCCCCcCCCCCCcCcCCCCCCCCCeecCCCCceEEECCC-CCCCCcc--cCcceeEE
Confidence 48999999999999999999999999999999999999999989999999999999999999 6998742 56899999
Q ss_pred echhhhhhCCCCCCccCHHHHHHCCCCCCCCCCCCCCeEEeecCC
Q 028582 155 NLKDIEAAGFLEGDEVSLETLKKKGLINPSGRERKLPLKVQIMTF 199 (207)
Q Consensus 155 NL~~L~~~r~d~~~~It~e~L~~~glv~~~g~~~~~~VKILa~~~ 199 (207)
||++|++ .++++++||+++|++.++|+.+ ...||||+.|-
T Consensus 78 NL~~L~~-~~~~g~~i~~~~L~~~gli~~~----~~~vKvLg~G~ 117 (145)
T TIGR01071 78 NLGKLAK-LFPNGEVVTLETLKEKGLITKK----IKFVKVLGNGK 117 (145)
T ss_pred EHHHHhh-hhhcCCEecHHHHhhCccCcCC----CCceEEeCCCC
Confidence 9999984 3577889999999999999753 45799998874
No 3
>COG0200 RplO Ribosomal protein L15 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.7e-37 Score=252.88 Aligned_cols=117 Identities=50% Similarity=0.753 Sum_probs=107.0
Q ss_pred eecCCCCCCCCCCccccccccCCCCCCCCccccCCCCCCCCCCCC-CCCcccCCCCCeEEecccccCCCCCCCCCCC-ee
Q 028582 74 FRLNNLGPQPGSRKRGKRKGRGIAAGQGNSCGFGMRGQKSRSGPG-VRKGFEGGQMPLYRRIPKLRGIAGGMHAGLP-KY 151 (207)
Q Consensus 74 m~L~nL~p~pGark~rKRvGRG~GSG~GKTsGRGhKGQksRsG~~-~r~GFEGGQtPLyRRlPK~RGF~ng~~~~~~-~y 151 (207)
|+|++|+|..|+++.++|+|||++||+|||+|||||||+||+|+. +++||||||||||||||| +||+| ..+.+ +|
T Consensus 1 m~l~~l~~~~G~~~~~~rvgrG~~sG~Gkt~GRG~kGqkaRsg~~~~~~gfeGgq~Pl~rrlpK-~GF~~--~~~~~~~~ 77 (152)
T COG0200 1 MRLNDLKPARGSKKTRKRVGRGIGSGLGKTGGRGHKGQKARSGHKWVRPGFEGGQMPLYRRLPK-RGFTN--SKFKKVEY 77 (152)
T ss_pred CcccccCcCCCCccccCCcccCCCCCCCCCCCCCCCCCccccCCceecceeecCCcchhhhcCC-CCCcc--ccccccce
Confidence 689999999999999999999999999999999999999999854 999999999999999999 69997 23444 89
Q ss_pred eeeechhhhhhCCCCCCccCHHHHHHCCCCCCCCCCCCCCeEEeecC
Q 028582 152 VPVNLKDIEAAGFLEGDEVSLETLKKKGLINPSGRERKLPLKVQIMT 198 (207)
Q Consensus 152 ~~VNL~~L~~~r~d~~~~It~e~L~~~glv~~~g~~~~~~VKILa~~ 198 (207)
.+|||++|+. .++++++||+++|.+.++|... ++.||||+.|
T Consensus 78 ~~vn~~~l~~-~~~~~~~v~~~~l~~~~~i~~~----~~~vKvLg~G 119 (152)
T COG0200 78 AVVNLGKLAE-LLPEGEEVTLASLKAAGVIRKL----KDLVKVLGNG 119 (152)
T ss_pred eEEEHHHhhh-hccccccccHHHHhhCCeEecc----ccccEEeccC
Confidence 9999999984 6889999999999999999876 6779999988
No 4
>KOG0846 consensus Mitochondrial/chloroplast ribosomal protein L15/L10 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-34 Score=253.86 Aligned_cols=121 Identities=45% Similarity=0.829 Sum_probs=105.7
Q ss_pred CCCeeecCCCCCCCCCCccccccccCCCCCCCCccccCCCCCCCCCCCCCCCcccCCCCCeEEecccccCCCCCCCCCCC
Q 028582 70 TNVRFRLNNLGPQPGSRKRGKRKGRGIAAGQGNSCGFGMRGQKSRSGPGVRKGFEGGQMPLYRRIPKLRGIAGGMHAGLP 149 (207)
Q Consensus 70 ~~~rm~L~nL~p~pGark~rKRvGRG~GSG~GKTsGRGhKGQksRsG~~~r~GFEGGQtPLyRRlPK~RGF~ng~~~~~~ 149 (207)
-.+|+.|+||+|++|+++ +||+|||++||+|||||||||||++|++ ..++||||||||||||+||+ ||.++ .++
T Consensus 18 ~~sr~~L~dLrpn~gskk-~kR~GRg~~sG~Gkt~GrG~KGqkqR~~-~~~lGfEgGqtP~yrr~Pk~-~~~~~---~~r 91 (274)
T KOG0846|consen 18 ALSRVRLNDLRPNPGSKK-KKRKGRGISSGLGKTSGRGHKGQKQRGG-RKILGFEGGQTPLYRRFPKF-GFGNG---GRR 91 (274)
T ss_pred hhhhhhhhccCCCCCccc-ccccCCCcCCCCccccCCCCcchhhccC-CCccccccCCchhHHhcccc-ccccc---ccc
Confidence 567999999999999999 7799999999999999999999999987 44559999999999999995 88764 467
Q ss_pred eeeeeechhhh----hhCCCCCCccCHHHHHHCCCCCCCCCCCCCCeEEeecC
Q 028582 150 KYVPVNLKDIE----AAGFLEGDEVSLETLKKKGLINPSGRERKLPLKVQIMT 198 (207)
Q Consensus 150 ~y~~VNL~~L~----~~r~d~~~~It~e~L~~~glv~~~g~~~~~~VKILa~~ 198 (207)
+|.+++|.+|+ .++||++++|||++|++.|+|.+.+ +..+|++.+.|
T Consensus 92 ~~~pl~L~rlq~lID~grid~~q~Idm~tL~~~g~i~p~~--~eyGv~L~~~G 142 (274)
T KOG0846|consen 92 QYLPLSLGRLQKLIDTGRIDPSQPIDMKTLKDSGLINPKG--REYGVQLTADG 142 (274)
T ss_pred cCCcccHHHHHHHHHhcCCCccCceeHHHHHhccCCCccc--cccCceeeccC
Confidence 99999999984 5899999999999999999887654 44567776554
No 5
>PF00828 Ribosomal_L18e: Ribosomal protein L18e/L15; InterPro: IPR021131 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 entry represents both L15 and L18e ribosomal proteins, which share a common structure consisting mainly of parallel beta sheets (beta-alpha-beta units) with a core of three turns of irregular (beta-beta-alpha)n superhelix [, ].; PDB: 3O58_Y 1S1I_V 3O5H_Y 3IZS_O 3IZR_R 2OTL_L 1M1K_M 3G6E_L 1VQ9_L 1YIT_L ....
Probab=99.82 E-value=3.2e-22 Score=157.63 Aligned_cols=91 Identities=41% Similarity=0.614 Sum_probs=73.7
Q ss_pred CCCccccCCCCCCCCCCC-CCCCcccCCCCCeEEecccccCCCCCCC-CCCCeeeeeechhhhhh--CCCCC-CccCHHH
Q 028582 100 QGNSCGFGMRGQKSRSGP-GVRKGFEGGQMPLYRRIPKLRGIAGGMH-AGLPKYVPVNLKDIEAA--GFLEG-DEVSLET 174 (207)
Q Consensus 100 ~GKTsGRGhKGQksRsG~-~~r~GFEGGQtPLyRRlPK~RGF~ng~~-~~~~~y~~VNL~~L~~~--r~d~~-~~It~e~ 174 (207)
+|+|||||||||++|+|. ..+.+|||||||+|||||| +||++.+. .++.+|.+|||++|++. .+... .++|.+.
T Consensus 3 ~gkt~grG~kG~~~rsG~~~~~~~feggq~pl~rr~pK-~Gf~~~~~~~~~~~~~~vnL~~L~~~i~~~~~~~~~~~~~~ 81 (129)
T PF00828_consen 3 KGKTRGRGHKGGRGRSGGHKHRPGFEGGQMPLYRRLPK-RGFNNPHLRKNRREYPPVNLSKLQELIEKLKIDGTEIDGKI 81 (129)
T ss_dssp SSSSSSSSSSSSSSSTTTSSTSSHHHHHHSHHHHHSSS-SSHHHCCHCSGTCCCEEEEHHHHHHHTTTSSSSSCECTTSE
T ss_pred CCccCcccCCCCCCCCCCCCCCchhcccccccccccCc-ccccccccccCcceeEeeeHHHHHHHHHhccccccccCCce
Confidence 699999999999999997 7889999999999999999 69987432 13468999999999851 12111 2789999
Q ss_pred HHHCCCCCCCCCCCCCCeEEeecC
Q 028582 175 LKKKGLINPSGRERKLPLKVQIMT 198 (207)
Q Consensus 175 L~~~glv~~~g~~~~~~VKILa~~ 198 (207)
|++.+++ .+.+|||+.|
T Consensus 82 ~~~~~~~-------~~~~KvLg~G 98 (129)
T PF00828_consen 82 LVDAGLI-------KGYVKVLGKG 98 (129)
T ss_dssp EEECCEE-------SSEEEEESSS
T ss_pred eeecccc-------ccceeeeccC
Confidence 9999988 2669999765
No 6
>PRK06419 rpl15p 50S ribosomal protein L15P; Reviewed
Probab=98.31 E-value=3.2e-06 Score=69.70 Aligned_cols=56 Identities=14% Similarity=0.054 Sum_probs=37.1
Q ss_pred ecccccCCCCCCCCCCCeeeeeechhhhhhCCCCCCccCHHHHHHCCCCCCCCC------CCCCCeEEeecCC
Q 028582 133 RIPKLRGIAGGMHAGLPKYVPVNLKDIEAAGFLEGDEVSLETLKKKGLINPSGR------ERKLPLKVQIMTF 199 (207)
Q Consensus 133 RlPK~RGF~ng~~~~~~~y~~VNL~~L~~~r~d~~~~It~e~L~~~glv~~~g~------~~~~~VKILa~~~ 199 (207)
-||| +||++. +..+.+|.+|||++|++ + ++.|.+.+++...+. .....+|||+.|-
T Consensus 54 ~fpK-~GF~~~-~~~~~~~~~INL~~L~~--l-------~~~l~~~g~i~~~~~~~vid~~~~g~~KVLG~G~ 115 (148)
T PRK06419 54 WYGK-HGFKRP-PKLIKEVSTINVGELDE--L-------ADLLKAEGKAEEEDGKIVVDLTELGYDKVLGGGK 115 (148)
T ss_pred CCCC-CCccCC-CcCcceeeeEEHHHHHH--h-------HHHHHHCCcccccCCcceeeeccCCceEEeCCCc
Confidence 3799 699874 23246899999999974 2 155777777654210 0124699998874
No 7
>PTZ00160 60S ribosomal protein L27a; Provisional
Probab=97.02 E-value=0.00069 Score=56.31 Aligned_cols=67 Identities=31% Similarity=0.424 Sum_probs=42.7
Q ss_pred ccccccccCCCCCCCCccccCCCCCCCCCCCCCCCcccCCCCCeEEecccc-------cCCCCCCCCCCCee--eeeech
Q 028582 87 KRGKRKGRGIAAGQGNSCGFGMRGQKSRSGPGVRKGFEGGQMPLYRRIPKL-------RGIAGGMHAGLPKY--VPVNLK 157 (207)
Q Consensus 87 k~rKRvGRG~GSG~GKTsGRGhKGQksRsG~~~r~GFEGGQtPLyRRlPK~-------RGF~ng~~~~~~~y--~~VNL~ 157 (207)
+++.|.=|| -.|||.|..||. |.-.+ -.|..|||-.-+..+-|+ .||+.. +..+.++ .+|||+
T Consensus 5 ~kK~rK~RG-----~rt~G~G~~gkh-R~~~G-GrG~AG~~kH~~~~~~ky~p~~fGK~Gfr~~-~~~~~~~~~~~INl~ 76 (147)
T PTZ00160 5 FKKCRKMRG-----HVSHGYGRVGKH-RKHPG-GRGNAGGQHHHRINFDKYHPGYFGKVGMRHF-HLKKNKYYCPTINVD 76 (147)
T ss_pred cccccCCCC-----CCccCCCCCCCC-CCCCC-CCcccCCCcceEEEeeecCCCccCCCCccCC-ccccccccCceeEHH
Confidence 344566688 478999988764 32111 248999997766555543 466542 3333455 899999
Q ss_pred hhhh
Q 028582 158 DIEA 161 (207)
Q Consensus 158 ~L~~ 161 (207)
+|++
T Consensus 77 ~L~~ 80 (147)
T PTZ00160 77 KLWS 80 (147)
T ss_pred HHHH
Confidence 9964
No 8
>PRK04005 50S ribosomal protein L18e; Provisional
Probab=96.55 E-value=0.00059 Score=54.45 Aligned_cols=36 Identities=28% Similarity=0.556 Sum_probs=26.8
Q ss_pred CCeEEecccccCCCCCCCCCCCeeeeeechhhhhhCC-CCCCccC
Q 028582 128 MPLYRRIPKLRGIAGGMHAGLPKYVPVNLKDIEAAGF-LEGDEVS 171 (207)
Q Consensus 128 tPLyRRlPK~RGF~ng~~~~~~~y~~VNL~~L~~~r~-d~~~~It 171 (207)
-|||+++++ | +. ..+.+|.+|||++|+. | +++++|+
T Consensus 18 ~~~~~~v~~-r-l~----~~r~~y~vVNL~~L~~--~~~~~~vv~ 54 (111)
T PRK04005 18 APIWKDVAE-R-LE----KPRRRRAEVNLSKINR--YAKEGDTVV 54 (111)
T ss_pred CcHHHHHHH-H-Hh----CCCCccceEEHHHHHh--hccCCCEEE
Confidence 489999999 4 32 3467999999999983 5 3555553
No 9
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=19.62 E-value=51 Score=23.31 Aligned_cols=27 Identities=33% Similarity=0.532 Sum_probs=17.6
Q ss_pred eeeeeechhhhh----hCCCCCCccCHHHHH
Q 028582 150 KYVPVNLKDIEA----AGFLEGDEVSLETLK 176 (207)
Q Consensus 150 ~y~~VNL~~L~~----~r~d~~~~It~e~L~ 176 (207)
.|.||+|++|.. ..++..+.|+...|.
T Consensus 21 ~YePI~L~el~~~L~~~g~~~~~~~~~~~l~ 51 (64)
T PF09494_consen 21 MYEPINLEELHAWLKASGIGFDRKVDPSKLK 51 (64)
T ss_pred cCCCccHHHHHHHHHHcCCCccceeCHHHHH
Confidence 599999999953 223333467766663
No 10
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=15.48 E-value=2.7e+02 Score=26.07 Aligned_cols=11 Identities=18% Similarity=0.404 Sum_probs=5.3
Q ss_pred CeeecCCCCCC
Q 028582 72 VRFRLNNLGPQ 82 (207)
Q Consensus 72 ~rm~L~nL~p~ 82 (207)
+++.+.++.+.
T Consensus 369 ~~~~~~~~~~~ 379 (456)
T PRK10590 369 PRIAIPGYEPD 379 (456)
T ss_pred cccccCCCccC
Confidence 44555555443
Done!