Query 035394
Match_columns 51
No_of_seqs 106 out of 191
Neff 3.7
Searched_HMMs 29240
Date Mon Mar 25 03:41:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035394.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/035394hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3u5e_l L46, YL40, 60S ribosoma 100.0 1.2E-37 4.1E-42 174.8 3.3 51 1-51 1-51 (51)
2 3iz5_o 60S ribosomal protein L 100.0 1.5E-37 5.1E-42 174.5 3.4 51 1-51 1-51 (51)
3 4a18_B RPL39, ribosomal protei 100.0 2.3E-37 7.8E-42 174.3 3.2 51 1-51 1-51 (52)
4 3j21_f 50S ribosomal protein L 100.0 7.2E-37 2.5E-41 171.6 2.0 50 1-50 1-50 (51)
5 1ffk_Y Ribosomal protein L39E; 100.0 2.3E-35 7.9E-40 164.5 4.9 48 3-50 1-48 (49)
6 1vq8_2 50S ribosomal protein L 100.0 2.9E-35 1E-39 164.7 1.8 48 3-50 2-49 (50)
7 3nfi_A DNA-directed RNA polyme 23.1 24 0.00082 23.1 0.7 25 2-26 1-25 (237)
8 3a4c_A DNA replication factor 20.1 42 0.0014 20.4 1.3 15 23-37 67-81 (106)
9 4htv_B Capsid protein; nuclear 12.2 32 0.0011 16.7 -0.6 8 41-48 16-23 (29)
10 2ost_A Putative endonuclease; 10.9 1.1E+02 0.0037 19.6 1.4 22 27-48 49-81 (151)
No 1
>3u5e_l L46, YL40, 60S ribosomal protein L39; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 2wwa_O 2ww9_O 3izc_o 3izs_o 2wwb_O 3o5h_e 3o58_e 3u5i_l 4b6a_l 3jyw_1
Probab=100.00 E-value=1.2e-37 Score=174.75 Aligned_cols=51 Identities=65% Similarity=1.174 Sum_probs=49.5
Q ss_pred CCCCchHHHHHHHHHHHhhcCCCCceEEEecCCceeecCcccccccccCCC
Q 035394 1 MPSHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLGF 51 (51)
Q Consensus 1 M~s~K~~~~K~rLaK~~kqNrpiP~Wv~~KT~~kiryn~kRRhWRRtkL~~ 51 (51)
|+|||||++|++||||++||+||||||+||||++|+|||||||||||+|+|
T Consensus 1 M~s~Kt~~~K~rLaK~~kqNr~iP~Wv~~KT~~kir~n~KRRhWRRtkL~~ 51 (51)
T 3u5e_l 1 MAAQKSFRIKQKMAKAKKQNRPLPQWIRLRTNNTIRYNAKRRNWRRTKMNI 51 (51)
T ss_dssp -CCSCCHHHHHHHHHHHHTCSCCCGGGGGSTTCCCCSCTTCCCTTTCCCCC
T ss_pred CCCcchHHHHHHHHHHHhccCCCCceEEEeCCCccccCCccccccccccCC
Confidence 999999999999999999999999999999999999999999999999997
No 2
>3iz5_o 60S ribosomal protein L39 (L39E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} PDB: 3izr_o 2zkr_3
Probab=100.00 E-value=1.5e-37 Score=174.45 Aligned_cols=51 Identities=92% Similarity=1.444 Sum_probs=50.5
Q ss_pred CCCCchHHHHHHHHHHHhhcCCCCceEEEecCCceeecCcccccccccCCC
Q 035394 1 MPSHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLGF 51 (51)
Q Consensus 1 M~s~K~~~~K~rLaK~~kqNrpiP~Wv~~KT~~kiryn~kRRhWRRtkL~~ 51 (51)
|+|||||++|++||||++||+||||||+||||++|+|||||||||||+|+|
T Consensus 1 M~s~Kt~~~K~rLaK~~kqNr~iP~Wv~~KT~~kir~n~kRRhWRRtkL~~ 51 (51)
T 3iz5_o 1 MPSHKTFRIKQKLAKKQRQNRPIPYWIRMRTDNTIRYNAKRRHWRRTKLGF 51 (51)
T ss_dssp CCSSCCHHHHHHHHHHHHHSSCCCGGGGTSCSSCCCCCCCCCCSSSSCCCC
T ss_pred CCCcchHHHHHHHHHHHhccCCCCceEEEeCCCccccCCccccccccccCC
Confidence 999999999999999999999999999999999999999999999999997
No 3
>4a18_B RPL39, ribosomal protein L37; ribosome, eukaryotic initiation factor 6, EIF6, transla large ribosomal subunit, rRNA; 3.52A {Tetrahymena thermophila} PDB: 4a19_B 4a1b_B 4a1d_B
Probab=100.00 E-value=2.3e-37 Score=174.27 Aligned_cols=51 Identities=53% Similarity=1.060 Sum_probs=49.4
Q ss_pred CCCCchHHHHHHHHHHHhhcCCCCceEEEecCCceeecCcccccccccCCC
Q 035394 1 MPSHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLGF 51 (51)
Q Consensus 1 M~s~K~~~~K~rLaK~~kqNrpiP~Wv~~KT~~kiryn~kRRhWRRtkL~~ 51 (51)
|||||||++|++||||++||+||||||+||||++|+|||||||||||+|++
T Consensus 1 M~s~Kt~~~K~rLaK~~kqNr~iP~Wv~~KT~~kir~n~KRRhWRRtkL~~ 51 (52)
T 4a18_B 1 MGANKTLNMKKRFGRKIKQNRPLPNWYRYKSDTNIRYNSKRRNWRRTKLKI 51 (52)
T ss_dssp -CCCCCHHHHHHHHHHHHTTSCCCTTGGGCSSCCCSSCTTCCCTTTSCCCC
T ss_pred CCCcchHHHHHHHHHHHhccCCCCceEEEeCCCccccCCccccccccccCc
Confidence 999999999999999999999999999999999999999999999999986
No 4
>3j21_f 50S ribosomal protein L39E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=100.00 E-value=7.2e-37 Score=171.59 Aligned_cols=50 Identities=42% Similarity=0.751 Sum_probs=49.5
Q ss_pred CCCCchHHHHHHHHHHHhhcCCCCceEEEecCCceeecCcccccccccCC
Q 035394 1 MPSHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLG 50 (51)
Q Consensus 1 M~s~K~~~~K~rLaK~~kqNrpiP~Wv~~KT~~kiryn~kRRhWRRtkL~ 50 (51)
|+|||||++|++||||++||+||||||+||||++|+|||||||||||+|+
T Consensus 1 M~s~Kt~~~K~rLaK~~kqNr~iP~Wv~~KT~~kir~n~KRRhWRRtkLk 50 (51)
T 3j21_f 1 MARNKPLAKKLRLAKALKQNRRVPVWVIVKTNRRVLTHPKRRYWRRTKLK 50 (51)
T ss_dssp CCCCCCHHHHHHHHHHHHHTSCCCHHHHHHHTSCCCSCTTCCCTTTCCCC
T ss_pred CCCcchHHHHHHHHHHHhccCCCCceEEEeCCCccccCCccccccccccC
Confidence 99999999999999999999999999999999999999999999999997
No 5
>1ffk_Y Ribosomal protein L39E; ribosome assembly, RNA-RNA, protein-RNA, protein-protein; 2.40A {Haloarcula marismortui} SCOP: a.137.1.1
Probab=100.00 E-value=2.3e-35 Score=164.53 Aligned_cols=48 Identities=38% Similarity=0.628 Sum_probs=47.2
Q ss_pred CCchHHHHHHHHHHHhhcCCCCceEEEecCCceeecCcccccccccCC
Q 035394 3 SHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLG 50 (51)
Q Consensus 3 s~K~~~~K~rLaK~~kqNrpiP~Wv~~KT~~kiryn~kRRhWRRtkL~ 50 (51)
|||||++|++||||++||+||||||+||||++|+|||||||||||+|+
T Consensus 1 ~~Kt~~~K~rLaK~~kQNrpiP~Wv~~KT~~kiryn~KRRhWRRtkL~ 48 (49)
T 1ffk_Y 1 GKKSKATKKRKAKLDNQNSRVPAYVMLKTDREVQRNHKRRHWRRNDTD 48 (49)
T ss_pred CCchHHHHHHHHHHHhccCCCCcEEEEecCCceecCCccccccccccC
Confidence 799999999999999999999999999999999999999999999997
No 6
>1vq8_2 50S ribosomal protein L39E; ribosome 50S, protein-protein complex, RNA-RNA complex, PROT complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: a.137.1.1 PDB: 1vq4_2* 1vq5_2* 1vq6_2* 1vq7_2* 1s72_2* 1vq9_2* 1vqk_2* 1vql_2* 1vqm_2* 1vqn_2* 1vqo_2* 1vqp_2* 1yhq_2* 1yi2_2* 1yij_2* 1yit_2* 1yj9_2* 1yjn_2* 1yjw_2* 2otj_2* ...
Probab=100.00 E-value=2.9e-35 Score=164.66 Aligned_cols=48 Identities=42% Similarity=0.740 Sum_probs=44.3
Q ss_pred CCchHHHHHHHHHHHhhcCCCCceEEEecCCceeecCcccccccccCC
Q 035394 3 SHKTFMIKKKLAKKMRQNRPIPHWIRMRTDNTIRYNAKRRHWRRTKLG 50 (51)
Q Consensus 3 s~K~~~~K~rLaK~~kqNrpiP~Wv~~KT~~kiryn~kRRhWRRtkL~ 50 (51)
|||||++|++||||++||+||||||+||||++|+|||||||||||+|+
T Consensus 2 s~Kt~~~K~rLaK~~kQNrpiP~Wv~~KT~~kiryn~KRRhWRRtkL~ 49 (50)
T 1vq8_2 2 GKKSKATKKRLAKLDNQNSRVPAWVMLKTDREVQRNHKRRHWRRNDTD 49 (50)
T ss_dssp CCCCHHHHHHHHHHHHHSSCCCHHHHHHTTC---CCTTCCCTTTCCCC
T ss_pred CcchHHHHHHHHHHHhccCCCCceEEEecCCceecCCccccccccccC
Confidence 799999999999999999999999999999999999999999999997
No 7
>3nfi_A DNA-directed RNA polymerase I subunit RPA49; winged helix, transcription, DNA binding, DN protein; HET: MSE PE4; 1.90A {Saccharomyces cerevisiae} PDB: 3nfh_A
Probab=23.13 E-value=24 Score=23.07 Aligned_cols=25 Identities=20% Similarity=0.341 Sum_probs=5.9
Q ss_pred CCCchHHHHHHHHHHHhhcCCCCce
Q 035394 2 PSHKTFMIKKKLAKKMRQNRPIPHW 26 (51)
Q Consensus 2 ~s~K~~~~K~rLaK~~kqNrpiP~W 26 (51)
+|++.+..+.-|.-+.-.++|||..
T Consensus 1 ~~~~~lpt~~el~~~~~~~r~iPp~ 25 (237)
T 3nfi_A 1 GSHMDLPTRAQMDEITSNDRPTPLA 25 (237)
T ss_dssp ------------------CCSSCCC
T ss_pred CCcccCCCHHHHHHHhhccCCCCCC
Confidence 5788888888999999999999973
No 8
>3a4c_A DNA replication factor CDT1; alpha-beta structure, cell cycle, DNA- binding, nucleus, phosphoprotein, proto-oncogene, UBL conjugation; HET: DNA; 1.89A {Mus musculus} PDB: 2rqq_A*
Probab=20.12 E-value=42 Score=20.37 Aligned_cols=15 Identities=27% Similarity=0.747 Sum_probs=12.9
Q ss_pred CCceEEEecCCceee
Q 035394 23 IPHWIRMRTDNTIRY 37 (51)
Q Consensus 23 iP~Wv~~KT~~kiry 37 (51)
+|.|+.+.+=++..|
T Consensus 67 lPdWls~~~vR~~~y 81 (106)
T 3a4c_A 67 LPDWLSLHRIRTDTY 81 (106)
T ss_dssp CTTTEEEEEETTEEE
T ss_pred Ccchheeeeeeccce
Confidence 799999998887776
No 9
>4htv_B Capsid protein; nuclear transporter, protein transport-viral protein complex; 3.00A {Beak and feather disease virus}
Probab=12.24 E-value=32 Score=16.73 Aligned_cols=8 Identities=50% Similarity=0.729 Sum_probs=4.9
Q ss_pred cccccccc
Q 035394 41 RRHWRRTK 48 (51)
Q Consensus 41 RRhWRRtk 48 (51)
||||+|..
T Consensus 16 RRyrrRrr 23 (29)
T 4htv_B 16 RRYRRRRR 23 (29)
T ss_pred HHHHHhhh
Confidence 56776643
No 10
>2ost_A Putative endonuclease; protein-DNA complex, restriction enzyme fold,PD-(D/E)-XK MOT homing endonuclease, group I intron, hydrolase-DNA complex; 3.10A {Synechocystis SP}
Probab=10.88 E-value=1.1e+02 Score=19.58 Aligned_cols=22 Identities=23% Similarity=0.446 Sum_probs=13.9
Q ss_pred EEEecC----Cceeec-------Cccccccccc
Q 035394 27 IRMRTD----NTIRYN-------AKRRHWRRTK 48 (51)
Q Consensus 27 v~~KT~----~kiryn-------~kRRhWRRtk 48 (51)
|++||+ ..++|+ .+||.|++..
T Consensus 49 IQvKta~~~~~~~~f~~d~~~~~~~~~~~~~~~ 81 (151)
T 2ost_A 49 VQVKSSWKSEKTGNYVVDNRRTRTNRRNIVRSP 81 (151)
T ss_dssp EEEEECEEETTTTEEEEECSEEECSSSSCEEEC
T ss_pred EEEEEEEEcCceeEEEeecceecccccccccCC
Confidence 566665 255555 5688998754
Done!