Query 035122
Match_columns 72
No_of_seqs 100 out of 141
Neff 2.8
Searched_HMMs 29240
Date Mon Mar 25 15:25:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035122.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/035122hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3u5c_e 40S ribosomal protein S 100.0 1.7E-34 5.7E-39 180.4 0.7 57 1-57 1-57 (63)
2 3iz6_Z 40S ribosomal protein S 100.0 5.8E-35 2E-39 182.1 -3.1 57 1-57 1-57 (62)
3 2xzm_X RPS30E; ribosome, trans 100.0 8.8E-32 3E-36 174.1 0.6 61 1-61 1-63 (80)
4 2xzm_9 RPS31E; ribosome, trans 96.3 0.0014 4.7E-08 46.4 1.8 25 10-35 75-99 (189)
5 1egw_A MADS box transcription 16.1 23 0.00079 21.5 -0.6 21 49-71 18-48 (77)
6 1m5n_Q PTHRP, PTH-RP, parathyr 9.8 94 0.0032 16.2 0.7 14 15-28 13-26 (28)
7 3v2d_F 50S ribosomal protein L 9.2 1.3E+02 0.0045 21.0 1.5 26 5-35 49-74 (210)
8 3ffd_P PTH-RP, PTHRP, parathyr 9.0 1.3E+02 0.0044 19.9 1.3 23 15-38 79-101 (108)
9 2i9f_A Nucleocapsid; assembly, 8.7 90 0.0031 19.1 0.4 10 5-14 37-47 (69)
10 1k6o_B SRF, serum response fac 8.1 72 0.0025 20.4 -0.2 39 31-71 9-57 (103)
No 1
>3u5c_e 40S ribosomal protein S30-A, 40S ribosomal protein S29-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_Z* 3j16_E 3u5g_e
Probab=99.98 E-value=1.7e-34 Score=180.37 Aligned_cols=57 Identities=60% Similarity=0.930 Sum_probs=53.1
Q ss_pred CCceecccccCCcccCCCCCcccccccCCCChhhhhhhhhchheeecchhhhhcccc
Q 035122 1 MGKVHGSLARAGKVRGQTPKVAKQDKKKRPRGRAYKRMQYNRRFVTAGQLIISHRFS 57 (72)
Q Consensus 1 mGKvHGSLarAGKVR~QTPKV~KqeKkk~~~GRak~R~qYnrRfvnv~~t~~~~r~~ 57 (72)
|||||||||+|||||+||||||++||+++++|||++|++||+||+|++++|+.++..
T Consensus 1 mgKvHGSLarAGKVR~QTPKV~k~eKkk~~~gRak~R~~YnrRfvnv~~~~gkrk~~ 57 (63)
T 3u5c_e 1 MAKVHGSLARAGKVKSQTPKVEKTEKPKKPKGRAYKRLLYTRRFVNVTLVNGKRRMN 57 (63)
T ss_dssp -CCCBCCCTTTTHHHHHSCCCCCCCCCCCCCTHHHHHHHHHHHHTSCCCCSSSCCSS
T ss_pred CCcccchhhhcccccCCCCCCcccccccCCchhHHHHHHhhhhheeecccCCcccCC
Confidence 999999999999999999999999999999999999999999999999999966543
No 2
>3iz6_Z 40S ribosomal protein S30 (S30E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
Probab=99.97 E-value=5.8e-35 Score=182.08 Aligned_cols=57 Identities=81% Similarity=1.039 Sum_probs=54.9
Q ss_pred CCceecccccCCcccCCCCCcccccccCCCChhhhhhhhhchheeecchhhhhcccc
Q 035122 1 MGKVHGSLARAGKVRGQTPKVAKQDKKKRPRGRAYKRMQYNRRFVTAGQLIISHRFS 57 (72)
Q Consensus 1 mGKvHGSLarAGKVR~QTPKV~KqeKkk~~~GRak~R~qYnrRfvnv~~t~~~~r~~ 57 (72)
|||||||||+|||||+||||||+|||+|+++|||++|++||+||+|++++|+.+|+-
T Consensus 1 mGKvHGSLarAGKVR~QTPKV~kqeKkk~~~gRak~R~~YnrRfvnv~~~~g~kr~~ 57 (62)
T 3iz6_Z 1 MGKVHGSLARAGKVRGQTPKVAKQDKKKKPRGRAHKRMQYNRRFVTAVVGFGKKRGP 57 (62)
T ss_dssp CHHHHHHHHHHHTTCCCCSSSSCCHHHHHHHHHHHHHHCCCCCCSCHHHHHHTTTCC
T ss_pred CCcccchhhccccccCCCCCcchhhhccCCchHHHHHHHhhhhhhhcccccCCccCC
Confidence 999999999999999999999999998889999999999999999999999998864
No 3
>2xzm_X RPS30E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_X 3j0o_X 3j0l_X 3j0p_X 3j0q_X
Probab=99.96 E-value=8.8e-32 Score=174.10 Aligned_cols=61 Identities=52% Similarity=0.782 Sum_probs=50.8
Q ss_pred CCceecccccCCcccCCCCCccccccc-CCCChhhhhhhhhchheeecch-hhhhccccccee
Q 035122 1 MGKVHGSLARAGKVRGQTPKVAKQDKK-KRPRGRAYKRMQYNRRFVTAGQ-LIISHRFSGLLN 61 (72)
Q Consensus 1 mGKvHGSLarAGKVR~QTPKV~KqeKk-k~~~GRak~R~qYnrRfvnv~~-t~~~~r~~~~~~ 61 (72)
|||+|||||+|||||+||||||+|||+ |.++|||++|++||+||+|+++ +|+.+|+..-.|
T Consensus 1 mGkvHGSLarAGKVR~QTPKV~kqeKk~K~~~GRak~R~~YnrRfv~~~~~~~gkrk~npn~~ 63 (80)
T 2xzm_X 1 MGRMHGTLAKAGKVRKQTPKVEKKDKPRKTPKGRSYKRILYNRRYAPHILATDPKKRKSPNWH 63 (80)
T ss_dssp ------CCTTTTHHHHHSCCCCCCCCSSCCCCSHHHHHHHHHHHSSTTTTTSCSSSCCCTTTC
T ss_pred CccchhhhhccccccccCCCcchhhhcccCCchhHHHHHHHHHhhhhhcccccccccCCCCcc
Confidence 999999999999999999999999998 8899999999999999999999 999999854433
No 4
>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9
Probab=96.32 E-value=0.0014 Score=46.39 Aligned_cols=25 Identities=20% Similarity=0.093 Sum_probs=20.9
Q ss_pred cCCcccCCCCCcccccccCCCChhhh
Q 035122 10 RAGKVRGQTPKVAKQDKKKRPRGRAY 35 (72)
Q Consensus 10 rAGKVR~QTPKV~KqeKkk~~~GRak 35 (72)
|+ |+..||||++++++++.+.+..+
T Consensus 75 rk-K~~~~tPK~~k~~kKkvkl~~Lk 99 (189)
T 2xzm_9 75 KK-KKSYTTKKKTKHRHVHTKLGALA 99 (189)
T ss_dssp CC-CCCCCSSSCCCCCCCCCCCSCCC
T ss_pred cc-ccccCCCccccccccccCCceee
Confidence 77 99999999999999877665543
No 5
>1egw_A MADS box transcription enhancer factor 2, polypeptide A; MADS-box transcription factor, DNA/protein complex, transcription/DNA; HET: DNA; 1.50A {Homo sapiens} SCOP: d.88.1.1 PDB: 1c7u_A 3mu6_A*
Probab=16.10 E-value=23 Score=21.45 Aligned_cols=21 Identities=19% Similarity=0.468 Sum_probs=13.0
Q ss_pred hhhhhcccccc----------eeeeEEEEEEee
Q 035122 49 QLIISHRFSGL----------LNIRVCFCIVFS 71 (72)
Q Consensus 49 ~t~~~~r~~~~----------~~~~~~~~~~~~ 71 (72)
.||..|| .|| -+..||. |+||
T Consensus 18 vTfsKRr-~GL~KKA~ELsvLCdaeV~l-ivfs 48 (77)
T 1egw_A 18 VTFTKRK-FGLMKKAYELSVLCDCEIAL-IIFN 48 (77)
T ss_dssp HHHHHHH-HHHHHHHHHHHHHTTCEEEE-EEEC
T ss_pred HHHHHhH-HHHHHHHHHHhcccCCeEEE-EEEC
Confidence 4665555 555 5778886 4565
No 6
>1m5n_Q PTHRP, PTH-RP, parathyroid hormone-related protein; all helical protein, heat repeats, protein transport; 2.90A {Homo sapiens}
Probab=9.76 E-value=94 Score=16.25 Aligned_cols=14 Identities=29% Similarity=0.290 Sum_probs=8.0
Q ss_pred cCCCCCcccccccC
Q 035122 15 RGQTPKVAKQDKKK 28 (72)
Q Consensus 15 R~QTPKV~KqeKkk 28 (72)
..|.+|.+-+.||+
T Consensus 13 keqplk~~~KkKk~ 26 (28)
T 1m5n_Q 13 KEQPLKTPGKKKKG 26 (28)
T ss_dssp SSGGGCSSCCCCCC
T ss_pred ccCCcccccccccC
Confidence 45666766554443
No 7
>3v2d_F 50S ribosomal protein L4; ribosome associated inhibitor A, RAIA, protein Y, stress RES stationary phase, ribosome hibernation, ribosome; 2.70A {Thermus thermophilus} PDB: 2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F 2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F 2wro_F 2wrr_F 2x9s_F 2x9u_F ...
Probab=9.19 E-value=1.3e+02 Score=20.97 Aligned_cols=26 Identities=31% Similarity=0.350 Sum_probs=18.2
Q ss_pred ecccccCCcccCCCCCcccccccCCCChhhh
Q 035122 5 HGSLARAGKVRGQTPKVAKQDKKKRPRGRAY 35 (72)
Q Consensus 5 HGSLarAGKVR~QTPKV~KqeKkk~~~GRak 35 (72)
|.+.++ +.|++=+-|+-+| +-+||||
T Consensus 49 ~~tktr-aEv~G~grKp~rQ----KGTGrAR 74 (210)
T 3v2d_F 49 ASTKTR-GEVAYSGRKIWPQ----KHTGRAR 74 (210)
T ss_dssp CCCCCT-TTSSCCCCCSSCS----SSSSSCC
T ss_pred cCCCcc-ccccCCCCCCCCC----CCCCccC
Confidence 556666 5688888777766 3578887
No 8
>3ffd_P PTH-RP, PTHRP, parathyroid hormone-related protein; PTHRP complexed to FAB, alternative splicing, calcium, cleavage on PAIR of basic residues; 2.00A {Homo sapiens} PDB: 1bzg_A
Probab=9.00 E-value=1.3e+02 Score=19.93 Aligned_cols=23 Identities=26% Similarity=0.302 Sum_probs=12.7
Q ss_pred cCCCCCcccccccCCCChhhhhhh
Q 035122 15 RGQTPKVAKQDKKKRPRGRAYKRM 38 (72)
Q Consensus 15 R~QTPKV~KqeKkk~~~GRak~R~ 38 (72)
..|..|.+.+ |||-..|+.|-..
T Consensus 79 kdqp~k~~~K-KkK~r~Gkrre~e 101 (108)
T 3ffd_P 79 KEQPLKTPGK-KKKGKPGKRKEQE 101 (108)
T ss_pred cccccccccc-ccccCCccchHHH
Confidence 3465555655 5555567666433
No 9
>2i9f_A Nucleocapsid; assembly, viral protein; 2.00A {Equine arteritis virus} SCOP: d.254.1.1
Probab=8.71 E-value=90 Score=19.06 Aligned_cols=10 Identities=60% Similarity=0.959 Sum_probs=7.2
Q ss_pred ecccc-cCCcc
Q 035122 5 HGSLA-RAGKV 14 (72)
Q Consensus 5 HGSLa-rAGKV 14 (72)
||||+ -||-.
T Consensus 37 hgsltadaggl 47 (69)
T 2i9f_A 37 HGSLTADAGGL 47 (69)
T ss_dssp CSEEEECSSSE
T ss_pred ccceeecCCCc
Confidence 89998 56643
No 10
>1k6o_B SRF, serum response factor; protein/DNA complex, transcription factor, combinatorial gene regulation, ETS proteins, MADS-box proteins; 3.19A {Homo sapiens} SCOP: d.88.1.1
Probab=8.05 E-value=72 Score=20.43 Aligned_cols=39 Identities=23% Similarity=0.307 Sum_probs=21.8
Q ss_pred Chhhhhhhhhchheeecchhhhhccccc----------ceeeeEEEEEEee
Q 035122 31 RGRAYKRMQYNRRFVTAGQLIISHRFSG----------LLNIRVCFCIVFS 71 (72)
Q Consensus 31 ~GRak~R~qYnrRfvnv~~t~~~~r~~~----------~~~~~~~~~~~~~ 71 (72)
.||.|-.++|-..-.+-..||..|| .| |-+..||+. |||
T Consensus 9 mgR~Ki~ik~Ien~~~R~vTFsKRr-~GL~KKA~ELsvLCda~Vali-vfs 57 (103)
T 1k6o_B 9 RGRVKIKMEFIDNKLRRYTTFSKRK-TGIMKKAYELSTLTGTQVLLL-VAS 57 (103)
T ss_dssp CCSCCCCSSCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHTTCEEEEE-EEC
T ss_pred CCcceeEEEEecCchHHHHhHhHhh-HhHHHHHHHHHhhhCCceEEE-EEe
Confidence 5666654444433333446777766 45 446788854 454
Done!