Query 039493
Match_columns 749
No_of_seqs 137 out of 172
Neff 3.9
Searched_HMMs 29240
Date Mon Mar 25 17:33:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039493.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/039493hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3gvo_A Pumilio 2, pumilio homo 82.7 0.17 5.7E-06 53.0 -1.3 31 718-748 90-120 (351)
2 3k62_A FEM-3 mRNA-binding fact 58.1 1.1 3.6E-05 48.8 -2.3 28 721-748 107-134 (412)
3 3bwt_A Protein PUF4; pumilio, 56.0 1.4 4.7E-05 45.4 -1.8 27 721-747 80-106 (333)
4 3v71_A PUF (pumilio/FBF) domai 37.7 5.1 0.00017 42.8 -1.0 24 724-747 95-118 (382)
5 3k49_A MRNA-binding protein PU 28.8 7.3 0.00025 40.9 -1.6 23 723-745 64-86 (369)
6 2npt_A Dual specificity mitoge 17.5 15 0.00053 33.2 -1.6 29 90-121 69-100 (106)
7 2i5o_A DNA polymerase ETA; zin 13.6 78 0.0027 24.1 1.6 12 125-136 28-39 (39)
8 1sn9_A BBAT, tetrameric beta-B 8.5 1.7E+02 0.0057 20.4 1.7 12 21-32 8-19 (26)
9 3k62_A FEM-3 mRNA-binding fact 5.7 77 0.0026 34.3 -1.7 29 721-749 143-173 (412)
10 2d3o_1 Trigger factor, TF; rib 5.5 4E+02 0.014 23.5 3.2 30 20-57 21-52 (112)
No 1
>3gvo_A Pumilio 2, pumilio homolog 2; RNA-binding, PUF domain, RNA binding protein; HET: DTD; 1.60A {Mus musculus} SCOP: a.118.1.8 PDB: 3gvt_A 3q0q_A 3q0r_A 3q0s_A 1ib2_A 1m8w_A 1m8x_A 1m8y_A 1m8z_A 3q0l_A 3q0m_A 3q0n_A 3q0o_A 3q0p_A 2yjy_A 3bsx_A 3bsb_A 3h3d_X
Probab=82.70 E-value=0.17 Score=52.98 Aligned_cols=31 Identities=16% Similarity=0.192 Sum_probs=25.5
Q ss_pred ceeecccccceeEeecCcccchhhhhhhhcc
Q 039493 718 CFELSEIAGHVVEFRYAMLLAHLMLHFSAVL 748 (749)
Q Consensus 718 ~~EL~DI~GhvvEFs~DQ~GSRFIQ~~~~~~ 748 (749)
..=+..|.|||+++|.|+||+|+||+.+..+
T Consensus 90 ~~i~~~i~g~~~~l~~~~~G~rvvQk~le~~ 120 (351)
T 3gvo_A 90 LALATRIRGHVLPLALQMYGCRVIQKALESI 120 (351)
T ss_dssp HHHHHHHTTCHHHHHTSTTHHHHHHHHHHHS
T ss_pred HHHHHHHHhhHHHHhhCHHhHHHHHHHHHhC
Confidence 3345678999999999999999999977643
No 2
>3k62_A FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding factor, PUF, RNA-binding specificity, base flipping, base stacking; 1.90A {Caenorhabditis elegans} PDB: 3k5y_A 3k5z_A 3k61_A 3k5q_A 3k64_A 3qg9_A 3v6y_A 3v74_A 3qgc_A 3qgb_A
Probab=58.07 E-value=1.1 Score=48.76 Aligned_cols=28 Identities=4% Similarity=0.044 Sum_probs=23.8
Q ss_pred ecccccceeEeecCcccchhhhhhhhcc
Q 039493 721 LSEIAGHVVEFRYAMLLAHLMLHFSAVL 748 (749)
Q Consensus 721 L~DI~GhvvEFs~DQ~GSRFIQ~~~~~~ 748 (749)
+.-|.|||+++|.|+||+|+||+-+..+
T Consensus 107 ~~~l~g~v~~L~~~~~GsrvvQk~le~~ 134 (412)
T 3k62_A 107 KNFISSQMTDMCLDKFACRVIQSSLQNM 134 (412)
T ss_dssp HHHHHHTHHHHHHSTTHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHcChhhhHHHHHHHHhC
Confidence 4567899999999999999999876543
No 3
>3bwt_A Protein PUF4; pumilio, RNA binding, HO endonuclease, transcription, RNA binding protein; 2.69A {Saccharomyces cerevisiae} PDB: 4dzs_A 3bx2_A 3bx3_A
Probab=55.98 E-value=1.4 Score=45.39 Aligned_cols=27 Identities=11% Similarity=0.011 Sum_probs=22.0
Q ss_pred ecccccceeEeecCcccchhhhhhhhc
Q 039493 721 LSEIAGHVVEFRYAMLLAHLMLHFSAV 747 (749)
Q Consensus 721 L~DI~GhvvEFs~DQ~GSRFIQ~~~~~ 747 (749)
+..+.|||++++.|+||+|.||.-+..
T Consensus 80 ~~~~~~~~~~l~~~~~G~rviQ~~l~~ 106 (333)
T 3bwt_A 80 TKISSPHFVEISLNPHGTRALQKLIEC 106 (333)
T ss_dssp HHHHGGGHHHHHHSTTHHHHHHHHHHH
T ss_pred HHHHHhHHHHHHhcccccHHHHHHHHh
Confidence 445679999999999999999986654
No 4
>3v71_A PUF (pumilio/FBF) domain-containing protein 7, CO transcript evidence; PUF repeats, RNA binding protein-RNA complex; HET: EPE; 2.90A {Caenorhabditis elegans}
Probab=37.67 E-value=5.1 Score=42.79 Aligned_cols=24 Identities=8% Similarity=0.052 Sum_probs=19.8
Q ss_pred cccceeEeecCcccchhhhhhhhc
Q 039493 724 IAGHVVEFRYAMLLAHLMLHFSAV 747 (749)
Q Consensus 724 I~GhvvEFs~DQ~GSRFIQ~~~~~ 747 (749)
|.|||++.|.|+||+|+||.-+..
T Consensus 95 l~g~v~~Ls~~~~G~rvvQk~ie~ 118 (382)
T 3v71_A 95 IDGGLLAMCKDKFACRVVQLALQK 118 (382)
T ss_dssp HHTCHHHHHTSTTHHHHHHHHHHH
T ss_pred hcchHHHHHhCccchHHHHHHHHH
Confidence 469999999999999999976654
No 5
>3k49_A MRNA-binding protein PUF3; PUF3, pumilio, RNA binding, mitochondrial mRNA,, membrane, mitochondrion; HET: CIT; 2.50A {Saccharomyces cerevisiae} SCOP: a.118.1.0 PDB: 3k4e_A
Probab=28.76 E-value=7.3 Score=40.90 Aligned_cols=23 Identities=17% Similarity=0.271 Sum_probs=11.8
Q ss_pred ccccceeEeecCcccchhhhhhh
Q 039493 723 EIAGHVVEFRYAMLLAHLMLHFS 745 (749)
Q Consensus 723 DI~GhvvEFs~DQ~GSRFIQ~~~ 745 (749)
+|.||++|.++|+||+..||+.+
T Consensus 64 el~~~~~~L~~d~~gn~vvQkll 86 (369)
T 3k49_A 64 EIRDDAIELSNDVFGNYVIQKFF 86 (369)
T ss_dssp HHGGGHHHHHHSTTTHHHHHHHH
T ss_pred HHHHHHHHHhhCcccccHHHHHH
Confidence 34555555555555555555443
No 6
>2npt_A Dual specificity mitogen-activated protein kinase; MAP2K5, MEK5, MKK PRKMK5, MAP kinase kinase 5, PHOX, PHOX-domain; 1.75A {Homo sapiens} SCOP: d.15.2.2 PDB: 2o2v_A 1wi0_A
Probab=17.50 E-value=15 Score=33.19 Aligned_cols=29 Identities=52% Similarity=0.805 Sum_probs=19.9
Q ss_pred CCCChhhhccCcccceeeccCCC---CCCCCCCCC
Q 039493 90 GFSSEEELRSDPAYLSYYYSNVN---LNPRLPPPL 121 (749)
Q Consensus 90 ~~~seeelRsdPAYl~YYYSnvn---LNPRLPPPL 121 (749)
.+-|+||+. |.|+|||.-++ .|=-||-||
T Consensus 69 TVRSDeE~k---AMlsyy~~~~~Eq~~~g~~~~PL 100 (106)
T 2npt_A 69 TVRSDEEMK---AMLSYYYSTVMEQQVNGQLIEPL 100 (106)
T ss_dssp EECSHHHHH---HHHHHHHHHHHHHHTTTCCCCCE
T ss_pred EEcchHHHH---HHHHHHHHHHHHHHhcCCCCCCc
Confidence 378999998 89999986432 344444444
No 7
>2i5o_A DNA polymerase ETA; zinc finger, DNA polymerase,POL ETA, UBZ, ubiquitin-binding zinc finger, translesion synthesis, ubiquitin-binding domain; HET: DNA; NMR {Homo sapiens}
Probab=13.55 E-value=78 Score=24.09 Aligned_cols=12 Identities=33% Similarity=0.562 Sum_probs=0.0
Q ss_pred hhHHHHHHhhCC
Q 039493 125 EDWRFAQRLRGE 136 (749)
Q Consensus 125 EdwR~aqRl~~g 136 (749)
+||.||+.|+.+
T Consensus 28 ~D~H~A~~Lq~s 39 (39)
T 2i5o_A 28 MDYHFALELQKS 39 (39)
T ss_dssp HHHHHHHHHTTC
T ss_pred hhHHHHHHHhcC
No 8
>1sn9_A BBAT, tetrameric beta-BETA-alpha mini-protein; protein design, domain swapping, oligomerization, de novo protein; HET: DBZ; 1.20A {Synthetic} SCOP: k.14.1.1 PDB: 1sna_A* 1sne_A* 1xof_B* 1xof_A*
Probab=8.54 E-value=1.7e+02 Score=20.39 Aligned_cols=12 Identities=50% Similarity=0.891 Sum_probs=0.0
Q ss_pred hHHHHHHHHHhh
Q 039493 21 DFEKEIGMLLRE 32 (749)
Q Consensus 21 dle~eLg~ll~~ 32 (749)
||.+||..||+.
T Consensus 8 dfadelakllrq 19 (26)
T 1sn9_A 8 DFADELAKLLRQ 19 (26)
T ss_dssp CHHHHHHHHHHH
T ss_pred chHHHHHHHHHH
No 9
>3k62_A FEM-3 mRNA-binding factor 2; FBF, FEM-3 binding factor, PUF, RNA-binding specificity, base flipping, base stacking; 1.90A {Caenorhabditis elegans} PDB: 3k5y_A 3k5z_A 3k61_A 3k5q_A 3k64_A 3qg9_A 3v6y_A 3v74_A 3qgc_A 3qgb_A
Probab=5.71 E-value=77 Score=34.28 Aligned_cols=29 Identities=10% Similarity=0.214 Sum_probs=0.0
Q ss_pred eccc--ccceeEeecCcccchhhhhhhhccC
Q 039493 721 LSEI--AGHVVEFRYAMLLAHLMLHFSAVLN 749 (749)
Q Consensus 721 L~DI--~GhvvEFs~DQ~GSRFIQ~~~~~~~ 749 (749)
+.++ .+||++.+.|++|+..||+-+..+.
T Consensus 143 v~eL~~~~~i~~L~~D~~GNhVIQK~Le~~~ 173 (412)
T 3k62_A 143 VQALPRDARLIAICVDQNANHVIQKVVAVIP 173 (412)
T ss_dssp HHTSCCSHHHHHHHHCTTTHHHHHHHHHHSC
T ss_pred HHHHhccccHHHHHhCccccHHHHHHHHhCC
No 10
>2d3o_1 Trigger factor, TF; ribosome, nascent chain, protein folding, SRP; 3.35A {Deinococcus radiodurans} PDB: 2aar_7
Probab=5.51 E-value=4e+02 Score=23.49 Aligned_cols=30 Identities=20% Similarity=0.477 Sum_probs=0.0
Q ss_pred chHHHHHHHHHhhhcccccccccccccc--ccCCCCCCCc
Q 039493 20 DDFEKEIGMLLREQRRQETDDCERELNL--YRSGSAPPTV 57 (749)
Q Consensus 20 ~dle~eLg~ll~~qr~~~~~~~erel~~--~RSGSAPPTv 57 (749)
+++++.+...+++-+ +..++ ||-|-||..|
T Consensus 21 ~~~~~~~~~~~~~~~--------k~~~ipGFRkGKvP~~v 52 (112)
T 2d3o_1 21 AEVNRAYDQVWAGLA--------RDVRVPGFRPGKAPRKV 52 (112)
T ss_dssp GGTHHHHHHHHHHHH--------TTSCBTTBCTTCCCSTT
T ss_pred HHHHHHHHHHHHHHH--------hhCCCCCcCCCCCCHHH
Done!