Query 042412
Match_columns 74
No_of_seqs 119 out of 1013
Neff 5.6
Searched_HMMs 29240
Date Mon Mar 25 09:57:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042412.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/042412hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1hbx_A SRF, serum response fac 100.0 6.6E-33 2.3E-37 174.0 4.2 66 4-71 4-70 (92)
2 1k6o_B SRF, serum response fac 100.0 1.8E-32 6.1E-37 175.0 4.3 66 4-71 3-69 (103)
3 1mnm_A Protein (MCM1 transcrip 100.0 5.1E-32 1.8E-36 172.1 4.6 65 5-71 11-76 (100)
4 1egw_A MADS box transcription 100.0 2.9E-31 9.9E-36 161.7 4.6 59 11-71 1-60 (77)
5 3p57_A Myocyte-specific enhanc 100.0 9.6E-31 3.3E-35 163.6 4.4 59 11-71 1-60 (90)
6 2lx9_A Ferrous iron transport 25.5 97 0.0033 17.4 3.9 44 13-67 8-51 (83)
7 3nrf_A APAG protein; structura 24.0 5.6 0.00019 24.9 -2.1 42 20-68 22-63 (106)
8 1wmh_B Partitioning defective- 23.6 42 0.0014 20.0 1.8 51 21-73 14-68 (86)
9 3izc_Z 60S ribosomal protein R 22.5 55 0.0019 21.5 2.3 27 42-70 4-34 (155)
10 4a17_T RPL24, 60S ribosomal pr 22.0 54 0.0019 21.6 2.3 27 42-70 6-36 (158)
No 1
>1hbx_A SRF, serum response factor; gene regulation, transcription complex; 3.15A {Homo sapiens} SCOP: d.88.1.1 PDB: 1srs_A*
Probab=99.97 E-value=6.6e-33 Score=173.98 Aligned_cols=66 Identities=33% Similarity=0.468 Sum_probs=62.5
Q ss_pred ccccccCcc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412 4 SDYNYTMGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK 71 (74)
Q Consensus 4 ~~~k~~mgR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~ 71 (74)
...|++||| ||+|++|+|+.+|++||+||+.||||||+|||+||||+||||||+|+ |++|+|+||+
T Consensus 4 ~~~k~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~V~livfs~~--gk~~~f~s~~ 70 (92)
T 1hbx_A 4 KPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTFATRK 70 (92)
T ss_dssp --CCSSCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECTT--SCEEEEECGG
T ss_pred CcCCCCCCcceEEEEEecChhHHHHHHHHhhhhHHHHHHHHHhhcCCceEEEEECCC--CCEEEecCCC
Confidence 356899999 99999999999999999999999999999999999999999999999 9999999985
No 2
>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=99.97 E-value=1.8e-32 Score=174.97 Aligned_cols=66 Identities=33% Similarity=0.468 Sum_probs=62.4
Q ss_pred ccccccCcc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412 4 SDYNYTMGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK 71 (74)
Q Consensus 4 ~~~k~~mgR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~ 71 (74)
...|++||| ||+|++|+|+.+|++||+||+.||||||+|||+||||+||||||+|+ |++|.|+|++
T Consensus 3 ~~~k~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~--gk~~~f~s~~ 69 (103)
T 1k6o_B 3 KPGKKTRGRVKIKMEFIDNKLRRYTTFSKRKTGIMKKAYELSTLTGTQVLLLVASET--GHVYTFATRK 69 (103)
T ss_dssp --CCSSCCSCCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECSS--SCEEEEECGG
T ss_pred CCCCCCCCcceeEEEEecCchHHHHhHhHhhHhHHHHHHHHHhhhCCceEEEEEeCC--CCeeeecCcc
Confidence 356889999 99999999999999999999999999999999999999999999999 9999999985
No 3
>1mnm_A Protein (MCM1 transcriptional regulator); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: d.88.1.1
Probab=99.97 E-value=5.1e-32 Score=172.11 Aligned_cols=65 Identities=38% Similarity=0.533 Sum_probs=60.1
Q ss_pred cccccCcc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412 5 DYNYTMGK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK 71 (74)
Q Consensus 5 ~~k~~mgR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~ 71 (74)
..+++||| ||+|++|+|+.+|++||+||+.||||||+|||+||||+||||||+|+ |++|.|+||+
T Consensus 11 ~~~~~mgR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valivfs~~--gk~~~f~sps 76 (100)
T 1mnm_A 11 NNGQQKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSET--GLVYTFSTPK 76 (100)
T ss_dssp ----CCCCCCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTT--CCEEEEECTT
T ss_pred CCCCCCCccceeeEEecCcchhhhhhhHhhhhHHHHHHHHHHhcCCcEEEEEecCC--CCcceecCCC
Confidence 35789999 99999999999999999999999999999999999999999999999 9999999995
No 4
>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=99.97 E-value=2.9e-31 Score=161.74 Aligned_cols=59 Identities=42% Similarity=0.724 Sum_probs=57.6
Q ss_pred cc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412 11 GK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK 71 (74)
Q Consensus 11 gR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~ 71 (74)
|| ||+|++|+|+.+|++||+||++||+|||+|||+||||+||||||+++ |++|.|+|++
T Consensus 1 GR~Ki~ik~I~n~~~R~vTfsKRr~GL~KKA~ELsvLCdaeV~livfs~~--gk~~~~~s~~ 60 (77)
T 1egw_A 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSS--NKLFQYASTD 60 (77)
T ss_dssp CCSCCCSSCCCSHHHHHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECTT--CCEEEEESSC
T ss_pred CCceeeeEEecCchHHHHHHHHhHHHHHHHHHHHhcccCCeEEEEEECCC--CCEeeCCCCC
Confidence 78 99999999999999999999999999999999999999999999999 9999999875
No 5
>3p57_A Myocyte-specific enhancer factor 2A; protein-DNA complex, transcription factor, transcriptional activation, zinc finger; HET: DNA; 2.19A {Homo sapiens} PDB: 3kov_A* 1tqe_P 1n6j_A
Probab=99.96 E-value=9.6e-31 Score=163.59 Aligned_cols=59 Identities=42% Similarity=0.724 Sum_probs=57.6
Q ss_pred cc-ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCC
Q 042412 11 GK-KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMK 71 (74)
Q Consensus 11 gR-Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~ 71 (74)
|| ||+|++|+|+.+|++||+||+.||||||+|||+||||+||||||+|+ |++|+|+|++
T Consensus 1 GR~Ki~ik~Ien~~~R~vTFsKRr~GL~KKA~ELsvLCda~Valiifs~~--gk~~~f~s~~ 60 (90)
T 3p57_A 1 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSS--NKLFQYASTD 60 (90)
T ss_dssp CCSCCCSSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHTCEEEEEEECTT--CCEEEEESSC
T ss_pred CCCcceeEEecCchHHHHHHHHhhhhHHHHHHHHHhccCCceEEEEECCC--CCEEEeCCCC
Confidence 89 99999999999999999999999999999999999999999999999 9999999975
No 6
>2lx9_A Ferrous iron transport protein A; FEOA; NMR {Escherichia coli}
Probab=25.52 E-value=97 Score=17.43 Aligned_cols=44 Identities=11% Similarity=0.203 Sum_probs=32.4
Q ss_pred ceeeEEecCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEe
Q 042412 13 KIEIKKIADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKF 67 (74)
Q Consensus 13 Ki~ik~I~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~ 67 (74)
+..|..|.+. -...+.++..||-+..|+.|.++-..|- |.|..+
T Consensus 8 ~~~I~~i~~~---------~~~~~~rrL~~mGl~pG~~V~Vi~~ap~--ggPi~v 51 (83)
T 2lx9_A 8 AWKITGFSRE---------ISPAYRQKLLSLGMLPGSSFNVVRVAPL--GDPIHI 51 (83)
T ss_dssp EEEEEECCSS---------SCHHHHHHHHHSSCCSSSEEEEEEECTT--TCCEEE
T ss_pred EEEEEEEECC---------CCHHHHHHHHHCCCCCCCEEEEEEeCCC--CCcEEE
Confidence 5556666553 1356788889999999999999999997 555544
No 7
>3nrf_A APAG protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, unknown function; 1.50A {Pseudomonas aeruginosa} PDB: 3sb3_A
Probab=24.04 E-value=5.6 Score=24.90 Aligned_cols=42 Identities=21% Similarity=0.334 Sum_probs=30.6
Q ss_pred cCcccchhhhhhhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEec
Q 042412 20 ADAKARQVTYAKRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFC 68 (74)
Q Consensus 20 ~~~~~R~~tf~KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~ 68 (74)
.++.....||.=.-..|.++.-+|+.+| ++.|+|. |+-|..-
T Consensus 22 ~~k~~ytktFdV~vaNl~~~~idLsk~C-----~~a~~~~--gkef~ld 63 (106)
T 3nrf_A 22 GDKHFRTQAFKVRLVNAAKSEISLKNSC-----LVAQSAA--GQSFRLD 63 (106)
T ss_dssp TTEEEEEEEEEEEEECCSSSCEECTTCE-----EEEEETT--SCEEEEE
T ss_pred CCeeEEEEEEEEEEecCCCCccccchhh-----heeeCcC--CCEEEec
Confidence 4445555666666777888888888777 9999998 7776543
No 8
>1wmh_B Partitioning defective-6 homolog alpha; kinase, PB1 domain, OPCA motif, APKC, cell polarity, transferase/cell cycle complex; 1.50A {Homo sapiens} SCOP: d.15.2.2
Probab=23.58 E-value=42 Score=19.96 Aligned_cols=51 Identities=14% Similarity=0.283 Sum_probs=34.2
Q ss_pred Ccccchhhhh----hhhhhHHHHhHhhhhhcCccEEEEEecCCCCCCeEEecCCCCC
Q 042412 21 DAKARQVTYA----KRKKSLIKKAREISVACGIDLVLITFSPTKRGRSTKFCSMKRF 73 (74)
Q Consensus 21 ~~~~R~~tf~----KRk~GL~KKa~ELs~Lc~~~v~liv~~~~~~g~~~~~~s~~~~ 73 (74)
+..-|+..+. ..-..|..+...+.-|-+.++. |.|.+. +|....+++++++
T Consensus 14 ~aE~RRFs~d~~~~~~fe~f~~lv~~lh~L~~~~f~-i~Y~D~-dGDLlpInnDdnl 68 (86)
T 1wmh_B 14 DAEFRRFALPRASVSGFQEFSRLLRAVHQIPGLDVL-LGYTDA-HGDLLPLTNDDSL 68 (86)
T ss_dssp TTEEEEEEEEGGGCCCHHHHHHHHHHHTTCTTCCCE-EEEECT-TSCEEECCSHHHH
T ss_pred CCeeeEeEccCCCCCCHHHHHHHHHHHcCCCCCCEE-EEEECC-CCCEeeecCHHHH
Confidence 4445555553 2456788899999888777765 444442 3999999887653
No 9
>3izc_Z 60S ribosomal protein RPL24 (L24E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_Z 3o58_V 3o5h_V 3u5e_W 3u5i_W 4b6a_W 1s1i_S 2x7n_D
Probab=22.54 E-value=55 Score=21.54 Aligned_cols=27 Identities=15% Similarity=0.177 Sum_probs=19.1
Q ss_pred hhhhhcCccE----EEEEecCCCCCCeEEecCC
Q 042412 42 EISVACGIDL----VLITFSPTKRGRSTKFCSM 70 (74)
Q Consensus 42 ELs~Lc~~~v----~liv~~~~~~g~~~~~~s~ 70 (74)
|+|..||..| +.+.+-.| |++|.|++.
T Consensus 4 ~~CsFcg~~IyPG~G~~fVr~D--gkvf~Fcss 34 (155)
T 3izc_Z 4 EIDSFSGAKIYPGRGTLFVRGD--SKIFRFQNS 34 (155)
T ss_dssp EECTTTCSEECTTCCEEEECTT--CCEEEESSH
T ss_pred eEecCcCCcccCCCCeEEEecC--CCEEEEEcH
Confidence 6788888887 34444445 789988874
No 10
>4a17_T RPL24, 60S ribosomal protein L21; eukaryotic ribosome, ribosome, eukaryotic initiation factor 60S, translation, large ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB: 4a1a_T 4a1c_T 4a1e_T
Probab=22.03 E-value=54 Score=21.63 Aligned_cols=27 Identities=15% Similarity=0.146 Sum_probs=19.1
Q ss_pred hhhhhcCccE----EEEEecCCCCCCeEEecCC
Q 042412 42 EISVACGIDL----VLITFSPTKRGRSTKFCSM 70 (74)
Q Consensus 42 ELs~Lc~~~v----~liv~~~~~~g~~~~~~s~ 70 (74)
|+|..||..| +.+.+-.| |++|.|+|.
T Consensus 6 ~~CsFcg~~IyPG~G~~fVr~D--gkvf~Fcss 36 (158)
T 4a17_T 6 GTCSFCEYRIYPGRGQRFIAKD--GRGFFFLTK 36 (158)
T ss_dssp EECTTTCCEECTTCCEEEECTT--SCEEEESCH
T ss_pred EEecCcCCcccCCCCeEEEeeC--CceEEEEcH
Confidence 6788898887 34444444 789988874
Done!