Query 005538
Match_columns 691
No_of_seqs 210 out of 415
Neff 3.3
Searched_HMMs 29240
Date Tue Mar 26 18:11:27 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/005538.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_2046-2050//hhsearch_pdb/005538hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3m91_B Prokaryotic ubiquitin-l 1.0 1 1 17.8 2.5 25 17-41 13-37 (44)
2 3m9d_G Prokaryotic ubiquitin-l 1.0 1 1 17.7 -0.9 25 16-40 36-60 (68)
3 3gn4_A Myosin-VI; unconvention 1.0 1 1 16.6 0.6 55 2-57 83-138 (148)
4 3dl3_A Tellurite resistance pr 1.0 1 1 15.2 0.5 25 585-612 78-103 (119)
5 2pa7_A DTDP-6-deoxy-3,4-keto-h 1.0 1 1 14.5 3.5 33 596-639 31-63 (141)
6 2ld3_A Myosin VI; molecular mo 1.0 1 1 14.2 0.0 54 2-57 18-73 (88)
7 2p6v_A Transcription initiatio 1.0 1 1 14.2 3.7 46 3-53 26-73 (114)
8 3l2o_B F-box only protein 4; s 1.0 1 1 13.8 -4.3 22 599-622 212-233 (312)
9 2imj_A Hypothetical protein DU 1.0 1 1 13.8 -0.5 57 611-683 60-118 (166)
10 3exa_A TRNA delta(2)-isopenten 1.0 1 1 13.6 -4.5 36 604-639 246-281 (322)
No 1
>3m91_B Prokaryotic ubiquitin-like protein PUP; coil COIL alpha helix, ATP-binding, chaperone, nucleotide-BI proteasome, S-nitrosylation; 1.80A {Mycobacterium tuberculosis}
Probab=1.00 E-value=1 Score=17.77 Aligned_cols=25 Identities=32% Similarity=0.574 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 3558867999999998255543235
Q 005538 17 PEQVNDVKDLLEDYVERNQDDFEEF 41 (691)
Q Consensus 17 peqV~~ikddld~YvE~NqdDF~e~ 41 (691)
.+.+++|-|+||.-||.|-++|+.-
T Consensus 13 ~~~~D~lLDeId~vLE~NAeeFV~~ 37 (44)
T 3m91_B 13 TEETDDLLDEIDDVLEENAEDFVRA 37 (44)
T ss_dssp HHHHHHHHHHHHHHHHHTC------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 6468999999999999759999999
No 2
>3m9d_G Prokaryotic ubiquitin-like protein PUP; alpha helix coil COIL, 5 beta-strand barrel, ATP-binding, CH nucleotide-binding, proteasome; 4.50A {Mycobacterium tuberculosis}
Probab=1.00 E-value=1 Score=17.68 Aligned_cols=25 Identities=32% Similarity=0.577 Sum_probs=18.7
Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 9355886799999999825554323
Q 005538 16 SPEQVNDVKDLLEDYVERNQDDFEE 40 (691)
Q Consensus 16 ~peqV~~ikddld~YvE~NqdDF~e 40 (691)
..+.+++|-|+||.-||.|-++|+.
T Consensus 36 ~~~~~D~lLDeId~vLe~NAeefV~ 60 (68)
T 3m9d_G 36 LTEETDDLLDEIDDVLEENAEDFVR 60 (68)
T ss_dssp TTTTTTTHHHHHTTTSSSCC-----
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 3546899999999999975999999
No 3
>3gn4_A Myosin-VI; unconventional myosin, motility, lever ARM, 3-helix bundle, actin-binding, ATP-binding, calmodulin-binding, coiled coil; 2.70A {Sus scrofa}
Probab=1.00 E-value=1 Score=16.61 Aligned_cols=55 Identities=13% Similarity=0.272 Sum_probs=39.9
Q ss_pred HHHHHHHHHHCCCCC-HHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCCCCC
Q ss_conf 289999864089999-35588679999999982555432355546653038986000
Q 005538 2 KLELILRLLDNDELS-PEQVNDVKDLLEDYVERNQDDFEEFSDVDELYHLLPLDKVE 57 (691)
Q Consensus 2 kLE~ilRlLdNd~l~-peqV~~ikddld~YvE~NqdDF~e~~d~eelYd~L~lde~e 57 (691)
+++.|+..|+.+.-. -.+|.+++.+||--+..=-++-..-+++|..|+.| +++.+
T Consensus 83 ~~~~i~~~Lk~~k~k~~~~v~~~~~~i~~~i~kIK~~~i~~~~Id~~y~~l-v~~~~ 138 (148)
T 3gn4_A 83 KFNEVVSALKDGKQEMSKQVKDLEISIDALMAKIKSTMMTREQIQKEYDAL-VKSSA 138 (148)
T ss_dssp ------------CCHHHHHHHHHHHHHHHHHHHHTTSCCCHHHHHHHHHHH-HHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH-HHHHH
T ss_conf 999999998545899999999999999999998636889999999999999-99999
No 4
>3dl3_A Tellurite resistance protein B; X-RAY NESG VFR98 Q5E3X2_VIBF1, structural genomics, PSI-2, protein structure initiative; 2.30A {Vibrio fischeri ES114} SCOP: b.82.2.13
Probab=1.00 E-value=1 Score=15.20 Aligned_cols=25 Identities=28% Similarity=0.736 Sum_probs=15.0
Q ss_pred HHHHHHHCCCCCCCCEEEEE-EECCCCCH
Q ss_conf 45775301487897304888-62078818
Q 005538 585 PAFWERLSLDSYGTDTLFFA-FYYQQNTY 612 (691)
Q Consensus 585 p~lfeKiKi~kfs~ETLFYI-FYs~PgD~ 612 (691)
|..|-|+. +++|+-|++ ||..|.|+
T Consensus 78 Pq~wHrVe---~sdD~~f~leFyc~~~dy 103 (119)
T 3dl3_A 78 PQYWHRIE---LSDDAQFNINFWSDQDKS 103 (119)
T ss_dssp TTCEEEEE---ECTTCEEEEEEEECC---
T ss_pred CCCEEEEE---ECCCEEEEEEEEECCHHH
T ss_conf 88448999---779969999999783677
No 5
>2pa7_A DTDP-6-deoxy-3,4-keto-hexulose isomerase; deoxysugar biosynthesis, S-layer biosynthesis, ketoisomerase; HET: TYD; 1.50A {Aneurinibacillus thermoaerophilus} SCOP: b.82.1.1 PDB: 2pae_A* 2pak_A* 2pam_A*
Probab=1.00 E-value=1 Score=14.49 Aligned_cols=33 Identities=9% Similarity=0.278 Sum_probs=25.6
Q ss_pred CCCCEEEEEEECCCCCHHHHHHHHHHHHCCCEEECCCCEEEECC
Q ss_conf 89730488862078818999999998423712111331554114
Q 005538 596 YGTDTLFFAFYYQQNTYQQYLAAKELKKQSWRYHRKYNTWFQRH 639 (691)
Q Consensus 596 fs~ETLFYIFYs~PgD~~QllAA~EL~~RgWRYHKk~k~Wf~R~ 639 (691)
|...-+|||+-+-|+.+ |+|..|++...||.-.
T Consensus 31 f~ikRvy~~~~~~~g~~-----------RG~H~Hk~~~q~li~l 63 (141)
T 2pa7_A 31 FSIKRVYYIFDTKGEEP-----------RGFHAHKKLEQVLVCL 63 (141)
T ss_dssp SCCCEEEEEESCCSSCC-----------EEEEEESSCCEEEEEE
T ss_pred CCCCEEEEEEECCCCCE-----------ECCCCCCCCEEEEEEE
T ss_conf 77038999996699989-----------8868588725899998
No 6
>2ld3_A Myosin VI; molecular motor, lever arm extension, motor prote; NMR {Mus musculus}
Probab=1.00 E-value=1 Score=14.23 Aligned_cols=54 Identities=11% Similarity=0.236 Sum_probs=37.1
Q ss_pred HHHHHHHHHHCCCCC-HHHHHHHHHHHHHHHHHCCC-CCCCCCCHHHHHHCCCCCCCC
Q ss_conf 289999864089999-35588679999999982555-432355546653038986000
Q 005538 2 KLELILRLLDNDELS-PEQVNDVKDLLEDYVERNQD-DFEEFSDVDELYHLLPLDKVE 57 (691)
Q Consensus 2 kLE~ilRlLdNd~l~-peqV~~ikddld~YvE~Nqd-DF~e~~d~eelYd~L~lde~e 57 (691)
+++.|.+-|+.+.=+ -.+|.+++..||.-+..=-. + ..-++.|..|..| ++..+
T Consensus 18 ~m~eia~~LK~~k~~~~kqV~~l~~~Ie~~I~kIK~~~-itr~~Id~~y~~L-~~~~~ 73 (88)
T 2ld3_A 18 KFNEVVSALKDGKPEVNRQIKNLEISIDALMAKIKSTM-MTREQIQKEYDAL-VKSSE 73 (88)
No 7
>2p6v_A Transcription initiation factor TFIID subunit 4; alpha helix; HET: MLY; 2.00A {Homo sapiens} SCOP: a.277.1.1
Probab=1.00 E-value=1 Score=14.19 Aligned_cols=46 Identities=24% Similarity=0.424 Sum_probs=36.4
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCC--CCCCCCCHHHHHHCCCC
Q ss_conf 8999986408999935588679999999982555--43235554665303898
Q 005538 3 LELILRLLDNDELSPEQVNDVKDLLEDYVERNQD--DFEEFSDVDELYHLLPL 53 (691)
Q Consensus 3 LE~ilRlLdNd~l~peqV~~ikddld~YvE~Nqd--DF~e~~d~eelYd~L~l 53 (691)
|-.+|+|-.++...||-...|++.|..-|+..-+ +|... ||++|+.
T Consensus 26 L~tLi~las~~~~spev~~~Vr~LVq~Ll~~~i~~EeFt~~-----Lq~~lns 73 (114)
T 2p6v_A 26 LSTLIXLASSGXQSTETAANVXELVQNLLDGXIEAEDFTSR-----LYRELNS 73 (114)
T ss_dssp HHHHHHHHTSSSSCHHHHHHHHHHHHHHHTTSSCHHHHHHH-----HHHHTTC
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHH-----HHHHHCC
T ss_conf 99999997435668078999999999999744889999999-----9999759
No 8
>3l2o_B F-box only protein 4; small G protein fold, UBL conjugation pathway, ubiquitin Pro ligase, protein binding-cell cycle complex; 2.80A {Homo sapiens}
Probab=1.00 E-value=1 Score=13.79 Aligned_cols=22 Identities=9% Similarity=0.067 Sum_probs=8.1
Q ss_pred CEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf 304888620788189999999984
Q 005538 599 DTLFFAFYYQQNTYQQYLAAKELK 622 (691)
Q Consensus 599 ETLFYIFYs~PgD~~QllAA~EL~ 622 (691)
+.|-|+-=+.-++. +-|+.||.
T Consensus 212 dglIfVVDSsDreR--leak~EL~ 233 (312)
T 3l2o_B 212 DGFIYVANAEAHKR--HEWQDEFS 233 (312)
T ss_dssp SEEEECCBCBTTCC--CCHHHHHH
T ss_pred CEEEEEECCCCHHH--HHHHHHHH
T ss_conf 87999954772768--99999999
No 9
>2imj_A Hypothetical protein DUF1348; alpha beta protein, structural genomics, PSI-2, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5} SCOP: d.17.4.23
Probab=1.00 E-value=1 Score=13.78 Aligned_cols=57 Identities=19% Similarity=0.385 Sum_probs=23.5
Q ss_pred CHHHHHHHHHHHHCCCEEECCCCEEEECCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCEEE--CCCEEEECH
Q ss_conf 1899999999842371211133155411468765789510465999666667531256722343--477177321
Q 005538 611 TYQQYLAAKELKKQSWRYHRKYNTWFQRHEEPKVANDEFEQGTYVYFDFHIANDDLQHGWCQRI--KTEFTFEYN 683 (691)
Q Consensus 611 D~~QllAA~EL~~RgWRYHKk~k~Wf~R~~ePkv~Td~yErGsYiyFDpe~~~d~~~~~W~qr~--K~dFtfeY~ 683 (691)
.+..++..+=-+...+|.-|+ +|-....-.-| +=.|.+-|-. ..|- |. .++..|+.+
T Consensus 60 eI~~FLtrKW~rE~dYrLiKE--Lwaf~~nRIAV------RFaYEw~D~~-------gqWf-RsyGnEnWeFd~~ 118 (166)
T 2imj_A 60 EAKAFLTRKWAKELDYRLIKE--LWAFTDNRIAV------RYAYEWHDDS-------GNWF-RSYGNENWEFDEQ 118 (166)
T ss_dssp HHHHHHHHHHHHSEEEEEEEE--EEEEETTEEEE------EEEEEEECTT-------SCEE-EEEEEEEEEECTT
T ss_pred HHHHHHHHHHHHHCCCHHHHH--HHEECCCEEEE------EEEEEEECCC-------CCEE-HHCCCCCCEECCC
T ss_conf 999999998775505523434--11005976999------9876776488-------9773-3027756418878
No 10
>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A
Probab=1.00 E-value=1 Score=13.63 Aligned_cols=36 Identities=28% Similarity=0.493 Sum_probs=0.0
Q ss_pred EEECCCCCHHHHHHHHHHHHCCCEEECCCCEEEECC
Q ss_conf 862078818999999998423712111331554114
Q 005538 604 AFYYQQNTYQQYLAAKELKKQSWRYHRKYNTWFQRH 639 (691)
Q Consensus 604 IFYs~PgD~~QllAA~EL~~RgWRYHKk~k~Wf~R~ 639 (691)
+|-|+-|..--.-|...++...++|-|+..+||.+.
T Consensus 246 ~~~yL~G~~sl~eaie~i~~~TR~yAKRQ~TWfR~~ 281 (322)
T 3exa_A 246 MYDYLDGNVTLEEAIDTLKRNSRRYAKRQLTWFRNK 281 (322)
T ss_dssp HHHHHHTSSCHHHHHHHHHHHHHHHHHHHHHHHHTS
T ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 999977998899999999999999999999985689
Done!