Query psy17970
Match_columns 174
No_of_seqs 4 out of 6
Neff 1.8
Searched_HMMs 29240
Date Fri Aug 16 19:02:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17970.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/17970hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1n7d_A LDL receptor, low-densi 20.7 4.2E+02 0.014 23.1 15.3 108 55-162 461-575 (699)
2 3m0c_C LDL receptor, low-densi 7.5 1.2E+03 0.041 21.1 14.4 109 55-163 479-594 (791)
3 3lpe_B DNA-directed RNA polyme 5.1 1.5E+02 0.0052 19.7 0.1 10 42-51 32-41 (59)
4 3ica_A Phenylalanyl-tRNA synth 4.8 2.9E+02 0.0099 20.7 1.5 17 31-47 48-64 (213)
5 1n7d_A LDL receptor, low-densi 4.5 1.6E+03 0.055 19.4 14.3 22 147-168 550-571 (699)
6 3ig2_A Phenylalanyl-tRNA synth 4.3 3.2E+02 0.011 20.4 1.4 17 31-47 48-64 (213)
7 1ijq_A LDL receptor, low-densi 4.1 1.2E+03 0.041 17.3 14.2 108 55-162 85-199 (316)
8 3p8b_A DNA-directed RNA polyme 3.9 2.1E+02 0.0071 20.4 0.1 11 42-52 55-65 (81)
9 1ryq_A DNA-directed RNA polyme 3.7 2.2E+02 0.0076 19.6 0.1 10 42-51 43-52 (69)
10 2bfd_A 2-oxoisovalerate dehydr 2.9 4.8E+02 0.016 21.8 1.3 12 26-37 15-26 (400)
No 1
>1n7d_A LDL receptor, low-density lipoprotein receptor; familial hypercholesterolemia, cholestero metabolism, lipid transport; HET: NAG BMA MAN KEG; 3.70A {Homo sapiens} SCOP: b.68.5.1 g.3.11.1 g.3.11.1 g.3.11.1 g.12.1.1 g.12.1.1 g.12.1.1 g.12.1.1 g.12.1.1 g.12.1.1 PDB: 2lgp_A 1xfe_A 1f5y_A 1ldl_A 1ldr_A 1d2j_A 1f8z_A
Probab=20.74 E-value=4.2e+02 Score=23.10 Aligned_cols=108 Identities=15% Similarity=0.118 Sum_probs=55.6
Q ss_pred cCCCCceeeecccccceeeecccccceeeec---CCCCceeeeCCCCCceeeecccc-cceeeecccccceEee--c-CC
Q psy17970 55 DPTLPEMTLMDPTLSEMTVMDPTLSEMTVMD---PTLPEMTVMDPTLPEMAVMDPTL-SEMTVMDPTLSEMTIM--D-PT 127 (174)
Q Consensus 55 ~P~~~~~~~l~Pttse~tv~~Pttse~Tv~~---Ptt~~~~VlnP~~~~~~VlnP~~-S~~~VlnP~~S~v~vl--n-P~ 127 (174)
|+..-++-+.|-....+.++++.....+++- -..|+--.+||....+-+-|--. ..|.++++-.+..+++ . -.
T Consensus 461 D~~~g~LY~tD~~~~~I~v~d~dg~~~~~l~~~~~~~P~giavDp~~g~ly~td~~~~~~I~~~~~dG~~~~~l~~~~l~ 540 (699)
T 1n7d_A 461 DWIHSNIYWTDSVLGTVSVADTKGVKRKTLFREQGSKPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENIQ 540 (699)
T ss_dssp CCSSSBCEECCTTTSCEEEEBSSSCCEEEECCCSSCCCCCEECCSSSSCCEECCCSSSCCEEBCCSSSCCCCEESCSSCS
T ss_pred EeeCCcEEEEeccCCeEEEEecCCCceEEEEeCCCCCcceEEEccCCCcEEEcccCCCCeEEEEeCCCCCeeEEEeCCCC
Confidence 4445555566665666666666655544432 13455566666655555555432 4556655554444432 1 12
Q ss_pred CCceEeecccccceEeecccccceEeeccccccee
Q psy17970 128 LPEMTVMDPTLSEMTVMDPTLSEMTVMDPTLSEMT 162 (174)
Q Consensus 128 ~~~v~VlnP~~S~v~VlnP~~S~v~VlnP~~S~~~ 162 (174)
.|+=-.+||....+-+-|--...+.++|+-.++.+
T Consensus 541 ~PnGlavd~~~~~LY~aD~~~~~I~~~d~dG~~~~ 575 (699)
T 1n7d_A 541 WPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRK 575 (699)
T ss_dssp SCCCEEECTTTCCEEEEETTTTEEEEECSSSSCCE
T ss_pred CccEEEEeccCCEEEEEecCCCeEEEEccCCCceE
Confidence 24444455555555555555555555555444433
No 2
>3m0c_C LDL receptor, low-density lipoprotein receptor; protein complex, beta propeller, cholesterol clearance, PCSK autocatalytic cleavage; 7.01A {Homo sapiens}
Probab=7.48 E-value=1.2e+03 Score=21.07 Aligned_cols=109 Identities=15% Similarity=0.129 Sum_probs=56.3
Q ss_pred cCCCCceeeecccccceeeecccccceeee---cCCCCceeeeCCCCCceeeecccc-cceeeecccccceEeecC---C
Q psy17970 55 DPTLPEMTLMDPTLSEMTVMDPTLSEMTVM---DPTLPEMTVMDPTLPEMAVMDPTL-SEMTVMDPTLSEMTIMDP---T 127 (174)
Q Consensus 55 ~P~~~~~~~l~Pttse~tv~~Pttse~Tv~---~Ptt~~~~VlnP~~~~~~VlnP~~-S~~~VlnP~~S~v~vlnP---~ 127 (174)
|+..-++-+.|.....+.+++...+..+++ +-..|.--++||...++-+-|--. ..|.+.+.-.+..+++=. .
T Consensus 479 D~~~~~LY~tD~~~~~I~v~~ldG~~~~~l~~~~l~~P~gIaVDp~~g~LYwtD~g~~~~I~~~~~dG~~~~~lv~~~l~ 558 (791)
T 3m0c_C 479 DWIHSNIYWTDSVLGTVSVADTKGVKRKTLFRENGSKPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENIQ 558 (791)
T ss_dssp ETTTTEEEEEETTTTEEEEEETTSSSEEEEEECTTCCEEEEEEETTTTEEEEEECSSSCEEEEEETTSCCEEEEECSSCS
T ss_pred eecCCcEEEEecCCCeEEEEeCCCCeEEEEEeCCCCCcceEEEecCCCCEEEecCCCCCeEEEEecCCCceEEEEeCCCC
Confidence 555555666666666666666655554443 112355556666655555555332 445666655555544321 1
Q ss_pred CCceEeecccccceEeecccccceEeecccccceee
Q psy17970 128 LPEMTVMDPTLSEMTVMDPTLSEMTVMDPTLSEMTV 163 (174)
Q Consensus 128 ~~~v~VlnP~~S~v~VlnP~~S~v~VlnP~~S~~~V 163 (174)
.|+=-.+||....+-+-|--...+.+.|.-.++.++
T Consensus 559 ~P~GLavD~~~~~LYwaD~~~~~I~~~d~dG~~~~~ 594 (791)
T 3m0c_C 559 WPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKT 594 (791)
T ss_dssp CEEEEEEETTTTEEEEEETTTTEEEEEETTSCSCEE
T ss_pred CceEEEEecCCCeEEEEeCCCCcEEEEecCCCceEE
Confidence 233344555555555555555555555554444433
No 3
>3lpe_B DNA-directed RNA polymerase subunit E''; transcription regulation, SPT4, SPT5, NUSG, archaea, evoluti directed RNA polymerase; 1.90A {Methanocaldococcus jannaschii} SCOP: g.41.9.0
Probab=5.08 E-value=1.5e+02 Score=19.65 Aligned_cols=10 Identities=40% Similarity=0.700 Sum_probs=4.1
Q ss_pred eeecccccee
Q psy17970 42 AVMDPTLSEM 51 (174)
Q Consensus 42 ~V~~P~~S~~ 51 (174)
+++||.-|++
T Consensus 32 ~i~dP~~Swv 41 (59)
T 3lpe_B 32 IVINPEKSEI 41 (59)
T ss_dssp EESCTTTCHH
T ss_pred EEeCCchhHH
Confidence 3444444433
No 4
>3ica_A Phenylalanyl-tRNA synthetase beta chain; APC61692.1, phenylalanyl-tRNA SYNT beta subunit, structural genomics, PSI-2; HET: TAM; 2.44A {Porphyromonas gingivalis}
Probab=4.78 E-value=2.9e+02 Score=20.71 Aligned_cols=17 Identities=29% Similarity=0.542 Sum_probs=8.5
Q ss_pred eeeeCccccceeeeccc
Q psy17970 31 MTIMDPTLSEMAVMDPT 47 (174)
Q Consensus 31 ~~i~~P~~S~~~V~~P~ 47 (174)
++|+||..++..+|=+.
T Consensus 48 v~l~NPls~e~~vmRts 64 (213)
T 3ica_A 48 VELMNPLSQELNCMRQT 64 (213)
T ss_dssp CBCSSBSCSSEEEECSS
T ss_pred EEecCCccHHHHHHHHH
Confidence 45555555555555444
No 5
>1n7d_A LDL receptor, low-density lipoprotein receptor; familial hypercholesterolemia, cholestero metabolism, lipid transport; HET: NAG BMA MAN KEG; 3.70A {Homo sapiens} SCOP: b.68.5.1 g.3.11.1 g.3.11.1 g.3.11.1 g.12.1.1 g.12.1.1 g.12.1.1 g.12.1.1 g.12.1.1 g.12.1.1 PDB: 2lgp_A 1xfe_A 1f5y_A 1ldl_A 1ldr_A 1d2j_A 1f8z_A
Probab=4.50 E-value=1.6e+03 Score=19.37 Aligned_cols=22 Identities=14% Similarity=0.166 Sum_probs=9.1
Q ss_pred cccceEeecccccceeeecccc
Q psy17970 147 TLSEMTVMDPTLSEMTVMDPRL 168 (174)
Q Consensus 147 ~~S~v~VlnP~~S~~~VlnP~~ 168 (174)
....+-+-|--...|.++|...
T Consensus 550 ~~~~LY~aD~~~~~I~~~d~dG 571 (699)
T 1n7d_A 550 LSGRLYWVDSKLHSISSIDVNG 571 (699)
T ss_dssp TTCCEEEEETTTTEEEEECSSS
T ss_pred cCCEEEEEecCCCeEEEEccCC
Confidence 3333444443344444444433
No 6
>3ig2_A Phenylalanyl-tRNA synthetase beta chain; phers, MCSG, structural genomics, midwest center for structural GE protein structure initiative; HET: MSE; 2.09A {Bacteroides fragilis}
Probab=4.29 E-value=3.2e+02 Score=20.44 Aligned_cols=17 Identities=18% Similarity=0.503 Sum_probs=8.8
Q ss_pred eeeeCccccceeeeccc
Q psy17970 31 MTIMDPTLSEMAVMDPT 47 (174)
Q Consensus 31 ~~i~~P~~S~~~V~~P~ 47 (174)
++|+||..++..+|=+.
T Consensus 48 v~l~NPls~e~~vmRts 64 (213)
T 3ig2_A 48 VMLLNPLSADLNCMRQT 64 (213)
T ss_dssp EEBSSGGGCSCCEECSC
T ss_pred EEEeCCcchhHHHHHHH
Confidence 45555555555555444
No 7
>1ijq_A LDL receptor, low-density lipoprotein receptor; beta-propeller, lipid transport; 1.50A {Homo sapiens} SCOP: b.68.5.1 g.3.11.1
Probab=4.15 E-value=1.2e+03 Score=17.31 Aligned_cols=108 Identities=15% Similarity=0.130 Sum_probs=49.8
Q ss_pred cCCCCceeeecccccceeeecccccceeee-c--CCCCceeeeCCCCCceeeecccc-cceeeecccccceEee---cCC
Q psy17970 55 DPTLPEMTLMDPTLSEMTVMDPTLSEMTVM-D--PTLPEMTVMDPTLPEMAVMDPTL-SEMTVMDPTLSEMTIM---DPT 127 (174)
Q Consensus 55 ~P~~~~~~~l~Pttse~tv~~Pttse~Tv~-~--Ptt~~~~VlnP~~~~~~VlnP~~-S~~~VlnP~~S~v~vl---nP~ 127 (174)
|+..-++-+.|.....+.++++..+..+++ + -..|.--.+||..-.+-+-|--. ..|.+.++-.+..+++ +-.
T Consensus 85 d~~~~~ly~~d~~~~~I~~~~~~g~~~~~~~~~~~~~P~~iavdp~~g~ly~~d~~~~~~I~~~~~dG~~~~~~~~~~~~ 164 (316)
T 1ijq_A 85 DWIHSNIYWTDSVLGTVSVADTKGVKRKTLFRENGSKPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSLVTENIQ 164 (316)
T ss_dssp ETTTTEEEEEETTTTEEEEEETTSSSEEEEEECTTCCEEEEEEETTTTEEEEEECSSSCEEEEEETTSCCEEEEECSSCS
T ss_pred eecCCeEEEEECCCCEEEEEeCCCCceEEEEECCCCCcceEEeCCCCCEEEEEccCCCCeEEEEcCCCCCeEEEEECCCC
Confidence 454555555555555566666554443322 1 12344445555555444444332 3455555554444433 111
Q ss_pred CCceEeecccccceEeecccccceEeeccccccee
Q psy17970 128 LPEMTVMDPTLSEMTVMDPTLSEMTVMDPTLSEMT 162 (174)
Q Consensus 128 ~~~v~VlnP~~S~v~VlnP~~S~v~VlnP~~S~~~ 162 (174)
.|+=-.+||....+-+-|--...+.+.|.-.++.+
T Consensus 165 ~P~gla~d~~~~~lY~~D~~~~~I~~~d~dg~~~~ 199 (316)
T 1ijq_A 165 WPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRK 199 (316)
T ss_dssp CEEEEEEETTTTEEEEEETTTTEEEEEETTSCSCE
T ss_pred CceEEEEeccCCEEEEEECCCCeEEEEecCCCceE
Confidence 23333345544455555544445555554444433
No 8
>3p8b_A DNA-directed RNA polymerase, subunit E''; transcription elongation factor, RNA polymerase, transferase transcription complex; 1.80A {Pyrococcus furiosus}
Probab=3.91 E-value=2.1e+02 Score=20.42 Aligned_cols=11 Identities=36% Similarity=0.437 Sum_probs=4.9
Q ss_pred eeeccccceee
Q psy17970 42 AVMDPTLSEMA 52 (174)
Q Consensus 42 ~V~~P~~S~~~ 52 (174)
+++||.-|++|
T Consensus 55 iI~dPe~S~IA 65 (81)
T 3p8b_A 55 IIVDVENSEIA 65 (81)
T ss_dssp EESCTTTCHHH
T ss_pred EEeCChHhHHH
Confidence 44444444443
No 9
>1ryq_A DNA-directed RNA polymerase, subunit E''; structural genomics, zinc, PSI, protein structure initiative; 1.38A {Pyrococcus furiosus} SCOP: g.41.9.3 PDB: 3qqc_E
Probab=3.70 E-value=2.2e+02 Score=19.61 Aligned_cols=10 Identities=30% Similarity=0.401 Sum_probs=4.3
Q ss_pred eeecccccee
Q psy17970 42 AVMDPTLSEM 51 (174)
Q Consensus 42 ~V~~P~~S~~ 51 (174)
+++||.-|++
T Consensus 43 iI~dPe~S~I 52 (69)
T 1ryq_A 43 IIVDVENSEI 52 (69)
T ss_dssp EESCGGGCHH
T ss_pred EEeCCchhHH
Confidence 3444444443
No 10
>2bfd_A 2-oxoisovalerate dehydrogenase alpha subunit; oxidoreductase, multi-enzyme complex, acylation, oxidative decarboxylation, maple syrup urine disease; HET: TDP; 1.39A {Homo sapiens} SCOP: c.36.1.11 PDB: 1v16_A* 2bfc_A* 1v1r_A* 1olu_A* 2bfb_A* 1v1m_A* 2bew_A* 1dtw_A* 1olx_A* 1ols_A* 1wci_A* 1x80_A* 2beu_A* 1u5b_A* 2bev_A* 1v11_A* 1x7x_A* 1x7y_A* 1x7w_A* 1x7z_A* ...
Probab=2.91 E-value=4.8e+02 Score=21.83 Aligned_cols=12 Identities=8% Similarity=0.440 Sum_probs=7.3
Q ss_pred CCCCceeeeCcc
Q psy17970 26 PTLPEMTIMDPT 37 (174)
Q Consensus 26 P~~~~~~i~~P~ 37 (174)
+|+.+++..+|.
T Consensus 15 ~~~~~~~~~~~~ 26 (400)
T 2bfd_A 15 EFIDKLEFIQPN 26 (400)
T ss_dssp CCCSSCCCCCCC
T ss_pred ccccceeeccCc
Confidence 466666666654
Done!