Query psy4504
Match_columns 219
No_of_seqs 174 out of 721
Neff 6.3
Searched_HMMs 29240
Date Fri Aug 16 18:53:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4504.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/4504hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2xov_A Rhomboid protease GLPG; 99.6 2.8E-16 9.5E-21 129.5 8.3 132 33-179 42-180 (181)
2 2nr9_A Protein GLPG homolog; i 99.6 4.6E-17 1.6E-21 135.9 3.5 137 32-183 46-189 (196)
3 2nr9_A Protein GLPG homolog; i 85.6 0.43 1.5E-05 38.7 2.7 33 3-36 96-128 (196)
4 2xov_A Rhomboid protease GLPG; 81.3 1.8 6E-05 34.6 4.6 32 4-36 92-123 (181)
5 3p5n_A RIBU, riboflavin uptake 12.5 3.2E+02 0.011 21.3 5.2 16 197-212 119-134 (189)
6 3hd7_A Vesicle-associated memb 12.3 3.4E+02 0.012 18.8 4.7 12 183-194 61-72 (91)
7 3vmt_A Monofunctional glycosyl 10.7 87 0.003 26.7 1.2 32 177-208 24-55 (263)
8 2vpz_C Hypothetical membrane s 10.3 3.7E+02 0.013 22.0 5.1 15 192-206 51-65 (253)
9 2knc_B Integrin beta-3; transm 8.0 3.9E+02 0.013 18.2 3.6 19 156-174 6-24 (79)
10 2kog_A Vesicle-associated memb 7.7 3.2E+02 0.011 20.1 3.2 7 185-191 91-97 (119)
No 1
>2xov_A Rhomboid protease GLPG; membrane protein, hydrolase, intramembrane protease; HET: BNG; 1.65A {Escherichia coli} PDB: 2ic8_A* 2nrf_A 2xtu_A* 2irv_A* 3b45_A* 2o7l_A* 2xow_A* 3txt_A* 2xtv_A* 3b44_A*
Probab=99.64 E-value=2.8e-16 Score=129.53 Aligned_cols=132 Identities=18% Similarity=0.163 Sum_probs=89.7
Q ss_pred HHHHHHhhcccccccChhHHHH----HHHHhcccC---ccchhhhhHHHHHHHhhhhhhhhccCCccchhhhhhHHHHHH
Q psy4504 33 AHLANVLLNYNQMEFGIVRLLA----IFVVGKFNT---TSFVQVSLITFFKDFLRGSLGTSVIDSDVYLVGASGGVYALL 105 (219)
Q Consensus 33 ah~~~~~~n~~~m~~G~~rll~----iyll~~~~e---g~~~r~~li~~l~gvi~Gsl~~~~~~p~~~~vGASGaifGLl 105 (219)
.++.||+.++.++|.+..|++. ++.++...| |+ +|+..+|+.+++ .|++.+...+|+. ++||||++||++
T Consensus 42 ~~~~wrl~T~~f~H~~~~Hl~~Nm~~l~~~g~~~E~~~G~-~~fl~~yl~~~i-~~~l~~~~~~~~~-~vGaSGai~gl~ 118 (181)
T 2xov_A 42 KFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGS-GKLIVITLISAL-LSGYVQQKFSGPW-FGGLSGVVYALM 118 (181)
T ss_dssp TTCTTHHHHGGGCCCSHHHHHHHHHHHHHHHHHHHHHHCH-HHHHHHHHHHHH-HHHHHHHHHHCSC-CCCSHHHHHHHH
T ss_pred CCCCHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHhCh-HHHHHHHHHHHH-HHHHHHHHhcCCC-ceeHHHHHHHHH
Confidence 4689999999999999999998 788899999 55 788776666665 5678887776654 999999999999
Q ss_pred HHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCcchhhhhHHHHHHHHHHHHHhc
Q psy4504 106 AAHLANVLLNYNQMEFGIVRLLAIFVVASADVGFAVYNRYAGELAGAGSGYPVSYVAHLTGALAGLTIGLLVLK 179 (219)
Q Consensus 106 ga~l~~~~~~~~~~~~~~~r~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~Vs~~AHlGG~i~G~llg~~~~~ 179 (219)
++.+..-.++.+. +.+..+...... .+.+.+.+ .. . .+|+|||+||+||+++|++++..+.|
T Consensus 119 g~~~~~~~~~p~~-~~~l~~~~~~~~--~~~~~~~~---~~-~-----~~~~v~~~aHlgG~l~G~l~~~~~~~ 180 (181)
T 2xov_A 119 GYVWLRGERDPQS-GIYLQRGLIIFA--LIWIVAGW---FD-L-----FGMSMANGAHIAGLAVGLAMAFVDSL 180 (181)
T ss_dssp HHHHHHHHHCGGG-SCCCCHHHHHHH--HHHHHHHH---TT-S-----SCCSSCHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhhCcCc-eeeeHHHHHHHH--HHHHHHHH---HH-h-----ccccchHHHHHHHHHHHHHHHHHHhc
Confidence 9875322222221 111111111111 11222222 21 1 14799999999999999999977543
No 2
>2nr9_A Protein GLPG homolog; intramembrane peptidase, rhomboid protease, membrane protein; HET: PA6 PQE; 2.20A {Haemophilus influenzae} SCOP: f.51.1.1 PDB: 3odj_A
Probab=99.64 E-value=4.6e-17 Score=135.89 Aligned_cols=137 Identities=16% Similarity=0.239 Sum_probs=91.7
Q ss_pred HHHHHHHhhcccccccChhHHHH----HHHHhcccC---ccchhhhhHHHHHHHhhhhhhhhccCCccchhhhhhHHHHH
Q psy4504 32 AAHLANVLLNYNQMEFGIVRLLA----IFVVGKFNT---TSFVQVSLITFFKDFLRGSLGTSVIDSDVYLVGASGGVYAL 104 (219)
Q Consensus 32 ~ah~~~~~~n~~~m~~G~~rll~----iyll~~~~e---g~~~r~~li~~l~gvi~Gsl~~~~~~p~~~~vGASGaifGL 104 (219)
-.++.||+.++.++|.|..|++. ++.++...| |+ +|+..+|+.+++ .|++.+...+|+. ++||||++||+
T Consensus 46 ~~~~~wrl~T~~flH~~~~Hl~~Nm~~l~~~G~~lE~~~G~-~~~l~~yl~~~~-~~~l~~~~~~~~~-~vGaSGai~gl 122 (196)
T 2nr9_A 46 QDSEVWRYISHTLVHLSNLHILFNLSWFFIFGGMIERTFGS-VKLLMLYVVASA-ITGYVQNYVSGPA-FFGLSGVVYAV 122 (196)
T ss_dssp GGGCTTHHHHGGGCCSSHHHHHHHHHHHHHHHHHHHHHHCH-HHHHHHHHHHHH-HHHHHHHHHHCSC-CCCSHHHHHHH
T ss_pred ccCCcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHCh-HHHHHHHHHHHH-HHHHHHHHhcCCC-eeeHHHHHHHH
Confidence 34689999999999999999998 788999999 55 788776666665 5678888776655 99999999999
Q ss_pred HHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCcchhhhhHHHHHHHHHHHHHhcchhh
Q psy4504 105 LAAHLANVLLNYNQMEFGIVRLLAIFVVASADVGFAVYNRYAGELAGAGSGYPVSYVAHLTGALAGLTIGLLVLKNFEQ 183 (219)
Q Consensus 105 lga~l~~~~~~~~~~~~~~~r~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~Vs~~AHlGG~i~G~llg~~~~~~~~~ 183 (219)
+++++..-.++.+....+. +.... . .+.+.+.+. ... .+++|||+||+||+++|++++..+.++.++
T Consensus 123 ~g~~~~~~~~~~~~~~~~~-~~~~~-~--~~~~~~~~~---~~~-----~~~~v~~~aHlgG~l~G~l~~~~~~~~~~~ 189 (196)
T 2nr9_A 123 LGYVFIRDKLNHHLFDLPE-GFFTM-L--LVGIALGFI---SPL-----FGVEMGNAAHISGLIVGLIWGFIDSKLRKN 189 (196)
T ss_dssp HHHHHHHHHSSTTSCCCCC-SSTTT-T--TTTTTHHHH---SCS-----SCCTTCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcchhhcchH-HHHHH-H--HHHHHHHHH---Hhc-----cCCCccHHHHHHHHHHHHHHHHHHHhcccc
Confidence 9987532112211110010 01111 0 011111211 110 146999999999999999999887655443
No 3
>2nr9_A Protein GLPG homolog; intramembrane peptidase, rhomboid protease, membrane protein; HET: PA6 PQE; 2.20A {Haemophilus influenzae} SCOP: f.51.1.1 PDB: 3odj_A
Probab=85.59 E-value=0.43 Score=38.74 Aligned_cols=33 Identities=21% Similarity=0.236 Sum_probs=27.4
Q ss_pred cceeeccccccccCCccccccchHhhHHHHHHHH
Q psy4504 3 VWLRRSLGTSVIDSDVYLVGASGGVYALLAAHLA 36 (219)
Q Consensus 3 ~~~~g~l~~~~~~~~~~l~gasgg~y~~~~ah~~ 36 (219)
.+++|++++..++|+. .+||||.+|.++|+...
T Consensus 96 ~~~~~~l~~~~~~~~~-~vGaSGai~gl~g~~~~ 128 (196)
T 2nr9_A 96 ASAITGYVQNYVSGPA-FFGLSGVVYAVLGYVFI 128 (196)
T ss_dssp HHHHHHHHHHHHHCSC-CCCSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCC-eeeHHHHHHHHHHHHHH
Confidence 3567888888888876 89999999999998754
No 4
>2xov_A Rhomboid protease GLPG; membrane protein, hydrolase, intramembrane protease; HET: BNG; 1.65A {Escherichia coli} PDB: 2ic8_A* 2nrf_A 2xtu_A* 2irv_A* 3b45_A* 2o7l_A* 2xow_A* 3txt_A* 2xtv_A* 3b44_A*
Probab=81.33 E-value=1.8 Score=34.56 Aligned_cols=32 Identities=25% Similarity=0.175 Sum_probs=26.5
Q ss_pred ceeeccccccccCCccccccchHhhHHHHHHHH
Q psy4504 4 WLRRSLGTSVIDSDVYLVGASGGVYALLAAHLA 36 (219)
Q Consensus 4 ~~~g~l~~~~~~~~~~l~gasgg~y~~~~ah~~ 36 (219)
+++|++.+..++|+. .+||||.+|.++++...
T Consensus 92 ~i~~~l~~~~~~~~~-~vGaSGai~gl~g~~~~ 123 (181)
T 2xov_A 92 ALLSGYVQQKFSGPW-FGGLSGVVYALMGYVWL 123 (181)
T ss_dssp HHHHHHHHHHHHCSC-CCCSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCC-ceeHHHHHHHHHHHHHH
Confidence 467788888888775 89999999999998754
No 5
>3p5n_A RIBU, riboflavin uptake protein; transporter, alpha-helical bundle, transport protein; HET: RBF; 3.60A {Staphylococcus aureus}
Probab=12.47 E-value=3.2e+02 Score=21.28 Aligned_cols=16 Identities=25% Similarity=0.177 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHhcC
Q psy4504 197 VYVACTIFAVIYNVTS 212 (219)
Q Consensus 197 ~~~~~~~~~i~~n~~~ 212 (219)
..++..+..+..|+++
T Consensus 119 G~~~~~i~~~~~n~~~ 134 (189)
T 3p5n_A 119 ATIVMTIVLSILNYFV 134 (189)
T ss_dssp HHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3456667778888774
No 6
>3hd7_A Vesicle-associated membrane protein 2; membrane protein, coiled-coil, 4-helical bundle, cell juncti cytoplasmic vesicle, membrane, phosphoprotein; HET: GGG; 3.40A {Rattus norvegicus} PDB: 3hd9_A 3ipd_A
Probab=12.25 E-value=3.4e+02 Score=18.84 Aligned_cols=12 Identities=8% Similarity=-0.072 Sum_probs=5.2
Q ss_pred hHHHHHHHHHHH
Q psy4504 183 QKLREQLMWWIA 194 (219)
Q Consensus 183 ~~~~~~~~~~~a 194 (219)
++.|.+-.++..
T Consensus 61 rkmwwkn~K~~i 72 (91)
T 3hd7_A 61 RKYWWKNLKMMI 72 (91)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 334444444443
No 7
>3vmt_A Monofunctional glycosyltransferase; transmembrane, bacterial cell WALL SYNT membrane; HET: LHI; 2.30A {Staphylococcus aureus} PDB: 3vmr_A* 3vms_A 3vmq_A*
Probab=10.75 E-value=87 Score=26.71 Aligned_cols=32 Identities=22% Similarity=0.265 Sum_probs=13.0
Q ss_pred HhcchhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4504 177 VLKNFEQKLREQLMWWIALGVYVACTIFAVIY 208 (219)
Q Consensus 177 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~i~~ 208 (219)
+-++.++++.+|.++|+.+++.++++++....
T Consensus 24 ~~~~~kk~~~~~~~~~~~~~~l~~~~~~~~~~ 55 (263)
T 3vmt_A 24 VGKPPKKKKSKRILLKILLTILIIIALFIGIM 55 (263)
T ss_dssp -----------CCTTHHHHHHHHHHHHHHHHH
T ss_pred cCCchhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445555667777777766666555554433
No 8
>2vpz_C Hypothetical membrane spanning protein; oxidoreductase, molybdopterin guanine dinucleotide, iron-sulfur, metal-binding, molybdopterin; HET: MGD; 2.40A {Thermus thermophilus} PDB: 2vpx_C* 2vpw_C* 2vpy_C*
Probab=10.33 E-value=3.7e+02 Score=21.96 Aligned_cols=15 Identities=13% Similarity=-0.104 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHHHH
Q psy4504 192 WIALGVYVACTIFAV 206 (219)
Q Consensus 192 ~~a~~~~~~~~~~~i 206 (219)
..++..+.+..++.+
T Consensus 51 ~~a~~~~~~g~~~l~ 65 (253)
T 2vpz_C 51 LYALMLIALDLFILW 65 (253)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 444444444444443
No 9
>2knc_B Integrin beta-3; transmembrane signaling, protein structure, cell A cleavage on PAIR of basic residues, disease mutation, disul bond, glycoprotein; NMR {Homo sapiens}
Probab=8.03 E-value=3.9e+02 Score=18.21 Aligned_cols=19 Identities=5% Similarity=0.020 Sum_probs=13.3
Q ss_pred CCcchhhhhHHHHHHHHHH
Q psy4504 156 YPVSYVAHLTGALAGLTIG 174 (219)
Q Consensus 156 ~~Vs~~AHlGG~i~G~llg 174 (219)
+.++..+=++|.++|+++.
T Consensus 6 ~~~n~~~Iv~gvi~gilli 24 (79)
T 2knc_B 6 KGPDILVVLLSVMGAILLI 24 (79)
T ss_dssp SSSCSHHHHHHHHHHHHHH
T ss_pred CCCCchhhHHHHHHHHHHH
Confidence 4567777778888886643
No 10
>2kog_A Vesicle-associated membrane protein 2; synaptobrevin, VAMP2, DPC micelle, snare, coiled coil, membrane fusion, transmembrane; NMR {Rattus norvegicus}
Probab=7.68 E-value=3.2e+02 Score=20.06 Aligned_cols=7 Identities=0% Similarity=-0.381 Sum_probs=2.6
Q ss_pred HHHHHHH
Q psy4504 185 LREQLMW 191 (219)
Q Consensus 185 ~~~~~~~ 191 (219)
.|.+-.+
T Consensus 91 mwwkn~K 97 (119)
T 2kog_A 91 YWWKNLK 97 (119)
T ss_dssp HSCHHHH
T ss_pred HHHHHHH
Confidence 3333333
Done!