Query psy5508
Match_columns 85
No_of_seqs 175 out of 1244
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 19:16:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5508.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5508hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00057 Ldl_recept_a: Low-den 99.5 2.2E-14 4.8E-19 76.6 3.6 37 25-62 1-37 (37)
2 cd00112 LDLa Low Density Lipop 99.5 4.1E-14 8.9E-19 74.6 2.7 35 27-62 1-35 (35)
3 smart00192 LDLa Low-density li 99.3 3E-12 6.6E-17 66.5 3.0 32 27-58 2-33 (33)
4 KOG1215|consensus 96.6 0.0011 2.3E-08 54.7 1.8 38 25-63 136-175 (877)
5 PF12999 PRKCSH-like: Glucosid 96.5 0.0025 5.5E-08 44.4 2.9 35 25-59 70-111 (176)
6 PF12999 PRKCSH-like: Glucosid 96.3 0.0025 5.4E-08 44.4 2.1 32 28-59 34-67 (176)
7 KOG1215|consensus 94.2 0.04 8.6E-07 45.5 2.8 39 25-64 258-296 (877)
8 KOG2397|consensus 87.1 0.47 1E-05 37.7 2.2 35 25-59 76-114 (480)
9 KOG3509|consensus 61.6 8.4 0.00018 33.3 2.9 39 22-60 70-109 (964)
10 KOG2397|consensus 61.3 5.1 0.00011 32.0 1.5 33 31-63 44-79 (480)
11 KOG3509|consensus 54.9 11 0.00023 32.7 2.5 39 25-64 30-68 (964)
12 PF08091 Toxin_21: Spider inse 24.2 41 0.00089 17.8 0.8 17 39-55 1-17 (39)
13 PF08099 Toxin_27: Scorpion ca 21.2 47 0.001 16.9 0.6 17 37-53 1-17 (33)
No 1
>PF00057 Ldl_recept_a: Low-density lipoprotein receptor domain class A This prints entry is specific to LDL receptor; InterPro: IPR002172 The low-density lipoprotein receptor (LDLR) is the major cholesterol-carrying lipoprotein of plasma, acting to regulate cholesterol homeostasis in mammalian cells. The LDL receptor binds LDL and transports it into cells by acidic endocytosis. In order to be internalized, the receptor-ligand complex must first cluster into clathrin-coated pits. Once inside the cell, the LDLR separates from its ligand, which is degraded in the lysosomes, while the receptor returns to the cell surface []. The internal dissociation of the LDLR with its ligand is mediated by proton pumps within the walls of the endosome that lower the pH. The LDLR is a multi-domain protein, containing: The ligand-binding domain contains seven or eight 40-amino acid LDLR class A (cysteine-rich) repeats, each of which contains a coordinated calcium ion and six cysteine residues involved in disulphide bond formation []. Similar domains have been found in other extracellular and membrane proteins []. The second conserved region contains two EGF repeats, followed by six LDLR class B (YWTD) repeats, and another EGF repeat. The LDLR class B repeats each contain a conserved YWTD motif, and is predicted to form a beta-propeller structure []. This region is critical for ligand release and recycling of the receptor []. The third domain is rich in serine and threonine residues and contains clustered O-linked carbohydrate chains. The fourth domain is the hydrophobic transmembrane region. The fifth domain is the cytoplasmic tail that directs the receptor to clathrin-coated pits. LDLR is closely related in structure to several other receptors, including LRP1, LRP1b, megalin/LRP2, VLDL receptor, lipoprotein receptor, MEGF7/LRP4, and LRP8/apolipoprotein E receptor2); these proteins participate in a wide range of physiological processes, including the regulation of lipid metabolism, protection against atherosclerosis, neurodevelopment, and transport of nutrients and vitamins []. This entry represents the LDLR class A (cyateine-rich) repeat, which contains 6 disulphide-bound cysteines and a highly conserved cluster of negatively charged amino acids, of which many are clustered on one face of the module []. In LDL receptors, the class A domains form the binding site for LDL and calcium. The acidic residues between the fourth and sixth cysteines are important for high-affinity binding of positively charged sequences in LDLR's ligands. The repeat consists of a beta-hairpin structure followed by a series of beta turns. In the absence of calcium, LDL-A domains are unstructured; the bound calcium ion imparts structural integrity. Following these repeats is a 350 residue domain that resembles part of the epidermal growth factor (EGF) precursor. Numerous familial hypercholestorolemia mutations of the LDL receptor alter the calcium coordinating residue of LDL-A domains or other crucial scaffolding residues. ; GO: 0005515 protein binding; PDB: 2I1P_A 3OJY_A 4E0S_B 3T5O_A 4A5W_B 1JRF_A 1K7B_A 1V9U_5 3DPR_E 2KNY_A ....
Probab=99.50 E-value=2.2e-14 Score=76.59 Aligned_cols=37 Identities=41% Similarity=0.924 Sum_probs=34.3
Q ss_pred CCCCCCeEeecCCceeccCcccCCcCCCCCCCCCCCCC
Q psy5508 25 HQCRISEYACENGRCISLDRFCNEYDDCGDKSDEPRYC 62 (85)
Q Consensus 25 ~~C~~~~f~C~~g~Ci~~~~~CDg~~DC~DgSDE~~~C 62 (85)
+.|+..+|+|.++.||+..++|||+.||.|||||.+ |
T Consensus 1 ~~C~~~~f~C~~~~CI~~~~~CDg~~DC~dgsDE~~-C 37 (37)
T PF00057_consen 1 PTCPPGEFRCGNGQCIPKSWVCDGIPDCPDGSDEQN-C 37 (37)
T ss_dssp SSSSTTEEEETTSSEEEGGGTTSSSCSSSSSTTTSS-H
T ss_pred CcCcCCeeEcCCCCEEChHHcCCCCCCCCCCccccc-C
Confidence 368999999999999999999999999999999975 5
No 2
>cd00112 LDLa Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure
Probab=99.46 E-value=4.1e-14 Score=74.58 Aligned_cols=35 Identities=51% Similarity=1.137 Sum_probs=32.6
Q ss_pred CCCCeEeecCCceeccCcccCCcCCCCCCCCCCCCC
Q psy5508 27 CRISEYACENGRCISLDRFCNEYDDCGDKSDEPRYC 62 (85)
Q Consensus 27 C~~~~f~C~~g~Ci~~~~~CDg~~DC~DgSDE~~~C 62 (85)
|++.+|+|.+++||+..++|||+.||.|||||.+ |
T Consensus 1 C~~~~f~C~~~~Ci~~~~~CDg~~DC~dgsDE~~-C 35 (35)
T cd00112 1 CPPNEFRCANGRCIPSSWVCDGEDDCGDGSDEEN-C 35 (35)
T ss_pred CCCCeEEcCCCCeeCHHHcCCCccCCCCCccccc-C
Confidence 6678999999999999999999999999999975 5
No 3
>smart00192 LDLa Low-density lipoprotein receptor domain class A. Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia.
Probab=99.28 E-value=3e-12 Score=66.50 Aligned_cols=32 Identities=53% Similarity=1.168 Sum_probs=30.3
Q ss_pred CCCCeEeecCCceeccCcccCCcCCCCCCCCC
Q psy5508 27 CRISEYACENGRCISLDRFCNEYDDCGDKSDE 58 (85)
Q Consensus 27 C~~~~f~C~~g~Ci~~~~~CDg~~DC~DgSDE 58 (85)
|+..+|+|.++.||+..++|||+.||.|||||
T Consensus 2 C~~~~f~C~~~~Ci~~~~~Cdg~~dC~dgsDE 33 (33)
T smart00192 2 CPPGEFQCDNGRCIPLSWVCDGVDDCSDGSDE 33 (33)
T ss_pred CCCCeEECCCCCEECchhhCCCcCcCcCCCCC
Confidence 66679999999999999999999999999998
No 4
>KOG1215|consensus
Probab=96.61 E-value=0.0011 Score=54.65 Aligned_cols=38 Identities=34% Similarity=0.879 Sum_probs=33.6
Q ss_pred CCCCCCeEeec--CCceeccCcccCCcCCCCCCCCCCCCCC
Q psy5508 25 HQCRISEYACE--NGRCISLDRFCNEYDDCGDKSDEPRYCS 63 (85)
Q Consensus 25 ~~C~~~~f~C~--~g~Ci~~~~~CDg~~DC~DgSDE~~~C~ 63 (85)
..|...+|+|. +++|++..|+||+..+|.||+||.. |.
T Consensus 136 ~~~~~~~~~c~~~~~~Cip~~~~cd~~~~C~dg~de~~-~~ 175 (877)
T KOG1215|consen 136 SHCCLDKFSCRTGSCKCIPGDWLCDGEADCPDGSDELN-CA 175 (877)
T ss_pred ccccCCCCCCcCccccCCCCceeCCCCCccccchhhhc-cc
Confidence 45666789998 7899999999999999999999986 76
No 5
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=96.50 E-value=0.0025 Score=44.37 Aligned_cols=35 Identities=37% Similarity=0.635 Sum_probs=31.0
Q ss_pred CCCCCCeEeecCC----ceeccCcccCCcCC---CCCCCCCC
Q psy5508 25 HQCRISEYACENG----RCISLDRFCNEYDD---CGDKSDEP 59 (85)
Q Consensus 25 ~~C~~~~f~C~~g----~Ci~~~~~CDg~~D---C~DgSDE~ 59 (85)
+.|+.+.|.|.|. .-|+.+++=||+=| |-|||||.
T Consensus 70 sAC~~~~FyC~N~g~~p~~i~~s~VnDGICDy~~CCDGSDE~ 111 (176)
T PF12999_consen 70 SACSNGKFYCENKGHIPRYIPSSRVNDGICDYDICCDGSDES 111 (176)
T ss_pred ccCcCceEeeccCCCCCceeehhhhcCCcCcccccCCCCCCC
Confidence 4688889999884 58999999999999 99999994
No 6
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=96.35 E-value=0.0025 Score=44.43 Aligned_cols=32 Identities=34% Similarity=0.776 Sum_probs=27.9
Q ss_pred CCCeEeecCCc-e-eccCcccCCcCCCCCCCCCC
Q psy5508 28 RISEYACENGR-C-ISLDRFCNEYDDCGDKSDEP 59 (85)
Q Consensus 28 ~~~~f~C~~g~-C-i~~~~~CDg~~DC~DgSDE~ 59 (85)
..+.|.|-+|. = |+.+++.|+.=||.|||||.
T Consensus 34 ~~~~f~Cl~~~~~~I~~~~iNDdyCDC~DGSDEP 67 (176)
T PF12999_consen 34 ENGKFTCLDGSKIVIPFSQINDDYCDCPDGSDEP 67 (176)
T ss_pred CCCceEecCCCCceecHHHccCcceeCCCCCCcc
Confidence 44679998874 4 89999999999999999996
No 7
>KOG1215|consensus
Probab=94.18 E-value=0.04 Score=45.52 Aligned_cols=39 Identities=31% Similarity=0.765 Sum_probs=34.2
Q ss_pred CCCCCCeEeecCCceeccCcccCCcCCCCCCCCCCCCCCC
Q psy5508 25 HQCRISEYACENGRCISLDRFCNEYDDCGDKSDEPRYCSR 64 (85)
Q Consensus 25 ~~C~~~~f~C~~g~Ci~~~~~CDg~~DC~DgSDE~~~C~~ 64 (85)
..|...++.|.++.|++....|||..||.||+||.. |..
T Consensus 258 ~~~~~~e~~~~~~~~~~~~~~~~g~~d~pdg~de~~-~~~ 296 (877)
T KOG1215|consen 258 ATCEAPEIECADGDCSDRQKLCDGDLDCPDGLDEDY-CKK 296 (877)
T ss_pred cccCCcceeecCCCCccceEEecCccCCCCcccccc-ccc
Confidence 456677999999999999999999999999999974 763
No 8
>KOG2397|consensus
Probab=87.11 E-value=0.47 Score=37.68 Aligned_cols=35 Identities=31% Similarity=0.525 Sum_probs=30.6
Q ss_pred CCCCCCeEeecCC----ceeccCcccCCcCCCCCCCCCC
Q psy5508 25 HQCRISEYACENG----RCISLDRFCNEYDDCGDKSDEP 59 (85)
Q Consensus 25 ~~C~~~~f~C~~g----~Ci~~~~~CDg~~DC~DgSDE~ 59 (85)
..|+.+.|+|.|. .-|+.+.+=||+=||-|||||.
T Consensus 76 sACpngkF~C~N~G~~p~~i~ssrV~DGICDCCDgSDE~ 114 (480)
T KOG2397|consen 76 SACPNGKFYCVNQGHQPKYIPSSRVNDGICDCCDGSDEY 114 (480)
T ss_pred ccCCCCceeeeecCCCceeeechhccCcccccccCCCCc
Confidence 3588889999873 4889999999999999999996
No 9
>KOG3509|consensus
Probab=61.63 E-value=8.4 Score=33.27 Aligned_cols=39 Identities=31% Similarity=0.616 Sum_probs=33.3
Q ss_pred cCCCCCCCCeEeecCC-ceeccCcccCCcCCCCCCCCCCC
Q psy5508 22 LQHHQCRISEYACENG-RCISLDRFCNEYDDCGDKSDEPR 60 (85)
Q Consensus 22 ~~~~~C~~~~f~C~~g-~Ci~~~~~CDg~~DC~DgSDE~~ 60 (85)
.++..|.+.++.|.+- ++...+..|+|.+||.|+++|..
T Consensus 70 ~~~s~~~~~~~~c~~~~~~~~~~~~~~g~~~~~~~~~~~~ 109 (964)
T KOG3509|consen 70 PSASDCKPTETQCRDRLRCNPQSFQCDGTNDCKDGSDEVG 109 (964)
T ss_pred ccccccCCcccccccchhcCCccccccCCCCCCccchhcc
Confidence 3445677788999887 79999999999999999999974
No 10
>KOG2397|consensus
Probab=61.26 E-value=5.1 Score=31.98 Aligned_cols=33 Identities=36% Similarity=0.756 Sum_probs=28.0
Q ss_pred eEeecCC-ceeccCcccCCcCCCCCCCCCCC--CCC
Q psy5508 31 EYACENG-RCISLDRFCNEYDDCGDKSDEPR--YCS 63 (85)
Q Consensus 31 ~f~C~~g-~Ci~~~~~CDg~~DC~DgSDE~~--~C~ 63 (85)
.|.|.+| +=|+..++=|+.-||.|||||.. .|+
T Consensus 44 ~~~CLdgs~~i~f~qlNDd~CDC~DGsDEPGtsACp 79 (480)
T KOG2397|consen 44 MFKCLDGSKTISFSQLNDDSCDCLDGSDEPGTSACP 79 (480)
T ss_pred ceeeccCCcccCHHHhccccccCCCCCCCCccccCC
Confidence 5999987 68899999999999999999963 265
No 11
>KOG3509|consensus
Probab=54.94 E-value=11 Score=32.69 Aligned_cols=39 Identities=26% Similarity=0.709 Sum_probs=34.5
Q ss_pred CCCCCCeEeecCCceeccCcccCCcCCCCCCCCCCCCCCC
Q psy5508 25 HQCRISEYACENGRCISLDRFCNEYDDCGDKSDEPRYCSR 64 (85)
Q Consensus 25 ~~C~~~~f~C~~g~Ci~~~~~CDg~~DC~DgSDE~~~C~~ 64 (85)
+.+++.+++|.++++.-..+.||.+.++++++++.+ |..
T Consensus 30 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 68 (964)
T KOG3509|consen 30 SACSPNEFKCNNPRCVQPEALLDADSTCGPNSTPSG-CNA 68 (964)
T ss_pred ccCCcchhccCCccccCchhhhccccccCCCCCcCC-ccc
Confidence 568889999999999999999999999999997765 653
No 12
>PF08091 Toxin_21: Spider insecticidal peptide; InterPro: IPR012626 This family consists of insecticidal peptides isolated from venom of spiders of Aptostichus schlingeri (Trap-door spider) and Calisoga sp. Nine insecticidal peptides were isolated from the venom of the A. schlinger spider and seven of these toxins cause flaccid paralysis to insect larvae within 10 min of injection. However, all nine peptides were lethal within 24 hours [].; GO: 0009405 pathogenesis, 0005576 extracellular region
Probab=24.24 E-value=41 Score=17.83 Aligned_cols=17 Identities=35% Similarity=0.690 Sum_probs=9.7
Q ss_pred eeccCcccCCcCCCCCC
Q psy5508 39 CISLDRFCNEYDDCGDK 55 (85)
Q Consensus 39 Ci~~~~~CDg~~DC~Dg 55 (85)
|+++.+-|....||-+|
T Consensus 1 C~s~~~PC~ns~dCC~g 17 (39)
T PF08091_consen 1 CISKRYPCSNSKDCCSG 17 (39)
T ss_pred CccccccCCCchhhccC
Confidence 45556666655565544
No 13
>PF08099 Toxin_27: Scorpion calcine family; InterPro: IPR012632 Toxins of the scorpion calcine family bind directly to ryanodine receptors (RyRs), intracellular channel targets of the endoplasmic reticulum, and induce long lasting channel openings in a mode of smaller conductance. They have the ability to translocate into cells by crossing the plasma membrane [, , ]. Toxins of scorpion calcine family are highly basic 33-amino acid peptides that present three disulphide bridges (C1-C4, C2-C5, and C3-C6) and fold along a knottin or inhibitor cystine knot motif (http://knottin.cbs.cnrs.fr) [, , ]. Their three dimensional structure consists of a compact disulphide-bonded core from which emerge loops and the N terminus. The main element of regular secondary structure is a double-stranded antiparallel beta-sheet. A third peripheral extended strand is almost perpendicular to the double-stranded antiparallel beta-sheet [, ]. Scorpion calcine mimic the activating segment of the dihydropyridine receptor II-III loop, which interacts with a region of the ryanodine receptor [, , ]. This family includes: Imperatoxin-A (IpTx A) from Pandinus imperator (Emperor scorpion). Opicalcin-1 and -2 from Opistophthalmus carinatus (African yellow leg scorpion). Maurocalcin (MCa) from Scorpio maurus palmatus (Chactoid scorpion). ; GO: 0019855 calcium channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1IE6_A.
Probab=21.19 E-value=47 Score=16.85 Aligned_cols=17 Identities=35% Similarity=0.858 Sum_probs=10.1
Q ss_pred CceeccCcccCCcCCCC
Q psy5508 37 GRCISLDRFCNEYDDCG 53 (85)
Q Consensus 37 g~Ci~~~~~CDg~~DC~ 53 (85)
|.|++...+|-...||-
T Consensus 1 gdclphlkrcken~dcc 17 (33)
T PF08099_consen 1 GDCLPHLKRCKENKDCC 17 (33)
T ss_dssp ---B-TTSB-SSGGGBS
T ss_pred CcchHHHHHHHhccchH
Confidence 46888889998888885
Done!