Query psy6537
Match_columns 66
No_of_seqs 163 out of 1286
Neff 7.4
Searched_HMMs 46136
Date Fri Aug 16 20:33:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6537.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6537hhsearch_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 1.2E-14 2.5E-19 70.7 3.2 36 28-64 2-37 (37)
2 cd00112 LDLa Low Density Lipop 99.5 2.3E-14 5E-19 68.8 2.6 35 29-64 1-35 (35)
3 smart00192 LDLa Low-density li 99.2 6.6E-12 1.4E-16 59.4 2.9 32 29-61 2-33 (33)
4 PF12999 PRKCSH-like: Glucosid 97.3 0.00029 6.3E-09 44.5 3.2 36 26-61 69-110 (176)
5 KOG1215|consensus 97.2 0.00061 1.3E-08 50.7 4.2 38 27-65 136-175 (877)
6 PF12999 PRKCSH-like: Glucosid 96.6 0.0015 3.3E-08 41.2 2.1 33 30-62 34-67 (176)
7 KOG1215|consensus 95.9 0.0091 2E-07 44.6 3.2 40 25-65 256-295 (877)
8 KOG2397|consensus 92.2 0.14 3E-06 36.8 2.7 37 26-62 75-114 (480)
9 KOG2397|consensus 66.3 3.8 8.2E-05 29.7 1.4 31 32-62 43-73 (480)
10 KOG3509|consensus 57.7 8.9 0.00019 30.1 2.2 40 25-64 71-110 (964)
11 KOG3509|consensus 35.5 28 0.0006 27.6 1.8 39 25-64 28-66 (964)
12 PF11049 KSHV_K1: Glycoprotein 23.6 49 0.0011 18.0 1.0 18 34-52 3-20 (71)
13 PF08091 Toxin_21: Spider inse 22.5 55 0.0012 15.7 1.0 10 40-50 17-26 (39)
14 smart00193 PTN Pleiotrophin / 21.1 80 0.0017 17.5 1.6 12 53-64 14-25 (80)
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=99.52 E-value=1.2e-14 Score=70.73 Aligned_cols=36 Identities=50% Similarity=1.022 Sum_probs=33.9
Q ss_pred CCCCCceeeCCCCceecCCcCCCCCCCCCCCCCCCCC
Q psy6537 28 SCAWSEFSCHDRLQCVPLSARCNGVSDCRDYSDEVNC 64 (66)
Q Consensus 28 ~C~~~~f~C~~~g~Ci~~~~~CDg~~dC~dgsDE~~C 64 (66)
.|+.++|+|.+ +.||+..|+|||+.||.|||||.+|
T Consensus 2 ~C~~~~f~C~~-~~CI~~~~~CDg~~DC~dgsDE~~C 37 (37)
T PF00057_consen 2 TCPPGEFRCGN-GQCIPKSWVCDGIPDCPDGSDEQNC 37 (37)
T ss_dssp SSSTTEEEETT-SSEEEGGGTTSSSCSSSSSTTTSSH
T ss_pred cCcCCeeEcCC-CCEEChHHcCCCCCCCCCCcccccC
Confidence 58899999999 8899999999999999999999876
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=99.48 E-value=2.3e-14 Score=68.84 Aligned_cols=35 Identities=49% Similarity=0.985 Sum_probs=32.8
Q ss_pred CCCCceeeCCCCceecCCcCCCCCCCCCCCCCCCCC
Q psy6537 29 CAWSEFSCHDRLQCVPLSARCNGVSDCRDYSDEVNC 64 (66)
Q Consensus 29 C~~~~f~C~~~g~Ci~~~~~CDg~~dC~dgsDE~~C 64 (66)
|+..+|+|.+ ++||+..++|||+.||.|+|||.+|
T Consensus 1 C~~~~f~C~~-~~Ci~~~~~CDg~~DC~dgsDE~~C 35 (35)
T cd00112 1 CPPNEFRCAN-GRCIPSSWVCDGEDDCGDGSDEENC 35 (35)
T ss_pred CCCCeEEcCC-CCeeCHHHcCCCccCCCCCcccccC
Confidence 5678999999 9999999999999999999999876
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=99.25 E-value=6.6e-12 Score=59.44 Aligned_cols=32 Identities=53% Similarity=1.076 Sum_probs=29.7
Q ss_pred CCCCceeeCCCCceecCCcCCCCCCCCCCCCCC
Q psy6537 29 CAWSEFSCHDRLQCVPLSARCNGVSDCRDYSDE 61 (66)
Q Consensus 29 C~~~~f~C~~~g~Ci~~~~~CDg~~dC~dgsDE 61 (66)
|+..+|+|.+ +.||+..++|||+.||.|+|||
T Consensus 2 C~~~~f~C~~-~~Ci~~~~~Cdg~~dC~dgsDE 33 (33)
T smart00192 2 CPPGEFQCDN-GRCIPLSWVCDGVDDCSDGSDE 33 (33)
T ss_pred CCCCeEECCC-CCEECchhhCCCcCcCcCCCCC
Confidence 6667999998 8999999999999999999998
No 4
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=97.29 E-value=0.00029 Score=44.46 Aligned_cols=36 Identities=36% Similarity=0.697 Sum_probs=32.0
Q ss_pred CCCCCCCceeeCCCC---ceecCCcCCCCCCC---CCCCCCC
Q psy6537 26 TVSCAWSEFSCHDRL---QCVPLSARCNGVSD---CRDYSDE 61 (66)
Q Consensus 26 ~~~C~~~~f~C~~~g---~Ci~~~~~CDg~~d---C~dgsDE 61 (66)
...|+.+.|.|.|.| .-|+..++-||+=| |-|||||
T Consensus 69 TsAC~~~~FyC~N~g~~p~~i~~s~VnDGICDy~~CCDGSDE 110 (176)
T PF12999_consen 69 TSACSNGKFYCENKGHIPRYIPSSRVNDGICDYDICCDGSDE 110 (176)
T ss_pred cccCcCceEeeccCCCCCceeehhhhcCCcCcccccCCCCCC
Confidence 356888899999965 68999999999999 9999999
No 5
>KOG1215|consensus
Probab=97.16 E-value=0.00061 Score=50.74 Aligned_cols=38 Identities=42% Similarity=0.962 Sum_probs=33.8
Q ss_pred CCCCCCceeeC--CCCceecCCcCCCCCCCCCCCCCCCCCC
Q psy6537 27 VSCAWSEFSCH--DRLQCVPLSARCNGVSDCRDYSDEVNCG 65 (66)
Q Consensus 27 ~~C~~~~f~C~--~~g~Ci~~~~~CDg~~dC~dgsDE~~C~ 65 (66)
..|....|+|. + .+||+..|+||+..+|.||+||.+|.
T Consensus 136 ~~~~~~~~~c~~~~-~~Cip~~~~cd~~~~C~dg~de~~~~ 175 (877)
T KOG1215|consen 136 SHCCLDKFSCRTGS-CKCIPGDWLCDGEADCPDGSDELNCA 175 (877)
T ss_pred ccccCCCCCCcCcc-ccCCCCceeCCCCCccccchhhhccc
Confidence 55677899998 6 89999999999999999999998873
No 6
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=96.59 E-value=0.0015 Score=41.23 Aligned_cols=33 Identities=33% Similarity=0.552 Sum_probs=27.7
Q ss_pred CCCceeeCCCCce-ecCCcCCCCCCCCCCCCCCC
Q psy6537 30 AWSEFSCHDRLQC-VPLSARCNGVSDCRDYSDEV 62 (66)
Q Consensus 30 ~~~~f~C~~~g~C-i~~~~~CDg~~dC~dgsDE~ 62 (66)
..+.|.|.++..= |+..++.|+.=||+|||||-
T Consensus 34 ~~~~f~Cl~~~~~~I~~~~iNDdyCDC~DGSDEP 67 (176)
T PF12999_consen 34 ENGKFTCLDGSKIVIPFSQINDDYCDCPDGSDEP 67 (176)
T ss_pred CCCceEecCCCCceecHHHccCcceeCCCCCCcc
Confidence 3457999984344 89999999999999999996
No 7
>KOG1215|consensus
Probab=95.87 E-value=0.0091 Score=44.63 Aligned_cols=40 Identities=33% Similarity=0.632 Sum_probs=34.8
Q ss_pred CCCCCCCCceeeCCCCceecCCcCCCCCCCCCCCCCCCCCC
Q psy6537 25 PTVSCAWSEFSCHDRLQCVPLSARCNGVSDCRDYSDEVNCG 65 (66)
Q Consensus 25 ~~~~C~~~~f~C~~~g~Ci~~~~~CDg~~dC~dgsDE~~C~ 65 (66)
....|...+|.|.+ +.|++..++|+|..||++|+||..|.
T Consensus 256 ~~~~~~~~e~~~~~-~~~~~~~~~~~g~~d~pdg~de~~~~ 295 (877)
T KOG1215|consen 256 SDATCEAPEIECAD-GDCSDRQKLCDGDLDCPDGLDEDYCK 295 (877)
T ss_pred eccccCCcceeecC-CCCccceEEecCccCCCCcccccccc
Confidence 34567777999988 99999999999999999999998775
No 8
>KOG2397|consensus
Probab=92.24 E-value=0.14 Score=36.80 Aligned_cols=37 Identities=35% Similarity=0.629 Sum_probs=32.5
Q ss_pred CCCCCCCceeeCCCC---ceecCCcCCCCCCCCCCCCCCC
Q psy6537 26 TVSCAWSEFSCHDRL---QCVPLSARCNGVSDCRDYSDEV 62 (66)
Q Consensus 26 ~~~C~~~~f~C~~~g---~Ci~~~~~CDg~~dC~dgsDE~ 62 (66)
...|+.+.|.|.|.| .-|+...+=||+=||-|||||.
T Consensus 75 tsACpngkF~C~N~G~~p~~i~ssrV~DGICDCCDgSDE~ 114 (480)
T KOG2397|consen 75 TSACPNGKFYCVNQGHQPKYIPSSRVNDGICDCCDGSDEY 114 (480)
T ss_pred cccCCCCceeeeecCCCceeeechhccCcccccccCCCCc
Confidence 457999999998865 5888999999999999999996
No 9
>KOG2397|consensus
Probab=66.31 E-value=3.8 Score=29.74 Aligned_cols=31 Identities=35% Similarity=0.515 Sum_probs=26.8
Q ss_pred CceeeCCCCceecCCcCCCCCCCCCCCCCCC
Q psy6537 32 SEFSCHDRLQCVPLSARCNGVSDCRDYSDEV 62 (66)
Q Consensus 32 ~~f~C~~~g~Ci~~~~~CDg~~dC~dgsDE~ 62 (66)
..|.|.+...-|+...+-|..-||.|||||-
T Consensus 43 ~~~~CLdgs~~i~f~qlNDd~CDC~DGsDEP 73 (480)
T KOG2397|consen 43 SMFKCLDGSKTISFSQLNDDSCDCLDGSDEP 73 (480)
T ss_pred cceeeccCCcccCHHHhccccccCCCCCCCC
Confidence 3789998557888889999999999999994
No 10
>KOG3509|consensus
Probab=57.72 E-value=8.9 Score=30.14 Aligned_cols=40 Identities=48% Similarity=0.999 Sum_probs=32.6
Q ss_pred CCCCCCCCceeeCCCCceecCCcCCCCCCCCCCCCCCCCC
Q psy6537 25 PTVSCAWSEFSCHDRLQCVPLSARCNGVSDCRDYSDEVNC 64 (66)
Q Consensus 25 ~~~~C~~~~f~C~~~g~Ci~~~~~CDg~~dC~dgsDE~~C 64 (66)
.+..|.+..+.|++.-++..+...|+|..+|.++++|..+
T Consensus 71 ~~s~~~~~~~~c~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 110 (964)
T KOG3509|consen 71 SASDCKPTETQCRDRLRCNPQSFQCDGTNDCKDGSDEVGC 110 (964)
T ss_pred cccccCCcccccccchhcCCccccccCCCCCCccchhccc
Confidence 3456777788898844788889999999999999999754
No 11
>KOG3509|consensus
Probab=35.51 E-value=28 Score=27.59 Aligned_cols=39 Identities=28% Similarity=0.548 Sum_probs=33.3
Q ss_pred CCCCCCCCceeeCCCCceecCCcCCCCCCCCCCCCCCCCC
Q psy6537 25 PTVSCAWSEFSCHDRLQCVPLSARCNGVSDCRDYSDEVNC 64 (66)
Q Consensus 25 ~~~~C~~~~f~C~~~g~Ci~~~~~CDg~~dC~dgsDE~~C 64 (66)
....+.+++|.|.+ +++.-..+.||.+.++.+++...+|
T Consensus 28 ~~~~~~p~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 66 (964)
T KOG3509|consen 28 IGSACSPNEFKCNN-PRCVQPEALLDADSTCGPNSTPSGC 66 (964)
T ss_pred ccccCCcchhccCC-ccccCchhhhccccccCCCCCcCCc
Confidence 34567888999988 9999999999999999999877665
No 12
>PF11049 KSHV_K1: Glycoprotein K1 of Kaposi's sarcoma-associated herpes virus; InterPro: IPR021022 This is a highly glycosylated cytoplasmic and membrane protein similar to the immunoglobulin receptor family that is expressed as an inducible early-lytic-cycle gene product in primary effusion lymphoma cell-lines. This domain would appear to be the cytoplasmic region of the protein [].
Probab=23.57 E-value=49 Score=17.98 Aligned_cols=18 Identities=33% Similarity=0.781 Sum_probs=10.5
Q ss_pred eeeCCCCceecCCcCCCCC
Q psy6537 34 FSCHDRLQCVPLSARCNGV 52 (66)
Q Consensus 34 f~C~~~g~Ci~~~~~CDg~ 52 (66)
+.|.+ ..-+|.+|.|+|.
T Consensus 3 ltC~s-~~sLPiswYcN~T 20 (71)
T PF11049_consen 3 LTCPS-NASLPISWYCNGT 20 (71)
T ss_pred eecCC-CCCCcccEEECCc
Confidence 34544 4566667777654
No 13
>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=22.46 E-value=55 Score=15.70 Aligned_cols=10 Identities=20% Similarity=0.235 Sum_probs=4.5
Q ss_pred CceecCCcCCC
Q psy6537 40 LQCVPLSARCN 50 (66)
Q Consensus 40 g~Ci~~~~~CD 50 (66)
|.|.. -|.|-
T Consensus 17 g~C~~-fWtC~ 26 (39)
T PF08091_consen 17 GNCGY-FWTCQ 26 (39)
T ss_pred CCccc-eEEEE
Confidence 44544 34443
No 14
>smart00193 PTN Pleiotrophin / midkine family. Heparin-binding domain family.
Probab=21.09 E-value=80 Score=17.49 Aligned_cols=12 Identities=33% Similarity=0.578 Sum_probs=5.5
Q ss_pred CCCCCCCCCCCC
Q psy6537 53 SDCRDYSDEVNC 64 (66)
Q Consensus 53 ~dC~dgsDE~~C 64 (66)
.||..|..|..|
T Consensus 14 gDCG~G~REgTC 25 (80)
T smart00193 14 KDCGLGTREGTC 25 (80)
T ss_pred CcccCcccccch
Confidence 344555544433
Done!