Query psy12307
Match_columns 106
No_of_seqs 52 out of 54
Neff 3.0
Searched_HMMs 46136
Date Fri Aug 16 15:42:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12307.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12307hhsearch_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 98.5 3.4E-08 7.3E-13 58.4 1.6 31 18-54 5-35 (37)
2 cd00112 LDLa Low Density Lipop 98.5 3.8E-08 8.3E-13 57.1 1.5 31 19-55 4-34 (35)
3 smart00192 LDLa Low-density li 98.3 4.4E-07 9.6E-12 51.8 2.5 28 20-53 6-33 (33)
4 PF12999 PRKCSH-like: Glucosid 97.8 1.8E-05 4E-10 61.0 3.9 40 28-67 34-84 (176)
5 PF15494 SRCR_2: Scavenger rec 96.3 0.002 4.4E-08 43.4 1.5 25 65-90 3-28 (98)
6 PF12999 PRKCSH-like: Glucosid 92.1 0.17 3.6E-06 39.3 3.3 45 7-58 56-115 (176)
7 KOG2397|consensus 91.1 0.25 5.5E-06 43.6 3.7 48 26-73 39-96 (480)
8 KOG1215|consensus 89.9 0.17 3.7E-06 45.0 1.6 34 19-56 141-174 (877)
9 KOG1215|consensus 81.5 0.93 2E-05 40.4 1.9 30 33-62 271-300 (877)
10 KOG2397|consensus 66.4 5.9 0.00013 35.3 3.0 46 6-55 61-115 (480)
11 PF04495 GRASP55_65: GRASP55/6 28.1 71 0.0015 23.4 2.9 35 68-102 1-38 (138)
12 PF07771 TSGP1: Tick salivary 22.0 82 0.0018 22.9 2.3 21 45-65 22-46 (120)
13 smart00202 SR Scavenger recept 21.7 64 0.0014 21.0 1.5 20 67-89 13-33 (101)
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=98.54 E-value=3.4e-08 Score=58.36 Aligned_cols=31 Identities=45% Similarity=1.046 Sum_probs=27.3
Q ss_pred CceecCCCCCCCCceeecCCCcccCCCCCCCCCCCCc
Q psy12307 18 MERFACPTPDHMGRYRCIDDHVLCDGFIDCPTGEDED 54 (106)
Q Consensus 18 ~de~~Cptpd~~gR~~CI~~~~LCDG~~DCpdGeDE~ 54 (106)
..+|.|.. +. ||...++|||+.||++||||.
T Consensus 5 ~~~f~C~~----~~--CI~~~~~CDg~~DC~dgsDE~ 35 (37)
T PF00057_consen 5 PGEFRCGN----GQ--CIPKSWVCDGIPDCPDGSDEQ 35 (37)
T ss_dssp TTEEEETT----SS--EEEGGGTTSSSCSSSSSTTTS
T ss_pred CCeeEcCC----CC--EEChHHcCCCCCCCCCCcccc
Confidence 46899992 33 999999999999999999995
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=98.53 E-value=3.8e-08 Score=57.10 Aligned_cols=31 Identities=42% Similarity=0.889 Sum_probs=27.6
Q ss_pred ceecCCCCCCCCceeecCCCcccCCCCCCCCCCCCcC
Q psy12307 19 ERFACPTPDHMGRYRCIDDHVLCDGFIDCPTGEDEDR 55 (106)
Q Consensus 19 de~~Cptpd~~gR~~CI~~~~LCDG~~DCpdGeDE~~ 55 (106)
.+|.|. . ..||+..++|||+.||++||||..
T Consensus 4 ~~f~C~-----~-~~Ci~~~~~CDg~~DC~dgsDE~~ 34 (35)
T cd00112 4 NEFRCA-----N-GRCIPSSWVCDGEDDCGDGSDEEN 34 (35)
T ss_pred CeEEcC-----C-CCeeCHHHcCCCccCCCCCccccc
Confidence 688998 3 569999999999999999999963
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=98.32 E-value=4.4e-07 Score=51.81 Aligned_cols=28 Identities=43% Similarity=0.907 Sum_probs=25.4
Q ss_pred eecCCCCCCCCceeecCCCcccCCCCCCCCCCCC
Q psy12307 20 RFACPTPDHMGRYRCIDDHVLCDGFIDCPTGEDE 53 (106)
Q Consensus 20 e~~Cptpd~~gR~~CI~~~~LCDG~~DCpdGeDE 53 (106)
+|.|. +.. ||+..++|||+.||++||||
T Consensus 6 ~f~C~-----~~~-Ci~~~~~Cdg~~dC~dgsDE 33 (33)
T smart00192 6 EFQCD-----NGR-CIPLSWVCDGVDDCSDGSDE 33 (33)
T ss_pred eEECC-----CCC-EECchhhCCCcCcCcCCCCC
Confidence 89998 333 99999999999999999998
No 4
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=97.84 E-value=1.8e-05 Score=61.02 Aligned_cols=40 Identities=30% Similarity=0.508 Sum_probs=32.1
Q ss_pred CCCceeecCCC-------cccCCCCCCCCCCCCcC---C-cceEEecCCCc
Q psy12307 28 HMGRYRCIDDH-------VLCDGFIDCPTGEDEDR---Q-NFLLENELCWG 67 (106)
Q Consensus 28 ~~gR~~CI~~~-------~LCDG~~DCpdGeDE~~---c-sC~Fyc~~~~p 67 (106)
.+|.|.|.+.. ++.|++=||||||||.- | .-+|||.|+.-
T Consensus 34 ~~~~f~Cl~~~~~~I~~~~iNDdyCDC~DGSDEPGTsAC~~~~FyC~N~g~ 84 (176)
T PF12999_consen 34 ENGKFTCLDGSKIVIPFSQINDDYCDCPDGSDEPGTSACSNGKFYCENKGH 84 (176)
T ss_pred CCCceEecCCCCceecHHHccCcceeCCCCCCccccccCcCceEeeccCCC
Confidence 44678885554 89999999999999974 5 45999999963
No 5
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=96.31 E-value=0.002 Score=43.43 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=21.7
Q ss_pred CCceeeeeccccccce-EEecCcchhc
Q psy12307 65 CWGLSIYKALDKSTGL-RSILNWSDLV 90 (106)
Q Consensus 65 ~~pLsVy~~l~~s~~l-~~~~nw~~~~ 90 (106)
+.-|+||++-+ ++|+ ||++||++..
T Consensus 3 ~s~LQV~~~~~-~~W~~VC~d~W~~~~ 28 (98)
T PF15494_consen 3 NSLLQVYSAAS-GSWLPVCSDNWNEAL 28 (98)
T ss_pred CcEEEEEecCC-CCEeeecccccCHHH
Confidence 35689999987 8899 9999999875
No 6
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=92.11 E-value=0.17 Score=39.30 Aligned_cols=45 Identities=33% Similarity=0.754 Sum_probs=32.7
Q ss_pred cccCCCCCCCCCce---ecCCCCCCCCceeecCC---------CcccCCCCC---CCCCCCCcCCcc
Q psy12307 7 MYLECPPAEDGMER---FACPTPDHMGRYRCIDD---------HVLCDGFID---CPTGEDEDRQNF 58 (106)
Q Consensus 7 ~~~~C~~~~~G~de---~~Cptpd~~gR~~CI~~---------~~LCDG~~D---CpdGeDE~~csC 58 (106)
-+=+||. |-|| .+|+ +++|||.+. +.+=||+=| |=|||||....|
T Consensus 56 dyCDC~D---GSDEPGTsAC~----~~~FyC~N~g~~p~~i~~s~VnDGICDy~~CCDGSDE~~~~C 115 (176)
T PF12999_consen 56 DYCDCPD---GSDEPGTSACS----NGKFYCENKGHIPRYIPSSRVNDGICDYDICCDGSDESGGKC 115 (176)
T ss_pred cceeCCC---CCCccccccCc----CceEeeccCCCCCceeehhhhcCCcCcccccCCCCCCCCCCC
Confidence 4557864 5555 4898 579999554 378899999 999999944333
No 7
>KOG2397|consensus
Probab=91.12 E-value=0.25 Score=43.62 Aligned_cols=48 Identities=23% Similarity=0.266 Sum_probs=34.5
Q ss_pred CCCCCceeecCCC------cccCCCCCCCCCCCCcC-Ccce---EEecCCCceeeeec
Q psy12307 26 PDHMGRYRCIDDH------VLCDGFIDCPTGEDEDR-QNFL---LENELCWGLSIYKA 73 (106)
Q Consensus 26 pd~~gR~~CI~~~------~LCDG~~DCpdGeDE~~-csC~---Fyc~~~~pLsVy~~ 73 (106)
|+..+.|.|.+.+ ++=|++-||++|+||-- -+|- |||++....++|-.
T Consensus 39 y~as~~~~CLdgs~~i~f~qlNDd~CDC~DGsDEPGtsACpngkF~C~N~G~~p~~i~ 96 (480)
T KOG2397|consen 39 YDASSMFKCLDGSKTISFSQLNDDSCDCLDGSDEPGTSACPNGKFYCVNQGHQPKYIP 96 (480)
T ss_pred cccccceeeccCCcccCHHHhccccccCCCCCCCCccccCCCCceeeeecCCCceeee
Confidence 3445567775444 89999999999999933 2666 99998865555543
No 8
>KOG1215|consensus
Probab=89.93 E-value=0.17 Score=45.00 Aligned_cols=34 Identities=47% Similarity=1.007 Sum_probs=27.4
Q ss_pred ceecCCCCCCCCceeecCCCcccCCCCCCCCCCCCcCC
Q psy12307 19 ERFACPTPDHMGRYRCIDDHVLCDGFIDCPTGEDEDRQ 56 (106)
Q Consensus 19 de~~Cptpd~~gR~~CI~~~~LCDG~~DCpdGeDE~~c 56 (106)
.+++|+. ++..||...++|||..+|++|+||..+
T Consensus 141 ~~~~c~~----~~~~Cip~~~~cd~~~~C~dg~de~~~ 174 (877)
T KOG1215|consen 141 DKFSCRT----GSCKCIPGDWLCDGEADCPDGSDELNC 174 (877)
T ss_pred CCCCCcC----ccccCCCCceeCCCCCccccchhhhcc
Confidence 4455551 367899999999999999999999754
No 9
>KOG1215|consensus
Probab=81.55 E-value=0.93 Score=40.45 Aligned_cols=30 Identities=47% Similarity=0.754 Sum_probs=23.7
Q ss_pred eecCCCcccCCCCCCCCCCCCcCCcceEEe
Q psy12307 33 RCIDDHVLCDGFIDCPTGEDEDRQNFLLEN 62 (106)
Q Consensus 33 ~CI~~~~LCDG~~DCpdGeDE~~csC~Fyc 62 (106)
-|+....+|||..|||+|+||+.+.-.+|+
T Consensus 271 ~~~~~~~~~~g~~d~pdg~de~~~~~~~~~ 300 (877)
T KOG1215|consen 271 DCSDRQKLCDGDLDCPDGLDEDYCKKKLYW 300 (877)
T ss_pred CCccceEEecCccCCCCcccccccccceee
Confidence 366777889999999999999977544443
No 10
>KOG2397|consensus
Probab=66.43 E-value=5.9 Score=35.25 Aligned_cols=46 Identities=33% Similarity=0.626 Sum_probs=34.5
Q ss_pred CcccCCCCCCCCCceecCCCCCCCCceeec---------CCCcccCCCCCCCCCCCCcC
Q psy12307 6 DMYLECPPAEDGMERFACPTPDHMGRYRCI---------DDHVLCDGFIDCPTGEDEDR 55 (106)
Q Consensus 6 ~~~~~C~~~~~G~de~~Cptpd~~gR~~CI---------~~~~LCDG~~DCpdGeDE~~ 55 (106)
+-+-+|++--+.--..+|| +|.|+|. ..+++=||+-||=+|+||..
T Consensus 61 Dd~CDC~DGsDEPGtsACp----ngkF~C~N~G~~p~~i~ssrV~DGICDCCDgSDE~~ 115 (480)
T KOG2397|consen 61 DDSCDCLDGSDEPGTSACP----NGKFYCVNQGHQPKYIPSSRVNDGICDCCDGSDEYL 115 (480)
T ss_pred cccccCCCCCCCCccccCC----CCceeeeecCCCceeeechhccCcccccccCCCCcc
Confidence 4456787643444568899 6899994 44489999999999999964
No 11
>PF04495 GRASP55_65: GRASP55/65 PDZ-like domain ; InterPro: IPR007583 GRASP55 (Golgi reassembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide-sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system [].; PDB: 3RLE_A 4EDJ_A.
Probab=28.11 E-value=71 Score=23.37 Aligned_cols=35 Identities=23% Similarity=0.488 Sum_probs=22.9
Q ss_pred eeeeeccccccce---EEecCcchhcccceeEeeeeec
Q psy12307 68 LSIYKALDKSTGL---RSILNWSDLVNLGLRIKWQGLE 102 (106)
Q Consensus 68 LsVy~~l~~s~~l---~~~~nw~~~~~~~~~~~~~~~~ 102 (106)
|.||++.....-. +=+.+|...-.||+.|+|+-.+
T Consensus 1 l~v~~~k~~~~R~v~i~ps~~w~~~g~LG~sv~~~~~~ 38 (138)
T PF04495_consen 1 LNVYNAKGQTTREVSIVPSKKWGGQGLLGISVRFESFE 38 (138)
T ss_dssp EEEEETTTSSEEEEEE---SSSSSSSSS-EEEEEEE-T
T ss_pred CceEECCCCeEEEEEEccCcccCCCCCCcEEEEEeccc
Confidence 5678775543333 3357899999999999998776
No 12
>PF07771 TSGP1: Tick salivary peptide group 1; InterPro: IPR011694 This entry contains a group of peptides derived from a salivary gland cDNA library of the tick Ixodes scapularis (Black-legged tick) []. Also present are peptides from a related tick species, Ixodes ricinus (Sheep tick). They are characterised by a putative signal peptide, indicative of secretion, and conserved cysteine residues.
Probab=21.96 E-value=82 Score=22.95 Aligned_cols=21 Identities=19% Similarity=0.170 Sum_probs=13.0
Q ss_pred CCCCCCC----CCcCCcceEEecCC
Q psy12307 45 IDCPTGE----DEDRQNFLLENELC 65 (106)
Q Consensus 45 ~DCpdGe----DE~~csC~Fyc~~~ 65 (106)
..|||+. +.....|.|||.+.
T Consensus 22 ~~Cp~~~r~~~~~~~~~C~YYC~~~ 46 (120)
T PF07771_consen 22 HGCPDKTRPASDTNREGCNYYCWND 46 (120)
T ss_pred hcCCCCCcCCCCCCCCCcEEEcCCC
Confidence 3566653 33334799999864
No 13
>smart00202 SR Scavenger receptor Cys-rich. The sea ucrhin egg peptide speract contains 4 repeats of SR domains that contain 6 conserved cysteines. May bind bacterial antigens in the protein MARCO.
Probab=21.67 E-value=64 Score=21.00 Aligned_cols=20 Identities=10% Similarity=0.101 Sum_probs=14.6
Q ss_pred ceeeeeccccccce-EEecCcchh
Q psy12307 67 GLSIYKALDKSTGL-RSILNWSDL 89 (106)
Q Consensus 67 pLsVy~~l~~s~~l-~~~~nw~~~ 89 (106)
-|.||. . ..|- ||..+|+..
T Consensus 13 ~leV~~--~-~~Wg~VC~~~w~~~ 33 (101)
T smart00202 13 RVEVYH--N-GQWGTVCDDGWDLR 33 (101)
T ss_pred EEEEEE--C-CEEeCeeCCCCChh
Confidence 466774 3 5788 999999764
Done!