Query 029898
Match_columns 185
No_of_seqs 12 out of 14
Neff 1.7
Searched_HMMs 46136
Date Fri Mar 29 05:23:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029898hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01848 PHA_reg_PhaR polyhyd 90.4 0.17 3.7E-06 39.7 1.8 35 147-181 2-49 (107)
2 PF07879 PHB_acc_N: PHB/PHA ac 89.8 0.21 4.6E-06 36.3 1.8 35 147-181 2-49 (64)
3 KOG2820 FAD-dependent oxidored 53.1 25 0.00055 33.1 4.8 108 60-176 227-358 (399)
4 PRK00044 psd phosphatidylserin 37.5 23 0.00049 30.4 1.9 24 51-74 44-71 (288)
5 PF11035 SnAPC_2_like: Small n 37.2 7 0.00015 36.1 -1.3 11 159-169 206-216 (344)
6 PRK03934 phosphatidylserine de 31.1 40 0.00087 28.6 2.3 24 51-74 34-59 (265)
7 smart00135 LY Low-density lipo 30.6 62 0.0013 18.2 2.4 29 155-183 7-38 (43)
8 TIGR02976 phageshock_pspB phag 29.1 18 0.00038 26.5 -0.1 16 144-159 19-34 (75)
9 PF06667 PspB: Phage shock pro 26.4 19 0.0004 26.5 -0.4 16 144-159 19-34 (75)
10 smart00294 4.1m putative band 25.2 28 0.00061 21.7 0.3 20 111-130 2-21 (26)
11 PF00058 Ldl_recept_b: Low-den 22.8 1E+02 0.0022 19.1 2.6 16 167-182 2-18 (42)
12 PF01436 NHL: NHL repeat; Int 21.6 1.1E+02 0.0023 17.6 2.3 17 164-180 11-27 (28)
No 1
>TIGR01848 PHA_reg_PhaR polyhydroxyalkanoate synthesis repressor PhaR. Poly-B-hydroxyalkanoates are lipidlike carbon/energy storage polymers found in granular inclusions. PhaR is a regulatory protein found in general near other proteins associated with polyhydroxyalkanoate (PHA) granule biosynthesis and utilization. It is found to be a DNA-binding homotetramer that is also capable of binding short chain hydroxyalkanoic acids and PHA granules. PhaR may regulate the expression of itself, of the phasins that coat granules, and of enzymes that direct carbon flux into polymers stored in granules.
Probab=90.37 E-value=0.17 Score=39.68 Aligned_cols=35 Identities=46% Similarity=0.674 Sum_probs=29.8
Q ss_pred eehhcccccCCCCc------------ceeecceEEEeecCcce-eeee
Q 029898 147 LVKHYRNRRLGDPE------------FVLDFEEIYVIDSKTKS-ITRA 181 (185)
Q Consensus 147 l~khyrnrr~~dp~------------fvldfeeiyvids~tks-itra 181 (185)
++|-|-|||+=|.+ +|.+=+++-|+|+||+. |||+
T Consensus 2 ~IKKY~NRRLYDT~tS~YITLedi~~lV~~g~~f~V~DakTgeDiT~~ 49 (107)
T TIGR01848 2 IIKKYPNRRLYDTETSSYVTLEDIRDLVREGREFQVVDSKSGDDLTRS 49 (107)
T ss_pred cccccCCCcccCCCccceeeHHHHHHHHHCCCeEEEEECCCCchhHHH
Confidence 68999999998875 78999999999999975 5553
No 2
>PF07879 PHB_acc_N: PHB/PHA accumulation regulator DNA-binding domain; InterPro: IPR012909 This domain is found at the N terminus of the polyhydroxyalkanoate (PHA) synthesis regulators. These regulators have been shown to directly bind DNA and PHA []. The invariant nature of this domain compared to the C-terminal IPR007897 from INTERPRO domain(s) suggests that it contains the DNA-binding function.
Probab=89.82 E-value=0.21 Score=36.27 Aligned_cols=35 Identities=49% Similarity=0.700 Sum_probs=29.3
Q ss_pred eehhcccccCCCCc------------ceeecceEEEeecCcce-eeee
Q 029898 147 LVKHYRNRRLGDPE------------FVLDFEEIYVIDSKTKS-ITRA 181 (185)
Q Consensus 147 l~khyrnrr~~dp~------------fvldfeeiyvids~tks-itra 181 (185)
++|-|-|||+=|.+ +|.+=+++-|+|++|+. |||+
T Consensus 2 iIKKY~NRRLYDT~~s~YiTL~di~~lV~~g~~~~V~D~ktgeDiT~~ 49 (64)
T PF07879_consen 2 IIKKYPNRRLYDTETSSYITLEDIAQLVREGEDFKVVDAKTGEDITRS 49 (64)
T ss_pred cccccCCCccccCCCceeEeHHHHHHHHHCCCeEEEEECCCCcccHHH
Confidence 58999999998875 67888999999999874 5653
No 3
>KOG2820 consensus FAD-dependent oxidoreductase [General function prediction only]
Probab=53.07 E-value=25 Score=33.09 Aligned_cols=108 Identities=25% Similarity=0.360 Sum_probs=67.7
Q ss_pred ceeecccccccccCCCCCCCCcccceeeeecCCCCce----eecccccCCCchhhhhhhhccCccc--cccCCCCCCCCC
Q 029898 60 HKISLMECDFFIRKPPDPDNDVYDFREMYVTPPDTDI----YAIPKVLAPMPQKYIRCAVSDYGCY--NVTEPPIDAPRD 133 (185)
Q Consensus 60 Hkisl~dcdffirk~PDpD~dVyDFREMYVTpPdTDv----YSIPrVl~pMPqky~rC~~s~yg~y--~vtePPid~pRd 133 (185)
--|+|-.|- |++|.+-|-- ..+=-+-|+-||.-|. ||.|- --|.+-++-.|+.= -++.+|--+|--
T Consensus 227 ~~i~ltvcy-wk~~~~~~~~-l~~d~~f~~F~~~~~~~~~~ya~p~------~eYpg~~k~~yh~g~~v~~~~~~~p~~~ 298 (399)
T KOG2820|consen 227 APIQLTVCY-WKTKKNMPVY-LFDDDCFYAFPPYPDTKLIKYALPG------YEYPGLMKVDYHEGSKVVPIDPDGPPKR 298 (399)
T ss_pred ceeEeehhh-heeecCCcee-ecCCCCceeccCCCCcceEEeccCC------CCCcceEEEeecCCCcCCCCCCCCCccc
Confidence 347788885 5677776632 2222356777777665 88887 66776666665543 355555555555
Q ss_pred ccchhhHHhhhheeehhcccc--------------cCCCCcceeec----ceEEEeecCcc
Q 029898 134 PMYKSEREIHKVFLVKHYRNR--------------RLGDPEFVLDF----EEIYVIDSKTK 176 (185)
Q Consensus 134 P~yk~E~ei~kVfl~khyrnr--------------r~~dp~fvldf----eeiyvids~tk 176 (185)
|.-+ +-+++.-|+.+|--.. -..|.+||+|+ ++|+|=-.-++
T Consensus 299 s~~~-~idl~~~f~~~~~p~l~~~~p~~t~~C~YT~TpD~~FviD~~P~~~Nv~Vg~G~SG 358 (399)
T KOG2820|consen 299 SLPK-AIDLMRRFLRTFGPDLDDRSPINTKMCMYTDTPDANFVIDKHPQYDNVFVGGGGSG 358 (399)
T ss_pred Ccch-HHHHHHHHHHHhCccccCCCcceeeEEEeeCCCCcCeeeecCCCcccEEEecCCCC
Confidence 6555 6677777877763221 15688999984 78887554443
No 4
>PRK00044 psd phosphatidylserine decarboxylase; Reviewed
Probab=37.54 E-value=23 Score=30.37 Aligned_cols=24 Identities=33% Similarity=0.551 Sum_probs=17.9
Q ss_pred EeecCccccce--eeccc--ccccccCC
Q 029898 51 DYRIDEDEFHK--ISLME--CDFFIRKP 74 (185)
Q Consensus 51 dY~inEdEFHk--isl~d--cdffirk~ 74 (185)
.|.||-+|+.+ ++=+. .|||+||.
T Consensus 44 ~~~i~~~E~~~~~~~~y~s~~~FF~R~l 71 (288)
T PRK00044 44 KYKVDMSEAQKPDPAAYKTFNDFFTRAL 71 (288)
T ss_pred HhCCCHHHHccCChhhCCCHHHhceecc
Confidence 58899999886 44343 48999994
No 5
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=37.20 E-value=7 Score=36.06 Aligned_cols=11 Identities=64% Similarity=1.259 Sum_probs=10.1
Q ss_pred CcceeecceEE
Q 029898 159 PEFVLDFEEIY 169 (185)
Q Consensus 159 p~fvldfeeiy 169 (185)
-+|++|||+||
T Consensus 206 ~d~~VDFEKIY 216 (344)
T PF11035_consen 206 GDFVVDFEKIY 216 (344)
T ss_pred cceeeeHHHHH
Confidence 57999999999
No 6
>PRK03934 phosphatidylserine decarboxylase; Provisional
Probab=31.06 E-value=40 Score=28.63 Aligned_cols=24 Identities=25% Similarity=0.391 Sum_probs=19.8
Q ss_pred EeecCccccceeecccc--cccccCC
Q 029898 51 DYRIDEDEFHKISLMEC--DFFIRKP 74 (185)
Q Consensus 51 dY~inEdEFHkisl~dc--dffirk~ 74 (185)
.|+||.+|+..++=+.| |||+||.
T Consensus 34 ~~~i~~~e~~~~~~y~sfn~FF~R~l 59 (265)
T PRK03934 34 IFKIDMSEFKPPENYKSLNALFTRSL 59 (265)
T ss_pred HHCCCHHHhcCcccCCCHHHhccccC
Confidence 68999999976666665 9999996
No 7
>smart00135 LY Low-density lipoprotein-receptor YWTD domain. Type "B" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin.
Probab=30.63 E-value=62 Score=18.15 Aligned_cols=29 Identities=28% Similarity=0.496 Sum_probs=21.3
Q ss_pred cCCCCc-ceeec--ceEEEeecCcceeeeeee
Q 029898 155 RLGDPE-FVLDF--EEIYVIDSKTKSITRAKV 183 (185)
Q Consensus 155 r~~dp~-fvldf--eeiyvids~tksitrakv 183 (185)
....|+ +.+|. ..+|-.|+....|.|++.
T Consensus 7 ~~~~~~~la~d~~~~~lYw~D~~~~~I~~~~~ 38 (43)
T smart00135 7 GLGHPNGLAVDWIEGRLYWTDWGLDVIEVANL 38 (43)
T ss_pred CCCCcCEEEEeecCCEEEEEeCCCCEEEEEeC
Confidence 344454 55555 579999999999999874
No 8
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=29.09 E-value=18 Score=26.46 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=11.9
Q ss_pred hheeehhcccccCCCC
Q 029898 144 KVFLVKHYRNRRLGDP 159 (185)
Q Consensus 144 kVfl~khyrnrr~~dp 159 (185)
-.+|.+|||++|....
T Consensus 19 p~wl~lHY~~k~~~~~ 34 (75)
T TIGR02976 19 PLWLILHYRSKRKTAA 34 (75)
T ss_pred HHHHHHHHHhhhccCC
Confidence 3568999998876554
No 9
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=26.40 E-value=19 Score=26.46 Aligned_cols=16 Identities=25% Similarity=0.630 Sum_probs=12.1
Q ss_pred hheeehhcccccCCCC
Q 029898 144 KVFLVKHYRNRRLGDP 159 (185)
Q Consensus 144 kVfl~khyrnrr~~dp 159 (185)
-++|+.|||++|....
T Consensus 19 p~WL~lHY~sk~~~~~ 34 (75)
T PF06667_consen 19 PIWLILHYRSKWKSSQ 34 (75)
T ss_pred HHHHHHHHHHhcccCC
Confidence 3568899999986543
No 10
>smart00294 4.1m putative band 4.1 homologues' binding motif.
Probab=25.20 E-value=28 Score=21.71 Aligned_cols=20 Identities=30% Similarity=0.406 Sum_probs=16.6
Q ss_pred hhhhhccCccccccCCCCCC
Q 029898 111 IRCAVSDYGCYNVTEPPIDA 130 (185)
Q Consensus 111 ~rC~~s~yg~y~vtePPid~ 130 (185)
.||..++.|.|++.||+...
T Consensus 2 yry~~R~kGSY~t~E~kg~~ 21 (26)
T smart00294 2 YRYKHRDEGSYHTHEPKGXX 21 (26)
T ss_pred cEEEecccCceEcCCCCCcc
Confidence 37889999999999998543
No 11
>PF00058 Ldl_recept_b: Low-density lipoprotein receptor repeat class B; InterPro: IPR000033 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 classB (YWTD) repeat, the structure of which has been solved []. The six YWTD repeats together fold into a six-bladed beta-propeller. Each blade of the propeller consists of four antiparallel beta-strands; the innermost strand of each blade is labeled 1 and the outermost strand, 4. The sequence repeats are offset with respect to the blades of the propeller, such that any given 40-residue YWTD repeat spans strands 24 of one propeller blade and strand 1 of the subsequent blade. This offset ensures circularization of the propeller because the last strand of the final sequence repeat acts as an innermost strand 1 of the blade that harbors strands 24 from the first sequence repeat. The repeat is found in a variety of proteins that include, vitellogenin receptor from Drosophila melanogaster, low-density lipoprotein (LDL) receptor [], preproepidermal growth factor, and nidogen (entactin).; PDB: 3S2K_A 3S8Z_A 3S8V_B 4A0P_A 3SOB_B 3S94_B 4DG6_A 3SOV_A 3SOQ_A 1NPE_A ....
Probab=22.75 E-value=1e+02 Score=19.15 Aligned_cols=16 Identities=44% Similarity=0.538 Sum_probs=14.4
Q ss_pred eEEEeecCcc-eeeeee
Q 029898 167 EIYVIDSKTK-SITRAK 182 (185)
Q Consensus 167 eiyvids~tk-sitrak 182 (185)
+||-.|..++ +|-+|+
T Consensus 2 ~iYWtD~~~~~~I~~a~ 18 (42)
T PF00058_consen 2 KIYWTDWSQDPSIERAN 18 (42)
T ss_dssp EEEEEETTTTEEEEEEE
T ss_pred EEEEEECCCCcEEEEEE
Confidence 6899999999 999886
No 12
>PF01436 NHL: NHL repeat; InterPro: IPR001258 The NHL repeat, named after NCL-1, HT2A and Lin-41, is found largely in a large number of eukaryotic and prokaryotic proteins. For example, the repeat is found in a variety of enzymes of the copper type II, ascorbate-dependent monooxygenase family which catalyse the C terminus alpha-amidation of biological peptides []. In many it occurs in tandem arrays, for example in the ringfinger beta-box, coiled-coil (RBCC) eukaryotic growth regulators []. The 'Brain Tumor' protein (Brat) is one such growth regulator that contains a 6-bladed NHL-repeat beta-propeller [, ]. The NHL repeats are also found in serine/threonine protein kinase (STPK) in diverse range of pathogenic bacteria. These STPK are transmembrane receptors with a intracellular N-terminal kinase domain and extracellular C-terminal sensor domain. In the STPK, PknD, from Mycobacterium tuberculosis, the sensor domain forms a rigid, six-bladed b-propeller composed of NHL repeats with a flexible tether to the transmembrane domain.; GO: 0005515 protein binding; PDB: 3FVZ_A 3FW0_A 1RWL_A 1RWI_A 1Q7F_A.
Probab=21.60 E-value=1.1e+02 Score=17.64 Aligned_cols=17 Identities=29% Similarity=0.360 Sum_probs=13.2
Q ss_pred ecceEEEeecCcceeee
Q 029898 164 DFEEIYVIDSKTKSITR 180 (185)
Q Consensus 164 dfeeiyvids~tksitr 180 (185)
+=.+|||.|+....|.+
T Consensus 11 ~~g~i~VaD~~n~rV~v 27 (28)
T PF01436_consen 11 SDGNIYVADSGNHRVQV 27 (28)
T ss_dssp TTSEEEEEECCCTEEEE
T ss_pred CCCCEEEEECCCCEEEE
Confidence 34689999999887754
Done!