RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031564
(157 letters)
>gnl|CDD|178347 PLN02746, PLN02746, hydroxymethylglutaryl-CoA lyase.
Length = 347
Score = 140 bits (355), Expect = 2e-41
Identities = 60/86 (69%), Positives = 67/86 (77%)
Query: 68 YLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKL 127
+ YSSS + + +KLL +P FVKIVEVGPRDGLQNEKNIVP VKVELI+
Sbjct: 17 SFKEHQYSSSSNEVGVAHMHNKLLKGLPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQR 76
Query: 128 LVSSGLPVVEATSFVSPKWVPQVADA 153
LVSSGLPVVEATSFVSPKWVPQ+ADA
Sbjct: 77 LVSSGLPVVEATSFVSPKWVPQLADA 102
>gnl|CDD|163676 cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase,
catalytic TIM barrel domain.
3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes
the cleavage of HMG-CoA to acetyl-CoA and acetoacetate,
one of the terminal steps in ketone body generation and
leucine degradation, and is a key enzyme in the pathway
that supplies metabolic fuel to extrahepatic tissues.
Mutations in HMGL cause a human autosomal recessive
disorder called primary metabolic aciduria that affects
ketogenesis and leucine catabolism and can be fatal due
to an inability to tolerate hypoglycemia. HMGL has a
TIM barrel domain with a catalytic center containing a
divalent cation-binding site formed by a cluster of
invariant residues that cap the core of the barrel. The
cleavage of HMG-CoA requires the presence of a divalent
cation like Mg2+ or Mn2+, and the reaction is thought to
involve general acid/base catalysis. This family
belongs to the DRE-TIM metallolyase superfamily.
DRE-TIM metallolyases include 2-isopropylmalate synthase
(IPMS), alpha-isopropylmalate synthase (LeuA),
3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
aldolase, re-citrate synthase, transcarboxylase 5S,
pyruvate carboxylase, AksA, and FrbC. These members all
share a conserved triose-phosphate isomerase (TIM)
barrel domain consisting of a core beta(8)-alpha(8)
motif with the eight parallel beta strands forming an
enclosed barrel surrounded by eight alpha helices. The
domain has a catalytic center containing a divalent
cation-binding site formed by a cluster of invariant
residues that cap the core of the barrel. In addition,
the catalytic site includes three invariant residues -
an aspartate (D), an arginine (R), and a glutamate (E) -
which is the basis for the domain name "DRE-TIM".
Length = 274
Score = 112 bits (283), Expect = 3e-31
Identities = 37/54 (68%), Positives = 43/54 (79%)
Query: 100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
IVEVGPRDGLQNEK +P K+ELI L ++GL +E TSFVSPKWVPQ+ADA
Sbjct: 1 IVEVGPRDGLQNEKTFIPTEDKIELIDALSAAGLRRIEVTSFVSPKWVPQMADA 54
>gnl|CDD|180206 PRK05692, PRK05692, hydroxymethylglutaryl-CoA lyase; Provisional.
Length = 287
Score = 108 bits (271), Expect = 2e-29
Identities = 38/59 (64%), Positives = 44/59 (74%)
Query: 95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
P VKIVEVGPRDGLQNEK +P K+ LI L ++GL +E SFVSPKWVPQ+ADA
Sbjct: 2 PKRVKIVEVGPRDGLQNEKRFIPTADKIALIDRLSAAGLSYIEVASFVSPKWVPQMADA 60
>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily.
The DRE-TIM metallolyase superfamily includes
2-isopropylmalate synthase (IPMS), alpha-isopropylmalate
synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase,
homocitrate synthase, citramalate synthase,
4-hydroxy-2-oxovalerate aldolase, re-citrate synthase,
transcarboxylase 5S, pyruvate carboxylase, AksA, and
FrbC. These members all share a conserved
triose-phosphate isomerase (TIM) barrel domain
consisting of a core beta(8)-alpha(8) motif with the
eight parallel beta strands forming an enclosed barrel
surrounded by eight alpha helices. The domain has a
catalytic center containing a divalent cation-binding
site formed by a cluster of invariant residues that cap
the core of the barrel. In addition, the catalytic site
includes three invariant residues - an aspartate (D), an
arginine (R), and a glutamate (E) - which is the basis
for the domain name "DRE-TIM".
Length = 265
Score = 74.4 bits (184), Expect = 7e-17
Identities = 19/53 (35%), Positives = 28/53 (52%)
Query: 101 VEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
+ RDGLQ+E K+E+ + L +G+ +E S SPK VPQ+ D
Sbjct: 1 TDTTLRDGLQSEGATFSTEDKLEIAEALDEAGVDSIEVGSGASPKAVPQMEDD 53
>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases
[Amino acid transport and metabolism].
Length = 409
Score = 53.4 bits (129), Expect = 5e-09
Identities = 14/57 (24%), Positives = 22/57 (38%)
Query: 98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADAL 154
V I + RDG Q K+ + K L G+ +EA V+ + A+
Sbjct: 3 VIIFDTTLRDGEQAPGVSFSVEEKIRIAKALDDLGVDYIEAGFPVASPGDFEFVRAI 59
>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like. This family contains a diverse
set of enzymes. These include various aldolases and a
region of pyruvate carboxylase.
Length = 236
Score = 44.2 bits (105), Expect = 5e-06
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 107 DGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT-SFVSPKWVPQVADA 153
DG Q K+ + + L +G+ +E F+SP V
Sbjct: 1 DGEQALGAAFSVEEKLAIARALDEAGVDEIEVGFPFMSPTDFESVRAI 48
>gnl|CDD|152354 pfam11919, DUF3437, Domain of unknown function (DUF3437). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 142 to 163 amino acids in length.
Length = 89
Score = 26.8 bits (60), Expect = 2.4
Identities = 6/16 (37%), Positives = 10/16 (62%)
Query: 135 VVEATSFVSPKWVPQV 150
+V A + P W+P+V
Sbjct: 16 LVLAFPYEVPPWIPKV 31
>gnl|CDD|238985 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK) catalyzes
the phosphorylation of adenosine 5'-phosphosulfate to
form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The
end-product PAPS is a biologically "activated" sulfate
form important for the assimilation of inorganic
sulfate.
Length = 149
Score = 26.3 bits (59), Expect = 5.2
Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 122 VELIKLLVSSGLPVVEATSFVSP 144
E+ KLL +GL V+ +F+SP
Sbjct: 61 AEVAKLLADAGLIVI--AAFISP 81
>gnl|CDD|177953 PLN02319, PLN02319, aminomethyltransferase.
Length = 404
Score = 26.6 bits (59), Expect = 6.5
Identities = 14/46 (30%), Positives = 21/46 (45%)
Query: 67 GYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNE 112
GY + + S DL LL + G V++ +G RD L+ E
Sbjct: 223 GYTGEDGFEISVPSEHAVDLAKALLEKSEGKVRLTGLGARDSLRLE 268
>gnl|CDD|107256 cd01543, PBP1_XylR, Ligand-binding domain of DNA transcription
repressor specific for xylose (XylR). Ligand-binding
domain of DNA transcription repressor specific for
xylose (XylR), a member of the LacI-GalR family of
bacterial transcription regulators. The ligand-binding
domain of XylR is structurally homologous to the
periplasmic sugar-binding domain of ABC-type
transporters and both domains contain the type I
periplasmic binding protein-like fold. The LacI-GalR
family repressors are composed of two functional
domains: an N-terminal HTH (helix-turn-helix) domain,
which is responsible for the DNA-binding specificity,
and a C-terminal ligand-binding domain, which is
homologous to the type I periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcription
repressor undergoes a conformational change upon ligand
binding which in turn changes the DNA binding affinity
of the repressor.
Length = 265
Score = 26.0 bits (58), Expect = 8.1
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 123 ELIKLLVSSGLPVVEATSFVSPKWVPQVA 151
E+ + L G+PVV+ + +P+V
Sbjct: 62 EMAEALQKLGIPVVDVSGSREKPGIPRVT 90
>gnl|CDD|217561 pfam03443, Glyco_hydro_61, Glycosyl hydrolase family 61.
Length = 234
Score = 25.7 bits (57), Expect = 9.8
Identities = 11/41 (26%), Positives = 13/41 (31%), Gaps = 11/41 (26%)
Query: 68 YLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDG 108
YL+K C L + KI E G DG
Sbjct: 107 YLAKC--GGDCATVDKTGL---------VWFKIDEDGLDDG 136
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.312 0.129 0.354
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,351,898
Number of extensions: 623330
Number of successful extensions: 322
Number of sequences better than 10.0: 1
Number of HSP's gapped: 321
Number of HSP's successfully gapped: 12
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (24.9 bits)