RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12130
(67 letters)
>gnl|CDD|130302 TIGR01235, pyruv_carbox, pyruvate carboxylase. This enzyme plays a
role in gluconeogensis but not glycolysis [Energy
metabolism, Glycolysis/gluconeogenesis].
Length = 1143
Score = 28.6 bits (64), Expect = 0.19
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 30 GAAMASYLKSAPYGVNGIGLSMDSLHSSLGYIPSANDI 67
G A+AS L + GV+ + +++DS+ S L PS I
Sbjct: 744 GIAVASMLAAVEAGVDVVDVAVDSM-SGLTSQPSLGAI 780
>gnl|CDD|163675 cd07937, DRE_TIM_PC_TC_5S, Pyruvate carboxylase and
Transcarboxylase 5S, carboxyltransferase domain. This
family includes the carboxyltransferase domains of
pyruvate carboxylase (PC) and the transcarboxylase (TC)
5S subunit. Transcarboxylase 5S is a cobalt-dependent
metalloenzyme subunit of the biotin-dependent
transcarboxylase multienzyme complex. Transcarboxylase
5S transfers carbon dioxide from the 1.3S biotin to
pyruvate in the second of two carboxylation reactions
catalyzed by TC. The first reaction involves the
transfer of carbon dioxide from methylmalonyl-CoA to the
1.3S biotin, and is catalyzed by the 12S subunit. These
two steps allow a carboxylate group to be transferred
from oxaloacetate to propionyl-CoA to yield pyruvate and
methylmalonyl-CoA. The catalytic domain of
transcarboxylase 5S has a canonical TIM-barrel fold with
a large C-terminal extension that forms a funnel leading
to the active site. Transcarboxylase 5S forms a
homodimer and there are six dimers per complex. In
addition to the catalytic domain, transcarboxylase 5S
has several other domains including a
carbamoyl-phosphate synthase domain, a biotin
carboxylase domain, a carboxyltransferase domain, and an
ATP-grasp domain. Pyruvate carboxylase, like TC, is a
biotin-dependent enzyme that catalyzes the carboxylation
of pyruvate to produce oxaloacetate. In mammals, PC has
critical roles in gluconeogenesis, lipogenesis,
glyceroneogenesis, and insulin secretion. Inherited PC
deficiencies are linked to serious diseases in humans
such as lactic acidemia, hypoglycemia, psychomotor
retardation, and death. PC is a single-chain enzyme and
is active only in its homotetrameric form. PC has three
domains, an N-terminal biotin carboxylase domain, a
carboxyltransferase domain (this alignment model), and a
C-terminal biotin-carboxyl carrier protein domain. 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 = 275
Score = 26.2 bits (59), Expect = 1.1
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 30 GAAMASYLKSAPYGVNGIGLSMDSLHSSLGY 60
G A+A+YL +A GV+ + ++ L S G
Sbjct: 204 GLAVATYLAAAEAGVDIVDTAISPL--SGGT 232
>gnl|CDD|223403 COG0326, HtpG, Molecular chaperone, HSP90 family
[Posttranslational modification, protein turnover,
chaperones].
Length = 623
Score = 25.7 bits (57), Expect = 1.6
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 45 NGIGLSMDSLHSSLGYI 61
NGIG++ D + +LG I
Sbjct: 81 NGIGMTKDEVIENLGTI 97
>gnl|CDD|233052 TIGR00612, ispG_gcpE, 1-hydroxy-2-methyl-2-(E)-butenyl
4-diphosphate synthase. This protein of previously
unknown biochemical function has now been identified as
an enzyme of the non-mevalonate pathway of IPP
biosynthesis. Chlamydial members of the family have a
long insert. The family is largely restricted to
Bacteria, where it is widely but not universally
distributed. No homology can be detected between the
GcpE family and other proteins [Biosynthesis of
cofactors, prosthetic groups, and carriers, Other].
Length = 346
Score = 25.5 bits (56), Expect = 2.3
Identities = 10/27 (37%), Positives = 11/27 (40%), Gaps = 2/27 (7%)
Query: 9 LGC--NADGELAFPSFGTSCGGGGAAM 33
+GC N GE G S G G A
Sbjct: 295 MGCVVNGPGEAKHADIGISGPGTGFAW 321
>gnl|CDD|173750 cd07857, STKc_MPK1, Catalytic domain of the Serine/Threonine
Kinase, Fungal Mitogen-Activated Protein Kinase MPK1.
Serine/Threonine Kinases (STKs), Fungal
Mitogen-Activated Protein Kinase (MAPK) MPK1 subfamily,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The MPK1 subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. This subfamily is
composed of the MAPKs MPK1 from Saccharomyces
cerevisiae, Pmk1 from Schizosaccharomyces pombe, and
similar proteins. MAPKs are important mediators of
cellular responses to extracellular signals. MPK1 (also
called Slt2) and Pmk1 (also called Spm1) are
stress-activated MAPKs that regulate the cell wall
integrity (CWI) pathway, and are therefore important in
the maintainance of cell shape, cell wall construction,
morphogenesis, and ion homeostasis. MPK1 is activated in
response to cell wall stress including heat stimulation,
osmotic shock, UV irradiation, and any agents that
interfere with cell wall biogenesis such as chitin
antagonists, caffeine, or zymolase. MPK1 is regulated by
the MAP2Ks Mkk1/2, which are regulated by the MAP3K
Bck1. Pmk1 is also activated by multiple stresses
including elevated temperatures, hyper- or hypotonic
stress, glucose deprivation, exposure to cell-wall
damaging compounds, and oxidative stress. It is
regulated by the MAP2K Pek1, which is regulated by the
MAP3K Mkh1.
Length = 332
Score = 25.1 bits (55), Expect = 3.1
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 9 LGCNADGELAFPSFGTSCG 27
L NAD EL FG + G
Sbjct: 136 LLVNADCELKICDFGLARG 154
>gnl|CDD|223968 COG1038, PycA, Pyruvate carboxylase [Energy production and
conversion].
Length = 1149
Score = 25.0 bits (55), Expect = 3.2
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 30 GAAMASYLKSAPYGVNGIGLSMDSLHSSLGYIPSANDI 67
G +A+YL + GV+ + ++M S+ S L PS N I
Sbjct: 749 GNGVATYLAAVEAGVDIVDVAMASM-SGLTSQPSLNSI 785
>gnl|CDD|184298 PRK13748, PRK13748, putative mercuric reductase; Provisional.
Length = 561
Score = 24.7 bits (54), Expect = 3.6
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 27 GGGGAAMASYLKSAPYG 43
G GGAAMA+ LK+ G
Sbjct: 105 GSGGAAMAAALKAVEQG 121
>gnl|CDD|217410 pfam03184, DDE_1, DDE superfamily endonuclease. This family of
proteins are related to pfam00665 and are probably
endonucleases of the DDE superfamily. Transposase
proteins are necessary for efficient DNA transposition.
This domain is a member of the DDE superfamily, which
contain three carboxylate residues that are believed to
be responsible for coordinating metal ions needed for
catalysis. The catalytic activity of this enzyme
involves DNA cleavage at a specific site followed by a
strand transfer reaction. Interestingly this family
also includes the CENP-B protein. This domain in that
protein appears to have lost the metal binding residues
and is unlikely to have endonuclease activity.
Centromere Protein B (CENP-B) is a DNA-binding protein
localised to the centromere.
Length = 215
Score = 24.6 bits (54), Expect = 3.6
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 2 KVKWTKMLGCNADG 15
K +WT ++ NA G
Sbjct: 39 KRRWTVVICANAAG 52
>gnl|CDD|233700 TIGR02053, MerA, mercuric reductase. This model represents the
mercuric reductase found in the mer operon for the
detoxification of mercury compounds. MerA is a
FAD-containing flavoprotein which reduces Hg(II) to
Hg(0) utilizing NADPH [Cellular processes,
Detoxification].
Length = 463
Score = 24.7 bits (54), Expect = 4.3
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 27 GGGGAAMASYLKSAPYGV 44
G G AA A+ +K+A G
Sbjct: 7 GSGAAAFAAAIKAAELGA 24
>gnl|CDD|188570 TIGR04055, rSAM_NirJ2, putative heme d1 biosynthesis radical SAM
protein NirJ2. Members of this radical SAM protein
subfamily, designated NirJ2, occur in genomic contexts
with a paralog NirJ1 and with other nitrite reductase
operon genes associated with heme d1 biosynthesis, as in
Heliobacillus mobilis and Heliophilum fasciatum. NirJ2
is presumed by bioinformatics analysis (Xiong, et al.)
to be a heme d1 biosynthesis protein by context.
Length = 325
Score = 24.6 bits (54), Expect = 4.6
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 33 MASYLKSAPYGVNGIGLSMDSLHS 56
+A LK A G +G+S+DSL +
Sbjct: 89 VARKLKKA--GAMRVGISLDSLDA 110
>gnl|CDD|183670 PRK12671, PRK12671, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 120
Score = 24.2 bits (53), Expect = 5.3
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 20 PSFGTSCGGGGAAMASYL 37
P+ GTS G GG +AS L
Sbjct: 46 PTLGTSWGAGGILIASIL 63
>gnl|CDD|225958 COG3424, BcsA, Predicted naringenin-chalcone synthase [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 356
Score = 23.9 bits (52), Expect = 7.2
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 19 FPSFGTSCGGGGAAMA---SYLKSAPYGV 44
P +G C G A +A Y ++AP
Sbjct: 131 VPVWGLGCAAGAAGLARARDYCRAAPDAN 159
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
0.316 0.134 0.414
Gapped
Lambda K H
0.267 0.0758 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,289,725
Number of extensions: 228227
Number of successful extensions: 218
Number of sequences better than 10.0: 1
Number of HSP's gapped: 218
Number of HSP's successfully gapped: 15
Length of query: 67
Length of database: 10,937,602
Length adjustment: 38
Effective length of query: 29
Effective length of database: 9,252,150
Effective search space: 268312350
Effective search space used: 268312350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.1 bits)