RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4919
(96 letters)
>gnl|CDD|223237 COG0159, TrpA, Tryptophan synthase alpha chain [Amino acid
transport and metabolism].
Length = 265
Score = 33.0 bits (76), Expect = 0.011
Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 10/58 (17%)
Query: 18 KPSFL----TDQELKHLILEAADGFLFVVACDTGRVVVTGLGLPCSDSVD--IEKVRE 69
P FL T E I EAA GF++ V+ G VTG P S V +++VR+
Sbjct: 149 DPIFLVAPTTPDERLKKIAEAASGFIYYVSR-MG---VTGARNPVSADVKELVKRVRK 202
>gnl|CDD|240075 cd04724, Tryptophan_synthase_alpha, Ttryptophan synthase (TRPS)
alpha subunit (TSA). TPRS is a bifunctional tetrameric
enzyme (2 alpha and 2 beta subunits) that catalyzes the
last two steps of L-tryptophan biosynthesis. Alpha and
beta subunit catalyze two distinct reactions which are
both strongly stimulated by the formation of the
complex. The alpha subunit catalyzes the cleavage of
indole 3-glycerol phosphate (IGP) to indole and
d-glyceraldehyde 3-phosphate (G3P). Indole is then
channeled to the active site of the beta subunit, a
PLP-dependent enzyme that catalyzes a replacement
reaction to convert L-serine into L-tryptophan.
Length = 242
Score = 32.4 bits (75), Expect = 0.019
Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 8/60 (13%)
Query: 23 TDQELKHLILEAADGFLFVVACDTGRVVVTGLGLPCSDSVD--IEKVREQLSTQEPQNAG 80
T E I E A GF++ V R VTG D + I+++R+ T P G
Sbjct: 140 TPDERIKKIAELASGFIYYV----SRTGVTGARTELPDDLKELIKRIRKY--TDLPIAVG 193
>gnl|CDD|163682 cd07944, DRE_TIM_HOA_like, 4-hydroxy-2-oxovalerate aldolase-like,
N-terminal catalytic TIM barrel domain. This family of
bacterial enzymes is sequence-similar to
4-hydroxy-2-oxovalerate aldolase (HOA) but its exact
function is unknown. This family includes the
Bacteroides vulgatus Bvu_2661 protein and 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 = 266
Score = 27.1 bits (61), Expect = 1.4
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 21 FLTDQELKHLILEAADGFLFVVACDTGRVVVTGLGLPCSDSVDIEKVR 68
F D+ L+ L+ ++ V D G + L P S SV ++ +R
Sbjct: 55 FCDDEFLRRLLGDSKGNTKIAVMVDYGNDDID-LLEPASGSV-VDMIR 100
>gnl|CDD|119334 cd06564, GH20_DspB_LnbB-like, Glycosyl hydrolase family 20 (GH20)
catalytic domain of dispersin B (DspB),
lacto-N-biosidase (LnbB) and related proteins.
Dispersin B is a soluble beta-N-acetylglucosamidase
found in bacteria that hydrolyzes the beta-1,6-linkages
of PGA (poly-beta-(1,6)-N-acetylglucosamine), a major
component of the extracellular polysaccharide matrix.
Lacto-N-biosidase hydrolyzes lacto-N-biose (LNB) type I
oligosaccharides at the nonreducing terminus to produce
lacto-N-biose as part of the GNB/LNB
(galacto-N-biose/lacto-N-biose I) degradation pathway.
The lacto-N-biosidase from Bifidobacterium bifidum has
this GH20 domain, a carbohydrate binding module 32, and
a bacterial immunoglobulin-like domain 2, as well as a
YSIRK signal peptide and a G5 membrane anchor at the N
and C termini, respectively. The GH20 hexosaminidases
are thought to act via a catalytic mechanism in which
the catalytic nucleophile is not provided by solvent or
the enzyme, but by the substrate itself.
Length = 326
Score = 26.9 bits (60), Expect = 1.5
Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 5/29 (17%)
Query: 8 TGNTSTDGTYKPSFLTDQELKHLILEAAD 36
T+ DG + T +E K LI A D
Sbjct: 70 YNLTANDG-----YYTKEEFKELIAYAKD 93
>gnl|CDD|238279 cd00501, Peptidase_C15, Pyroglutamyl peptidase (PGP) type I, also
known as pyrrolidone carboxyl peptidase (pcp) type I:
Enzymes responsible for cleaving pyroglutamate (pGlu)
from the N-terminal end of specialized proteins. The
N-terminal pGlu protects these proteins from
proteolysis by other proteases until the pGlu is
removed by a PGP. PGPs are cysteine proteases with a
Cys-His-Glu/Asp catalytic triad. Type I PGPs are found
in a wide variety of prokaryotes and eukaryotes. It is
not clear whether the functional form is a monomer, a
homodimer, or a homotetramer.
Length = 194
Score = 26.8 bits (60), Expect = 1.6
Identities = 9/32 (28%), Positives = 13/32 (40%)
Query: 46 TGRVVVTGLGLPCSDSVDIEKVREQLSTQEPQ 77
G V GL LP +E + E + +P
Sbjct: 31 LGGAEVVGLELPVVFQKAVEVLPELIEEHKPD 62
>gnl|CDD|221096 pfam11368, DUF3169, Protein of unknown function (DUF3169). Some
members in this family of proteins are annotated as
membrane proteins however this cannot be confirmed.
Currently there is no known function.
Length = 248
Score = 26.9 bits (60), Expect = 1.8
Identities = 10/39 (25%), Positives = 18/39 (46%)
Query: 16 TYKPSFLTDQELKHLILEAADGFLFVVACDTGRVVVTGL 54
Y+ S+ L +IL FLF+++ TG + +
Sbjct: 188 NYESSYKIYFVLNQVILPLLYVFLFIISILTGENQILAI 226
>gnl|CDD|238430 cd00834, KAS_I_II, Beta-ketoacyl-acyl carrier protein (ACP)
synthase (KAS), type I and II. KASs are responsible for
the elongation steps in fatty acid biosynthesis. KASIII
catalyses the initial condensation and KAS I and II
catalyze further elongation steps by Claisen
condensation of malonyl-acyl carrier protein (ACP) with
acyl-ACP.
Length = 406
Score = 26.3 bits (59), Expect = 2.9
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 48 RVVVTGLGLPCSDSVDIEKVREQL 71
RVV+TGLG +E+ E L
Sbjct: 2 RVVITGLGAVTPLGNGVEEFWEAL 25
>gnl|CDD|238599 cd01194, INT_Tn554A_C, Tn544A and related transposases, DNA
breaking-rejoining enzymes, integrase/recombinases,
C-terminal catalytic domain. This CD includes various
bacterial transposases similar to TnpA from transposon
Tn554.
Length = 186
Score = 25.9 bits (57), Expect = 3.1
Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 22 LTDQELKHLILEAA---DGFLFVVACDTGRVVVTGLGLPCSDSVDIEKVREQLSTQEPQN 78
LT E++ LI D FLF + +TG + LGL D E + ++ N
Sbjct: 1 LTPSEVQRLINACGNLRDKFLFALLYETGLRIGEALGLRIEDIDLAENQIWLVPREDNAN 60
Query: 79 AGRILDLKTGTVKK 92
R K+G ++
Sbjct: 61 GARA---KSGRERR 71
>gnl|CDD|235987 PRK07314, PRK07314, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 411
Score = 25.9 bits (58), Expect = 3.4
Identities = 8/9 (88%), Positives = 8/9 (88%)
Query: 48 RVVVTGLGL 56
RVVVTGLG
Sbjct: 3 RVVVTGLGA 11
>gnl|CDD|118121 pfam09585, Lin0512_fam, Conserved hypothetical protein
(Lin0512_fam). This family consists of few members,
broadly distributed. It occurs so far in several
Firmicutes (twice in Oceanobacillus), one
Cyanobacterium, one alpha Proteobacterium, and (with a
long prefix) in plants. The function is unknown. The
alignment includes a well conserved motif GxGxDxHG near
the N-terminus.
Length = 113
Score = 25.3 bits (56), Expect = 4.6
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 48 RVVVTGLGLPCSDSVDIEKVREQL 71
RV V +G+P + VD E V+ L
Sbjct: 50 RVQVK-VGVPRPEQVDEEAVKAVL 72
>gnl|CDD|200247 TIGR03150, fabF, beta-ketoacyl-acyl-carrier-protein synthase II.
3-oxoacyl-[acyl-carrier-protein] synthase 2 (KAS-II,
FabF) is involved in the condensation step of fatty
acid biosynthesis in which the malonyl donor group is
decarboxylated and the resulting carbanion used to
attack and extend the acyl group attached to the acyl
carrier protein. Most genomes encoding fatty acid
biosynthesis contain a number of condensing enzymes,
often of all three types: 1, 2 and 3. Synthase 2 is
mechanistically related to synthase 1 (KAS-I, FabB)
containing a number of absolutely conserved catalytic
residues in common. This model is based primarily on
genes which are found in apparent operons with other
essential genes of fatty acid biosynthesis
(GenProp0681). The large gap between the trusted cutoff
and the noise cutoff contains many genes which are not
found adjacent to genes of the fatty acid pathway in
genomes that often also contain a better hit to this
model. These genes may be involved in other processes
such as polyketide biosyntheses. Some genomes contain
more than one above-trusted hit to this model which may
result from recent paralogous expansions. Second hits
to this model which are not next to other fatty acid
biosynthesis genes may be involved in other processes.
FabB sequences should fall well below the noise cutoff
of this model [Fatty acid and phospholipid metabolism,
Biosynthesis].
Length = 407
Score = 25.5 bits (57), Expect = 4.7
Identities = 8/9 (88%), Positives = 8/9 (88%)
Query: 48 RVVVTGLGL 56
RVVVTGLG
Sbjct: 2 RVVVTGLGA 10
>gnl|CDD|188504 TIGR03989, Rxyl_3153, oxidoreductase, Rxyl_3153 family. This model
describes a clade within the family pfam00107 of
zinc-binding dehydrogenases. The family pfam00107
contains class III alcohol dehydrogenases, including
enzymes designated S-(hydroxymethyl)glutathione
dehydrogenase and NAD/mycothiol-dependent formaldehyde
dehydrogenase. Members of the current family occur only
in species that contain the very small protein
mycofactocin (TIGR03969), a possible cofactor precursor,
and radical SAM protein TIGR03962. We name this family
for Rxyl_3153, where the lone member of the family
co-clusters with these markers in Rubrobacter
xylanophilus [Unknown function, Enzymes of unknown
specificity].
Length = 369
Score = 25.4 bits (56), Expect = 5.2
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 46 TGRVVVTGLGLPCSDSVDI 64
GRVVVTGLG V +
Sbjct: 279 GGRVVVTGLGPMADVDVKV 297
>gnl|CDD|237285 PRK13111, trpA, tryptophan synthase subunit alpha; Provisional.
Length = 258
Score = 25.5 bits (57), Expect = 5.3
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 6/49 (12%)
Query: 23 TDQELKHLILEAADGFLFVVACDTGRVVVTGLGLPCSDSVD--IEKVRE 69
T E I A GF++ V+ G VTG + + + +++
Sbjct: 153 TTDERLKKIASHASGFVYYVSR-AG---VTGARSADAADLAELVARLKA 197
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 25.4 bits (57), Expect = 5.7
Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 6/41 (14%)
Query: 45 DTGRVVVTGLGLPCSDSVDIEKVREQLSTQEPQNAGRILDL 85
+ G TGL + +E++RE+L P R+ +
Sbjct: 402 EIGV---TGLDEDLFEEESLEELREELKEPTP---ERLFYI 436
>gnl|CDD|215136 PLN02245, PLN02245, ATP phosphoribosyl transferase.
Length = 403
Score = 25.1 bits (55), Expect = 7.1
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 4 SQERTGNTSTDGTY-KPSFLTDQELKHLILEAADGFL 39
++ER T TY P F+ D KH+ ADG L
Sbjct: 192 TEERPLRVVTGFTYLGPKFMKDNGFKHVTFSTADGAL 228
>gnl|CDD|107297 cd06302, PBP1_LsrB_Quorum_Sensing, Periplasmic binding domain of
autoinducer-2 (AI-2) receptor LsrB from Salmonella
typhimurium and its close homologs. Periplasmic binding
domain of autoinducer-2 (AI-2) receptor LsrB from
Salmonella typhimurium and its close homologs from other
bacteria. The members of this group are homologous to a
family of periplasmic pentose/hexose sugar-binding
proteins that function as the primary receptors for
chemotaxis and transporters of many sugar based solutes
in bacteria and archaea and that are a member of the
type I periplasmic binding protein superfamily. LsrB
binds a chemically distinct form of the AI-2 signal that
lacks boron, in contrast to the Vibrio harveyi AI-2
signaling molecule that has an unusual furanosyl borate
diester. Hence, many bacteria coordinate their gene
expression according to the local density of their
population by producing species specific AI-2. This
process of quorum sensing allows LsrB to function as a
periplasmic AI-2 binding protein in interspecies
signaling.
Length = 298
Score = 24.9 bits (55), Expect = 8.7
Identities = 9/11 (81%), Positives = 10/11 (90%)
Query: 47 GRVVVTGLGLP 57
G+V VTGLGLP
Sbjct: 211 GKVAVTGLGLP 221
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
0.313 0.132 0.371
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,736,857
Number of extensions: 391794
Number of successful extensions: 315
Number of sequences better than 10.0: 1
Number of HSP's gapped: 315
Number of HSP's successfully gapped: 23
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
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: 53 (24.2 bits)