RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12207
(69 letters)
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 38.0 bits (89), Expect = 2e-05
Identities = 14/39 (35%), Positives = 26/39 (66%), Gaps = 1/39 (2%)
Query: 19 PGDNGIYVTKIMDGGAAQVDGRLQVGDKLIAVRNSTVSK 57
GD GI+V++++ GGAA+ G LQ GD+++++ +
Sbjct: 21 DGDPGIFVSEVLPGGAAEAGG-LQEGDRILSINGQDLEN 58
>gnl|CDD|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of
Eumetazoan signaling molecules, often in tandem
arrangements. May be responsible for specific
protein-protein interactions, as most PDZ domains bind
C-terminal polypeptides, and binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this subfamily of PDZ domains an
N-terminal beta-strand forms the peptide-binding groove
base, a circular permutation with respect to PDZ
domains found in proteases.
Length = 82
Score = 35.2 bits (82), Expect = 2e-04
Identities = 12/30 (40%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 21 DNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 50
GI+V+++ GG A+ G L+VGD+++ V
Sbjct: 25 GGGIFVSRVEPGGPAE-RGGLRVGDRILEV 53
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some
PDZs have been shown to bind C-terminal polypeptides;
others appear to bind internal (non-C-terminal)
polypeptides. Different PDZs possess different binding
specificities.
Length = 85
Score = 33.9 bits (78), Expect = 0.001
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 21 DNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 50
G+ V+ ++ G A G L+VGD ++ V
Sbjct: 25 GGGVVVSSVVPGSPAAKAG-LRVGDVILEV 53
>gnl|CDD|238486 cd00986, PDZ_LON_protease, PDZ domain of ATP-dependent LON serine
proteases. Most PDZ domains bind C-terminal
polypeptides, though binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this bacterial subfamily of
protease-associated PDZ domains a C-terminal
beta-strand is thought to form the peptide-binding
groove base, a circular permutation with respect to PDZ
domains found in Eumetazoan signaling proteins.
Length = 79
Score = 30.1 bits (68), Expect = 0.025
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 22 NGIYVTKIMDGGAAQVDGRLQVGDKLIAVRNSTVSK 57
+G+YVT +++G A G+L+ GD +IAV +
Sbjct: 8 HGVYVTSVVEGMPAA--GKLKAGDHIIAVDGKPFKE 41
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization
through PDZ-PDZ domain interactions adds to the
domain's versatility, and PDZ domain-mediated
interactions may be modulated dynamically through
target phosphorylation. Some PDZ domains play a role in
scaffolding supramolecular complexes. PDZ domains are
found in diverse signaling proteins in bacteria,
archebacteria, and eurkayotes. This CD contains two
distinct structural subgroups with either a N- or
C-terminal beta-strand forming the peptide-binding
groove base. The circular permutation placing the
strand on the N-terminus appears to be found in
Eumetazoa only, while the C-terminal variant is found
in all three kingdoms of life, and seems to co-occur
with protease domains. PDZ domains have been named
after PSD95(post synaptic density protein), DlgA
(Drosophila disc large tumor suppressor), and ZO1, a
mammalian tight junction protein.
Length = 70
Score = 29.6 bits (67), Expect = 0.035
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 20 GDNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 50
+ G+ V + G A+ LQ GD ++AV
Sbjct: 11 TEGGVVVLSVEPGSPAE-RAGLQAGDVILAV 40
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function
in posttranslational protein processing, maturation,
and disassembly or degradation, in Bacteria, Archaea,
and plant chloroplasts. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 85
Score = 27.6 bits (62), Expect = 0.25
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 11 GGIGNQHIPGDNGIYVTKIMDGGAAQVDGRLQVGDKLIAVRNSTVSKGP 59
GGIG + D G+ +T ++ G A G ++ GD ++A+ V
Sbjct: 2 GGIGLELKYDDGGLVITSVLPGSPAAKAG-IKAGDIIVAIDGEPVDGLS 49
>gnl|CDD|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be
responsible for substrate recognition and/or binding,
as most PDZ domains bind C-terminal polypeptides, and
binding to internal (non-C-terminal) polypeptides and
even to lipids has been demonstrated. In this subfamily
of protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 79
Score = 25.7 bits (57), Expect = 1.0
Identities = 7/32 (21%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 25 YVTKIMDGGAAQVDGRLQVGDKLIAVRNSTVS 56
+ +++ G A G L+ GD+++A+ +
Sbjct: 15 VIGEVVPGSPAAKAG-LKAGDRILAINGQKIK 45
>gnl|CDD|238487 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
proteases, such as DegP/HtrA, which are oligomeric
proteins involved in heat-shock response, chaperone
function, and apoptosis. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in Eumetazoan signaling proteins.
Length = 90
Score = 25.7 bits (57), Expect = 1.1
Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 19 PGDNGIYVTKIMDGGAAQVDGRLQVGDKLIAVRNSTVS 56
G+ V + G A G L+ GD ++AV V
Sbjct: 21 KDTKGVLVASVDPGSPAAKAG-LKPGDVILAVNGKPVK 57
>gnl|CDD|132143 TIGR03099, dCO2ase_PEP1, pyridoxal-dependent decarboxylase,
exosortase A system-associated. The sequences in this
family contain the pyridoxal binding domain (pfam02784)
and C-terminal sheet domain (pfam00278) of a family of
Pyridoxal-dependent decarboxylases. Characterized
enzymes in this family decarboxylate substrates such as
ornithine, diaminopimelate and arginine. The genes of
the family modeled here, with the exception of those
observed in certain Burkholderia species, are all found
in the context of exopolysaccharide biosynthesis loci
containing the exosortase/PEP-CTERM protein sorting
system. More specifically, these are characteristic of
the type 1 exosortase system represented by the Genome
Property GenProp0652. The substrate of these enzymes may
be a precursor of the carrier or linker which is
hypothesized to release the PEP-CTERM protein from the
exosortase enzyme. These enzymes are apparently most
closely related to the diaminopimelate decarboxylase
modeled by TIGR01048 which may suggest a similarity (or
identity) of substrate.
Length = 398
Score = 26.2 bits (58), Expect = 1.3
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 18/74 (24%)
Query: 5 PIYNIAGGIGNQHIPGDNGIYVTKIMDGGAAQVD---------------GRLQVGDKLI- 48
+ NI GG G + PG+ + + + AA GR VG+ I
Sbjct: 227 RVINIGGGFGIPYFPGNPPLDLAPVGAALAALFARLRDALPEVEILLELGRYLVGEAGIY 286
Query: 49 --AVRNSTVSKGPT 60
V + +S+G T
Sbjct: 287 VCRVIDRKISRGET 300
>gnl|CDD|226011 COG3480, SdrC, Predicted secreted protein containing a PDZ domain
[Signal transduction mechanisms].
Length = 342
Score = 25.8 bits (57), Expect = 1.6
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 22 NGIYVTKIMDGGAAQVDGRLQVGDKLIAVRNSTVS 56
G+YV ++D + G+L+ GD +IAV +
Sbjct: 130 AGVYVLSVIDNSPFK--GKLEAGDTIIAVDGEPFT 162
>gnl|CDD|238275 cd00493, FabA_FabZ, FabA/Z, beta-hydroxyacyl-acyl carrier protein
(ACP)-dehydratases: One of several distinct enzyme types
of the dissociative, type II, fatty acid synthase system
(found in bacteria and plants) required to complete
successive cycles of fatty acid elongation. The third
step of the elongation cycle, the dehydration of
beta-hydroxyacyl-ACP to trans-2-acyl-ACP, is catalyzed
by FabA or FabZ. FabA is bifunctional and catalyzes an
additional isomerization reaction of trans-2-acyl-ACP to
cis-3-acyl-ACP, an essential reaction to unsaturated
fatty acid synthesis. FabZ is the primary dehydratase
that participates in the elongation cycles of saturated
as well as unsaturated fatty acid biosynthesis, whereas
FabA is more active in the dehydration of
beta-hydroxydecanoyl-ACP. The FabA structure is
homodimeric with two independent active sites located at
the dimer interface.
Length = 131
Score = 24.2 bits (53), Expect = 5.0
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 16 QHIPGDNGIYVTKI--MDGGAAQVDGRLQVGDKLIAVR 51
+PGD ++ + G + DGR V KL+A
Sbjct: 88 PVLPGDTLTLEVELLKVRRGLGKFDGRAYVDGKLVAEA 125
>gnl|CDD|235394 PRK05297, PRK05297, phosphoribosylformylglycinamidine synthase;
Provisional.
Length = 1290
Score = 24.0 bits (53), Expect = 9.0
Identities = 17/47 (36%), Positives = 19/47 (40%), Gaps = 22/47 (46%)
Query: 5 PIYNIAGGIGN---QHIPGDNGIYVTKIMDGGAAQVDGRLQVGDKLI 48
PI +AGGIGN H V K G + VG KLI
Sbjct: 405 PIM-LAGGIGNIRADH--------VQK----------GEIPVGAKLI 432
>gnl|CDD|219679 pfam07977, FabA, FabA-like domain. This enzyme domain has a HotDog
fold.
Length = 133
Score = 23.3 bits (51), Expect = 9.8
Identities = 14/53 (26%), Positives = 19/53 (35%), Gaps = 11/53 (20%)
Query: 8 NIAGGIGN-----QHIPGDN----GIYVTKIMD--GGAAQVDGRLQVGDKLIA 49
GI Q PGD + + +I+ G DGR V KL+
Sbjct: 78 RARFGIDEVKFRGQVTPGDKQLRYEVEIKRIIPRRGVIGIADGRALVDGKLVY 130
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
0.320 0.142 0.433
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,406,475
Number of extensions: 248681
Number of successful extensions: 207
Number of sequences better than 10.0: 1
Number of HSP's gapped: 202
Number of HSP's successfully gapped: 14
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.3 bits)