RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12206
(164 letters)
>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 = 47.2 bits (113), Expect = 6e-08
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 7/59 (11%)
Query: 42 ILDIELVKG-NKGLGFSIAGGIGNQHIPGDNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 99
+ + L K GLGFS+ GG + GI+V+++ GG A+ G L+VGD+++ V
Sbjct: 1 VRTVTLRKDPGGGLGFSLRGGKDS-----GGGIFVSRVEPGGPAE-RGGLRVGDRILEV 53
Score = 34.5 bits (80), Expect = 0.003
Identities = 12/30 (40%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 130 DNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 159
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 = 47.4 bits (113), Expect = 7e-08
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 41 KILDIELVKGNKGLGFSIAGGIGNQHIPGDNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 99
+ +EL KG GLGFS+ GG G+ V+ ++ G A G L+VGD ++ V
Sbjct: 1 EPRLVELEKGGGGLGFSLVGGKDE-----GGGVVVSSVVPGSPAAKAG-LRVGDVILEV 53
Score = 32.7 bits (75), Expect = 0.016
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 130 DNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 159
G+ V+ ++ G A G L+VGD ++ V
Sbjct: 25 GGGVVVSSVVPGSPAAKAG-LRVGDVILEV 53
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 43.8 bits (104), Expect = 1e-06
Identities = 22/50 (44%), Positives = 34/50 (68%), Gaps = 6/50 (12%)
Query: 50 GNKGLGFSIAGGIGNQHIPGDNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 99
G GLGFS+ GG GD GI+V++++ GGAA+ G LQ GD+++++
Sbjct: 8 GRGGLGFSLVGGS-----DGDPGIFVSEVLPGGAAEAGG-LQEGDRILSI 51
Score = 36.8 bits (86), Expect = 4e-04
Identities = 14/32 (43%), Positives = 25/32 (78%), Gaps = 1/32 (3%)
Query: 128 PGDNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 159
GD GI+V++++ GGAA+ G LQ GD+++++
Sbjct: 21 DGDPGIFVSEVLPGGAAEAGG-LQEGDRILSI 51
>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 = 31.9 bits (73), Expect = 0.027
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 8/48 (16%)
Query: 52 KGLGFSIAGGIGNQHIPGDNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 99
GLGFSI GG + G+ V + G A+ LQ GD ++AV
Sbjct: 1 GGLGFSIRGGT-------EGGVVVLSVEPGSPAE-RAGLQAGDVILAV 40
Score = 28.8 bits (65), Expect = 0.30
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 129 GDNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 159
+ G+ V + G A+ LQ GD ++AV
Sbjct: 11 TEGGVVVLSVEPGSPAE-RAGLQAGDVILAV 40
>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 = 28.6 bits (64), Expect = 0.51
Identities = 13/29 (44%), Positives = 21/29 (72%), Gaps = 2/29 (6%)
Query: 71 NGIYVTKIMDGGAAQVDGRLQVGDKLIAV 99
+G+YVT +++G A G+L+ GD +IAV
Sbjct: 8 HGVYVTSVVEGMPAA--GKLKAGDHIIAV 34
Score = 28.6 bits (64), Expect = 0.51
Identities = 13/29 (44%), Positives = 21/29 (72%), Gaps = 2/29 (6%)
Query: 131 NGIYVTKIMDGGAAQVDGRLQVGDKLIAV 159
+G+YVT +++G A G+L+ GD +IAV
Sbjct: 8 HGVYVTSVVEGMPAA--GKLKAGDHIIAV 34
>gnl|CDD|99782 cd06185, PDR_like, Phthalate dioxygenase reductase (PDR) is an
FMN-dependent reductase that mediates electron transfer
from NADH to FMN to an iron sulfur cluster. PDR has an
an N-terminal ferrredoxin reductase (FNR)-like NAD(H)
binding domain and a C-terminal iron-sulfur [2Fe-2S]
cluster domain. Although structurally homologous to FNR,
PDR binds FMN rather than FAD in it's FNR-like domain.
Electron transfer between pyrimidines and iron-sulfur
clusters (Rieske center [2Fe-2S]) or heme groups is
mediated by flavins in respiration, photosynthesis, and
oxygenase systems. Type I dioxygenase systems, including
the hydroxylate phthalate system, have 2 components, a
monomeric reductase consisting of a flavin and a 2Fe-2S
center and a multimeric oxygenase. In contrast to other
Rieske dioxygenases the ferredoxin like domain is C-,
not N-terminal.
Length = 211
Score = 27.8 bits (63), Expect = 2.0
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 81 GGAAQVDGRLQVGDKLIAV--RNSTSEDKRASPGIFLCNIAGGIG 123
GG+ + L+VGD+L RN D+ A + IAGGIG
Sbjct: 68 GGSRYMHELLRVGDELEVSAPRNLFPLDEAARRHLL---IAGGIG 109
>gnl|CDD|119282 pfam10762, DUF2583, Protein of unknown function (DUF2583). Some
members in this family of proteins are annotated as YchH
however currently no function is known.
Length = 89
Score = 27.0 bits (60), Expect = 2.1
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 20/91 (21%)
Query: 29 VRRKKVTRQGNMKILDIELVKGNKGLGFSIAGGIGNQHIPGDN-----------GIYVTK 77
++RK GN+ ++ + LV G+G+SI +P N I+V
Sbjct: 1 MKRKNAAILGNV-LMGLGLVTMVVGVGYSILA-----QVPQFNLPQFFAHGALLSIFVGA 54
Query: 78 IMDGGAAQVDGRLQVGDKLIAVRNSTSEDKR 108
++ A++ GR +V D+ V++ DKR
Sbjct: 55 LLWLVGARIGGREEVADRYWWVKHF---DKR 82
>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 = 26.4 bits (59), Expect = 2.5
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 60 GGIGNQHIPGDNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 99
GGIG + D G+ +T ++ G A G ++ GD ++A+
Sbjct: 2 GGIGLELKYDDGGLVITSVLPGSPAAKAG-IKAGDIIVAI 40
Score = 26.4 bits (59), Expect = 2.5
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 120 GGIGNQHIPGDNGIYVTKIMDGGAAQVDGRLQVGDKLIAV 159
GGIG + D G+ +T ++ G A G ++ GD ++A+
Sbjct: 2 GGIGLELKYDDGGLVITSVLPGSPAAKAG-IKAGDIIVAI 40
>gnl|CDD|182651 PRK10692, PRK10692, hypothetical protein; Provisional.
Length = 92
Score = 26.9 bits (60), Expect = 2.6
Identities = 26/90 (28%), Positives = 41/90 (45%), Gaps = 20/90 (22%)
Query: 30 RRKKVTRQGNMKILDIELVKGNKGLGFSIAGGIGNQHIPGDN-----------GIYVTKI 78
+RK + GN+ ++ + LV G+G+SI +P N I+V +
Sbjct: 2 KRKNASLLGNV-LMGLGLVVMVVGVGYSILN-----QLPQLNLPQFFAHGALLSIFVGAL 55
Query: 79 MDGGAAQVDGRLQVGDKLIAVRNSTSEDKR 108
+ A+V GR QV D+ VR+ DKR
Sbjct: 56 LWLAGARVGGREQVADRYWWVRHY---DKR 82
>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 = 27.8 bits (62), Expect = 2.7
Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 21/85 (24%)
Query: 56 FSIAGGIGNQHIPGDNGIYVTKIMDGGAAQVDGRLQVGDKLIAVRNSTSEDKRASPGIFL 115
+I GG G + PG+ + + + AA RL+ A P + +
Sbjct: 229 INIGGGFGIPYFPGNPPLDLAPVGAALAALFA-RLR----------------DALPEVEI 271
Query: 116 CNIAGGIGNQHIPGDNGIYVTKIMD 140
G +++ G+ GIYV +++D
Sbjct: 272 LLELG----RYLVGEAGIYVCRVID 292
Score = 27.8 bits (62), Expect = 2.8
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 115 LCNIAGGIGNQHIPGDNGIYVTKIMDGGAAQVD 147
+ NI GG G + PG+ + + + AA
Sbjct: 228 VINIGGGFGIPYFPGNPPLDLAPVGAALAALFA 260
>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 = 25.3 bits (56), Expect = 6.2
Identities = 7/26 (26%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 74 YVTKIMDGGAAQVDGRLQVGDKLIAV 99
+ +++ G A G L+ GD+++A+
Sbjct: 15 VIGEVVPGSPAAKAG-LKAGDRILAI 39
Score = 25.3 bits (56), Expect = 6.2
Identities = 7/26 (26%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 134 YVTKIMDGGAAQVDGRLQVGDKLIAV 159
+ +++ G A G L+ GD+++A+
Sbjct: 15 VIGEVVPGSPAAKAG-LKAGDRILAI 39
>gnl|CDD|224999 COG2088, SpoVG, Uncharacterized protein, involved in the
regulation of septum location [Cell envelope
biogenesis, outer membrane].
Length = 95
Score = 25.1 bits (55), Expect = 9.3
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 12/38 (31%)
Query: 29 VRRKKVTRQGNMK------------ILDIELVKGNKGL 54
VR +KV G MK + DI +++GN GL
Sbjct: 6 VRIRKVDTDGRMKAYVSVTLDNEFVVHDIRVIEGNNGL 43
>gnl|CDD|146585 pfam04026, SpoVG, SpoVG. Stage V sporulation protein G.
Essential for sporulation and specific to stage V
sporulation in Bacillus megaterium and subtilis. In B.
subtilis, expression decreases after 30-60 minutes of
cold shock.
Length = 83
Score = 24.8 bits (55), Expect = 9.6
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 12/38 (31%)
Query: 29 VRRKKVTRQGNMK------------ILDIELVKGNKGL 54
VR +KV +G +K + DI++++G KGL
Sbjct: 5 VRVRKVEGEGRLKAYASITFDNCFVVHDIKVIEGKKGL 42
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 0.141 0.409
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: 8,223,830
Number of extensions: 757498
Number of successful extensions: 556
Number of sequences better than 10.0: 1
Number of HSP's gapped: 541
Number of HSP's successfully gapped: 34
Length of query: 164
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 74
Effective length of database: 6,945,742
Effective search space: 513984908
Effective search space used: 513984908
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 (21.8 bits)
S2: 55 (25.0 bits)