RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7758
(235 letters)
>gnl|CDD|214614 smart00317, SET, SET (Su(var)3-9, Enhancer-of-zeste, Trithorax)
domain. Putative methyl transferase, based on outlier
plant homologues.
Length = 124
Score = 144 bits (364), Expect = 4e-44
Identities = 53/117 (45%), Positives = 75/117 (64%)
Query: 28 PPLEVFNTGSRGWGLKALTDLKRGQFVVEYVGEMIDQKELNRRRRDMDRNNDHNYYFLSL 87
LEVF + +GWG++A D+ +G+F+ EYVGE+I +E R + D + +Y +
Sbjct: 1 NKLEVFKSPGKGWGVRATEDIPKGEFIGEYVGEIITSEEAEERPKAYDTDGAKAFYLFDI 60
Query: 88 DNSRYIDAGKKGNLARFMNHSCEPNCTAEKWTVSGDTRVGLFALRDVPAGTELVFNY 144
D+ IDA +KGNLARF+NHSCEPNC V+GD R+ +FALRD+ G EL +Y
Sbjct: 61 DSDLCIDARRKGNLARFINHSCEPNCELLFVEVNGDDRIVIFALRDIKPGEELTIDY 117
>gnl|CDD|216155 pfam00856, SET, SET domain. SET domains are protein lysine
methyltransferase enzymes. SET domains appear to be
protein-protein interaction domains. It has been
demonstrated that SET domains mediate interactions with
a family of proteins that display similarity with
dual-specificity phosphatases (dsPTPases). A subset of
SET domains have been called PR domains. These domains
are divergent in sequence from other SET domains, but
also appear to mediate protein-protein interaction. The
SET domain consists of two regions known as SET-N and
SET-C. SET-C forms an unusual and conserved knot-like
structure of probably functional importance.
Additionally to SET-N and SET-C, an insert region
(SET-I) and flanking regions of high structural
variability form part of the overall structure.
Length = 113
Score = 117 bits (295), Expect = 6e-34
Identities = 44/112 (39%), Positives = 63/112 (56%), Gaps = 6/112 (5%)
Query: 39 GWGLKALTDLKRGQFVVEYVGEMIDQKELNRRRRDMDRN------NDHNYYFLSLDNSRY 92
G GL A D+ +G+ ++EYVGE+I +E R ++ +D + LD+
Sbjct: 1 GRGLFATRDIPKGELIIEYVGELITPEEAEERELLYNKEELRGLLSDLELFLSRLDSEYD 60
Query: 93 IDAGKKGNLARFMNHSCEPNCTAEKWTVSGDTRVGLFALRDVPAGTELVFNY 144
IDA GN+ARF+NHSCEPNC V+G R+ + ALRD+ G EL +Y
Sbjct: 61 IDATGLGNVARFINHSCEPNCEVRFVFVNGGDRIVVRALRDIKPGEELTIDY 112
>gnl|CDD|225491 COG2940, COG2940, Proteins containing SET domain [General function
prediction only].
Length = 480
Score = 92.2 bits (229), Expect = 1e-21
Identities = 51/149 (34%), Positives = 83/149 (55%), Gaps = 7/149 (4%)
Query: 28 PPLEVFNTGSRGWGLKALTDLKRGQFVVEYVGEMIDQKELNRRRRDMDRNNDHNYYFLSL 87
P V + +G+G+ AL +K+G+F++EY GE+I +KE R + D + + L
Sbjct: 332 EPNVVQESEIKGYGVFALESIKKGEFIIEYHGEIIRRKEAREREENYDLLGNEFSFGLLE 391
Query: 88 DNSRYIDAGKKGNLARFMNHSCEPNCTAEKWTVSGDTRVGLFALRDVPAGTELVFNYELQ 147
D + D+ K G++ARF+NHSC PNC A V+G ++ ++A+RD+ AG EL ++Y
Sbjct: 392 DKDKVRDSQKAGDVARFINHSCTPNCEASPIEVNGIFKISIYAIRDIKAGEELTYDYGPS 451
Query: 148 KADNDGMRR-------CMCGAASCSGFIG 169
DN +++ C CG CS +
Sbjct: 452 LEDNRELKKLLEKRWGCACGEDRCSHTMS 480
>gnl|CDD|238247 cd00433, Peptidase_M17, Cytosol aminopeptidase family, N-terminal
and catalytic domains. Family M17 contains zinc- and
manganese-dependent exopeptidases ( EC 3.4.11.1),
including leucine aminopeptidase. They catalyze removal
of amino acids from the N-terminus of a protein and play
a key role in protein degradation and in the metabolism
of biologically active peptides. They do not contain
HEXXH motif (which is used as one of the signature
patterns to group the peptidase families) in the
metal-binding site. The two associated zinc ions and the
active site are entirely enclosed within the C-terminal
catalytic domain in leucine aminopeptidase. The enzyme
is a hexamer, with the catalytic domains clustered
around the three-fold axis, and the two trimers related
to one another by a two-fold rotation. The N-terminal
domain is structurally similar to the ADP-ribose binding
Macro domain. This family includes proteins from
bacteria, archaea, animals and plants.
Length = 468
Score = 31.4 bits (72), Expect = 0.38
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 152 DGMRRCMCGAASCSGFIGA 170
DGM+ M GAA+ G + A
Sbjct: 258 DGMKYDMGGAAAVLGAMKA 276
>gnl|CDD|227067 COG4723, COG4723, Phage-related protein, tail component [Function
unknown].
Length = 198
Score = 29.3 bits (66), Expect = 1.4
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 58 VGEMIDQKELNRRRRDMDRNNDHNYYFLSLDNS 90
V +M+ K R D N N YF SLDN
Sbjct: 136 VAQMLAPKAKTPDYRATD-NGKQNTYFSSLDNM 167
>gnl|CDD|197795 smart00570, AWS, associated with SET domains. subdomain of
PRESET.
Length = 50
Score = 26.6 bits (59), Expect = 1.9
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 2 LYVECNPDSCPARTKCQNRDFETRNY 27
L++EC SCP + C N+ F+ R Y
Sbjct: 26 LFIEC-SSSCPCGSYCSNQRFQKRQY 50
>gnl|CDD|173881 cd08516, PBP2_NikA_DppA_OppA_like_11, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 457
Score = 28.4 bits (64), Expect = 3.3
Identities = 10/19 (52%), Positives = 10/19 (52%)
Query: 115 AEKWTVSGDTRVGLFALRD 133
AE W VS D F LRD
Sbjct: 48 AESWEVSDDGLTYTFKLRD 66
>gnl|CDD|133114 cd06904, M14_MpaA_like, Peptidase M14-like domain of Escherichia
coli Murein Peptide Amidase A and related proteins.
Peptidase M14-like domain of Escherichia coli Murein
Peptide Amidase A (MpaA) and related proteins. MpaA is a
member of the M14 family of metallocarboxypeptidases
(MCPs), however it has an exceptional type of activity,
it hydrolyzes the gamma-D-glutamyl-meso-diaminopimelic
acid (gamma-D-Glu-Dap) bond in murein peptides. MpaA is
specific for cleavage of the gamma-D-Glu-Dap bond of
free murein tripeptide; it may also cleave murein
tetrapeptide. MpaA has a different substrate specificity
and cellular role than endopeptidase I, ENP1 (ENP1 does
not belong to this group). MpaA works on free murein
peptide in the recycling pathway.
Length = 178
Score = 28.1 bits (63), Expect = 3.5
Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 15/64 (23%)
Query: 7 NPDSCPARTKCQ------NRDFETRNYPPLE---VFNTGSRGWG------LKALTDLKRG 51
NPD T+C NR+F T+++PP G + L L + +
Sbjct: 42 NPDGLLRATRCNANGVDLNRNFPTKDWPPGASRYRRYPGPKPGSEPESRALMDLIERFKP 101
Query: 52 QFVV 55
VV
Sbjct: 102 DVVV 105
>gnl|CDD|173858 cd08493, PBP2_DppA_like, The substrate-binding component of an
ABC-type dipeptide import system contains the type 2
periplasmic binding fold. This family represents the
substrate-binding domain of an ATP-binding cassette
(ABC)-type dipeptide import system. The DppA binds
dipeptides and some tripeptides and is involved in
chemotaxis toward dipeptides, whereas the OppA binds
peptides of a wide range of lengths (2-35 amino acid
residues) and plays a role in recycling of cell wall
peptides, which precludes any involvement in chemotaxis.
Most of other periplasmic binding proteins are
comprised of only two globular subdomains corresponding
to domains I and III of the dipeptide/oligopeptide
binding proteins. The structural topology of these
domains is most similar to that of the type 2
periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 482
Score = 28.3 bits (64), Expect = 3.7
Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 8/39 (20%)
Query: 115 AEKWTVSGDTRVGLFALR-DVP--AGTEL-----VFNYE 145
AE W VS D F LR V G VF++
Sbjct: 49 AESWEVSDDGLTYTFHLRKGVKFHDGRPFNADDVVFSFN 87
>gnl|CDD|173885 cd08520, PBP2_NikA_DppA_OppA_like_21, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 468
Score = 28.4 bits (64), Expect = 3.9
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 115 AEKWTVSGDTRVGLFALRD 133
AE W VS D F LR+
Sbjct: 49 AESWEVSEDGLTYTFHLRE 67
>gnl|CDD|206354 pfam14186, Aida_C2, Cytoskeletal adhesion. This is the C-terminal
domain of the axin-interacting protein family, and is a
distinct version of the C2 domain. This domain is
critical for interactions with cytoskeletal in the
context of cellular adhesion points.
Length = 149
Score = 27.3 bits (61), Expect = 4.2
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 6/63 (9%)
Query: 22 FETRNYPPLEVFNTGSRGWGLKALTDLKRGQFVVEYVGEMIDQKELNRRRRDMDRNNDHN 81
FE R+Y P + + W L ++K G +E + K + +R+ +
Sbjct: 88 FEFRHYKPKKRK-MSVKCWAFMELDEIKPGPATLE-----LYAKPTDFKRKKLKLLTKKP 141
Query: 82 YYF 84
Y
Sbjct: 142 LYL 144
>gnl|CDD|237038 PRK12286, rpmF, 50S ribosomal protein L32; Reviewed.
Length = 57
Score = 25.6 bits (57), Expect = 5.2
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 5/35 (14%)
Query: 190 RKALKARRRNRRGASSGGEKGEVPAVVEVCERCGA 224
RK K+R+R RR K + P +VE C CG
Sbjct: 6 RKTSKSRKRKRRAHF----KLKAPGLVE-CPNCGE 35
>gnl|CDD|173860 cd08495, PBP2_NikA_DppA_OppA_like_8, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 482
Score = 27.7 bits (62), Expect = 6.2
Identities = 10/19 (52%), Positives = 10/19 (52%)
Query: 115 AEKWTVSGDTRVGLFALRD 133
AE W VS D R F LR
Sbjct: 52 AESWEVSPDGRRWTFTLRP 70
>gnl|CDD|212573 cd11700, DHR2_DOCK11, Dock Homology Region 2, a GEF domain, of
Class D Dedicator of Cytokinesis 11. Dock11, also
called Zizimin2 or activated Cdc42-associated GEF (ACG),
is an atypical guanine nucleotide exchange factor (GEF)
that lacks the conventional Dbl homology (DH) domain. As
a GEF, it activates the small GTPase Cdc42 by exchanging
bound GDP for free GTP. Dock11 is predominantly
expressed in lymphocytes and is found in high levels in
germinal center B lymphocytes after T cell dependent
antigen immunization. DOCK proteins are divided into
four classes (A-D) based on sequence similarity and
domain architecture; class D includes Dock9, 10 and 11.
All DOCKs contain two homology domains: the DHR-1 (Dock
homology region-1), also called CZH1 (CED-5, Dock180,
and MBC-zizimin homology 1), and DHR-2 (also called CZH2
or Docker). The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of Dock11, which
contains the catalytic GEF activity for Cdc42. Class D
DOCKs also contain a Pleckstrin homology (PH) domain at
the N-terminus.
Length = 413
Score = 27.3 bits (60), Expect = 8.4
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 3/52 (5%)
Query: 47 DLKRGQFVVEYVGEMIDQKELNRRRRDMDRNNDHNYYFLSLDNSRYIDAGKK 98
D K V YV D KE+ R+ + +RN++ + + Y +GKK
Sbjct: 213 DPKYAHIQVTYVKPYFDDKEMAERKTEFERNHNIQRFVFE---TPYTLSGKK 261
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
0.319 0.135 0.418
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,837,443
Number of extensions: 1089110
Number of successful extensions: 956
Number of sequences better than 10.0: 1
Number of HSP's gapped: 953
Number of HSP's successfully gapped: 25
Length of query: 235
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 141
Effective length of database: 6,768,326
Effective search space: 954333966
Effective search space used: 954333966
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: 57 (25.8 bits)