RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5667
(79 letters)
>gnl|CDD|215619 PLN03185, PLN03185, phosphatidylinositol phosphate kinase;
Provisional.
Length = 765
Score = 39.8 bits (93), Expect = 2e-05
Identities = 24/67 (35%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 11 GVVQHGSFKY--DDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFP 68
G V G KY DG +Y G+W RG +HG G + P Y+G F G G G +
Sbjct: 17 GNVPEGPGKYLWSDGCMYEGEWR-RGMRHGNGKISWPSGATYEGEFSGGYMHGSGT--YT 73
Query: 69 DGANSTY 75
+TY
Sbjct: 74 GTDGTTY 80
Score = 32.9 bits (75), Expect = 0.008
Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 6 EEEYPGVVQHGSFKY--DDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLG 63
E E+ G HGS Y DGT Y G W KHG+G+ + P+ ++G++ GL G G
Sbjct: 58 EGEFSGGYMHGSGTYTGTDGTTYKGRW-RLNLKHGLGYQRYPNGDVFEGSWIQGLQEGPG 116
Score = 30.2 bits (68), Expect = 0.072
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 15 HGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDG 70
G + + +G +Y+GD + G+ G G + Y+G + +G+ G GV + DG
Sbjct: 115 PGKYTWANGNVYLGDM-KGGKMSGKGTLTWVSGDSYEGQWLDGMMHGFGVYTWSDG 169
Score = 27.1 bits (60), Expect = 0.93
Identities = 20/55 (36%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 16 GSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDG 70
G+ + G Y G W + G HG G D Y GT+ GL G GV +P G
Sbjct: 139 GTLTWVSGDSYEGQWLD-GMMHGFGVYTWSDGGCYVGTWTRGLKDGKGVF-YPAG 191
Score = 25.9 bits (57), Expect = 2.2
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 15 HGSFKYDDGTLYIGDWNERGQKHGMG 40
G + + DG Y+G W RG K G G
Sbjct: 161 FGVYTWSDGGCYVGTWT-RGLKDGKG 185
>gnl|CDD|197832 smart00698, MORN, Possible plasma membrane-binding motif in
junctophilins, PIP-5-kinases and protein kinases.
Length = 22
Score = 32.3 bits (75), Expect = 0.001
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 49 RYDGTFHNGLCSGLGVMRFPD 69
RY+G + NG G GV + +
Sbjct: 2 RYEGEWRNGKRHGRGVYTYAN 22
Score = 23.8 bits (53), Expect = 3.1
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 26 YIGDWNERGQKHGMGHMKLPD 46
Y G+W G++HG G +
Sbjct: 3 YEGEW-RNGKRHGRGVYTYAN 22
>gnl|CDD|202256 pfam02493, MORN, MORN repeat. The MORN (Membrane Occupation and
Recognition Nexus) repeat is found in multiple copies
in several proteins including junctophilins (See
Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat
protein has been identified in the parasite Toxoplasma
gondiis a dynamic component of cell division apparatus
in Toxoplasma gondii. It has been hypothesised to
functions as a linker protein between certain membrane
regions and the parasite's cytoskeleton.
Length = 23
Score = 30.4 bits (70), Expect = 0.007
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 50 YDGTFHNGLCSGLGVMRFPDG 70
Y+G + NG G GV +PDG
Sbjct: 1 YEGEWKNGKRHGKGVYTWPDG 21
Score = 23.5 bits (52), Expect = 3.4
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 26 YIGDWNERGQKHGMGHMKLPDHTR 49
Y G+W + G++HG G PD R
Sbjct: 1 YEGEW-KNGKRHGKGVYTWPDGDR 23
>gnl|CDD|226989 COG4642, COG4642, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 139
Score = 30.9 bits (70), Expect = 0.033
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 16 GSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLG 63
GS KYD+G +Y G + G+ +G G + Y+G F++G G G
Sbjct: 47 GSLKYDNGRIYTGTL-KNGKMNGQGTYTFANGDIYEGPFNSGKFRGQG 93
Score = 29.3 bits (66), Expect = 0.12
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 16 GSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDG 70
++ G + G+ G G +K + Y GT NG +G G F +G
Sbjct: 24 STYDILGCARVGGSLKQ-GKLAGKGSLKYDNGRIYTGTLKNGKMNGQGTYTFANG 77
Score = 27.8 bits (62), Expect = 0.38
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 16 GSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGA 71
G++ + +G +Y G +N G+ G G + Y G F G +G G + DG+
Sbjct: 70 GTYTFANGDIYEGPFNS-GKFRGQGTRGSFNGWLYIGRFTEGQANGKGFLLKEDGS 124
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 27.4 bits (62), Expect = 0.57
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 4/24 (16%)
Query: 47 HTRYDGTFHNGL----CSGLGVMR 66
H ++ F L CSGLGV+R
Sbjct: 314 HEKFAEKFDKILVDAPCSGLGVIR 337
>gnl|CDD|216683 pfam01758, SBF, Sodium Bile acid symporter family. This family
consists of Na+/bile acid co-transporters. These
transmembrane proteins function in the liver in the
uptake of bile acids from portal blood plasma a process
mediated by the co-transport of Na+. Also in the family
is ARC3 from S. cerevisiae, this is a putative
transmembrane protein involved in resistance to arsenic
compounds.
Length = 188
Score = 26.9 bits (60), Expect = 0.99
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 61 GLGVMRFPDGANSTYSDIR 79
GL +M F G Y D +
Sbjct: 3 GLFLMMFSMGLKVRYEDFK 21
>gnl|CDD|239284 cd02986, DLP, Dim1 family, Dim1-like protein (DLP) subfamily; DLP
is a novel protein which shares 38% sequence identity
to Dim1. Like Dim1, it is also implicated in pre-mRNA
splicing and cell cycle progression. DLP is located in
the nucleus and has been shown to interact with the U5
small nuclear ribonucleoprotein particle
(snRNP)-specific 102kD protein (or Prp6). Dim1 protein,
also known as U5 snRNP-specific 15kD protein is a
component of U5 snRNP, which pre-assembles with U4/U6
snRNPs to form a [U4/U6:U5] tri-snRNP complex required
for pre-mRNA splicing. Dim1 adopts a thioredoxin fold
but does not contain the redox active CXXC motif.
Length = 114
Score = 25.9 bits (57), Expect = 1.5
Identities = 9/19 (47%), Positives = 13/19 (68%), Gaps = 4/19 (21%)
Query: 41 HMKL----PDHTRYDGTFH 55
HMK+ PDHT++ G+F
Sbjct: 80 HMKVDYGSPDHTKFVGSFK 98
>gnl|CDD|181509 PRK08629, PRK08629, coproporphyrinogen III oxidase; Provisional.
Length = 433
Score = 26.2 bits (58), Expect = 2.1
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 5 DEEEYPGVVQHGSFKYDDGTLYIGDWN 31
D +EY GV GSF + DGTLY+ ++
Sbjct: 294 DYDEYLGV-GSGSFSFLDGTLYVNTFS 319
>gnl|CDD|180315 PRK05933, PRK05933, type III secretion system protein; Validated.
Length = 372
Score = 25.2 bits (55), Expect = 3.6
Identities = 16/41 (39%), Positives = 19/41 (46%), Gaps = 6/41 (14%)
Query: 2 SQKDEEEYPGVVQHGSFKYDDGTLYIGDWNERG-----QKH 37
Q +EE+ VV GSF D LY D E G Q+H
Sbjct: 224 CQLTQEEWHQVV-PGSFILLDSCLYDPDTEESGALLTIQRH 263
>gnl|CDD|240581 cd12946, NOPS_p54nrb_PSF_PSPC1, NOPS domain, including C-terminal
coiled-coil region, in p54nrb/PSF/PSPC1 family
proteins. The family contains a DBHS domain (for
Drosophila behavior, human splicing), which comprises
two conserved RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction NOPS (NONA and PSP1)
domain. This model corresponds to the NOPS domain, with
a long helical C-terminal extension, found in the
p54nrb/PSF/PSPC1 proteins. The NOPS domain specifically
binds to the second RNA recognition motif (RRM2) domain
of the partner DBHS protein via a substantial
interaction surface. Its highly conserved C-terminal
residues are critical for functional DBHS dimerization
while the highly conserved C-terminal helical
extension, forming a right-handed antiparallel
heterodimeric coiled-coil, is essential for
localization of these proteins to subnuclear bodies.
Members in the family include 54 kDa nuclear RNA- and
DNA-binding protein (p54nrb), polypyrimidine
tract-binding protein (PTB)-associated-splicing factor
(PSF) and paraspeckle protein component 1 (PSPC1 or
PSP1), which are ubiquitously expressed and are
conserved in vertebrates. p54nrb, also termed NONO or
NMT55, is a multi-functional protein involved in
numerous nuclear processes including transcriptional
regulation, splicing, DNA unwinding, nuclear retention
of hyperedited double-stranded RNA, viral RNA
processing, control of cell proliferation, and
circadian rhythm maintenance. PSF, also termed POMp100,
is a multi-functional protein that binds RNA,
single-stranded DNA (ssDNA), double-stranded DNA
(dsDNA) and many factors, and mediates diverse
activities in the cell. PSPC1 is a novel nucleolar
factor that accumulates within a new nucleoplasmic
compartment, termed paraspeckles, and diffusely
distributes in the nucleoplasm. The cellular function
of PSPC1 remains unknown currently. PSF has an
additional large N-terminal domain that differentiates
it from other family members.
Length = 93
Score = 25.1 bits (54), Expect = 3.6
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 1 MSQKDEEEYPGVVQHGSFKYD 21
K+ E+ P Q G+F+Y+
Sbjct: 28 QYHKEREQPPRFAQPGTFEYE 48
>gnl|CDD|240583 cd12948, NOPS_PSF, NOPS domain, including C-terminal coiled-coil
region, in polypyrimidine tract-binding protein
(PTB)-associated-splicing factor (PSF) and similar
proteins. This model contains the NOPS (NONA and PSP1)
domain PSF (also termed proline- and glutamine-rich
splicing factor, or 100 kDa DNA-pairing protein
(POMp100), or 100 kDa subunit of DNA-binding p52/p100
complex), with a long helical C-terminal extension. PSF
is a multifunctional protein that mediates diverse
activities in the cell. It is ubiquitously expressed
and highly conserved in vertebrates. PSF binds not only
RNA but also single-stranded DNA (ssDNA) as well as
double-stranded DNA (dsDNA) and facilitates the
renaturation of complementary ssDNAs. Additionally, it
promotes the formation of D-loops in superhelical
duplex DNA, and is involved in cell proliferation. PSF
can also interact with multiple factors. It is an
RNA-binding component of spliceosomes and binds to
insulin-like growth factor response element (IGFRE).
Moreover, PSF functions as a transcriptional repressor
interacting with Sin3A and mediating silencing through
the recruitment of histone deacetylases (HDACs) to the
DNA binding domain (DBD) of nuclear hormone receptors.
As an RNA-binding component of spliceosomes, PSF binds
to the insulin-like growth factor response element
(IGFRE), and acts as an independent negative regulator
of the transcriptional activity of the porcine P-450
cholesterol side-chain cleavage enzyme gene (P450scc)
IGFRE. PSF is an essential pre-mRNA splicing factor and
is dissociated from PTB and binds to U1-70K and
serine-arginine (SR) proteins during apoptosis. In
addition, PSF forms a heterodimer with the nuclear
protein p54nrb, also known as non-POU domain-containing
octamer-binding protein (NONO). The PSF/p54nrb complex
displays a variety of functions, such as DNA
recombination and RNA synthesis, processing, and
transport. PSF contains two conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), which are
responsible for interactions with RNA and for the
localization of the protein in speckles. It also
contains an N-terminal region rich in proline, glycine,
and glutamine residues, which may play a role in
interactions recruiting other molecules. The NOPS
domain specifically binds to the second RNA recognition
motif (RRM2) domain of the partner DBHS protein via a
substantial interaction surface. Its highly conserved
C-terminal residues are critical for functional DBHS
dimerization while the highly conserved C-terminal
helical extension, forming a right-handed antiparallel
heterodimeric coiled-coil, is essential for
localization of these proteins to subnuclear bodies.
Length = 97
Score = 24.7 bits (53), Expect = 4.7
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 1 MSQKDEEEYPGVVQHGSFKYD 21
M QK+ E P Q G+F+Y+
Sbjct: 28 MYQKERETPPRFAQPGTFEYE 48
>gnl|CDD|129268 TIGR00164, PS_decarb_rel, phosphatidylserine decarboxylase
precursor-related protein. Phosphatidylserine
decarboxylase is synthesized as a single chain
precursor. Generation of the pyruvoyl active site from a
Ser is coupled to cleavage of a Gly-Ser bond between the
larger (beta) and smaller (alpha chains). It is an
integral membrane protein. This protein has many regions
of homology to known phosphatidylserine decarboxylases,
including the Gly-Ser motif for chain cleavage and
active site generation, but has a shorter amino end and
a number of deletions along the length of the alignment
to the phosphatidylserine decarboxylases. It is unclear
whether this protein is a form of phosphatidylserine
decarboxylase or is a related enzyme. It is found in
Neisseria gonorrhoeae, Mycobacterium tuberculosis, and
several archaeal species, all of which lack known
phosphatidylserine decarboxylase [Unknown function,
General].
Length = 189
Score = 24.8 bits (54), Expect = 4.8
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 4 KDEEEYPGVVQHGSFKYDDGTLYI--GDWNERGQKHGM 39
K GVVQ F Y+ G+ RGQ+ GM
Sbjct: 113 KTASGEVGVVQIAGFVARRIVCYVKEGEKVSRGQRIGM 150
>gnl|CDD|199834 cd10276, BamB_YfgL, Beta-barrel assembly machinery (Bam) complex
component B and related proteins. BamB (YflG) is a
non-essential component of the beta-barrel assembly
machinery (Bam), a multi-subunit complex that inserts
proteins with beta-barrel topology into the outer
membrane. BamB has been found to interact with BamA,
which in turn binds and stabilizes pre-folded
beta-barrel proteins; it has been suggested that BamB
participates in the stabilization.
Length = 358
Score = 25.0 bits (55), Expect = 5.4
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 19 KYDDGTLYIGDWNER 33
Y DG +Y+G + R
Sbjct: 118 TYADGKIYVGTGDGR 132
>gnl|CDD|197753 smart00481, POLIIIAc, DNA polymerase alpha chain like domain.
DNA polymerase alpha chain like domain, incl. family of
hypothetical proteins.
Length = 67
Score = 23.8 bits (52), Expect = 6.0
Identities = 9/38 (23%), Positives = 17/38 (44%)
Query: 15 HGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDG 52
H + DG L + +R ++ G+ + + DH G
Sbjct: 5 HSDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFG 42
>gnl|CDD|217376 pfam03122, Herpes_MCP, Herpes virus major capsid protein. This
family represents the major capsid protein (MCP) of
herpes viruses. The capsid shell consists of 150 MCP
hexamers and 12 MCP pentamers. One pentamer is found at
each of the 12 apices of the icosahedral shell, and the
hexamers form the edges and 20 faces.
Length = 1352
Score = 24.5 bits (54), Expect = 6.8
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 6/27 (22%)
Query: 34 GQKHGMGHMKLPDHTR-YDGTFHNGLC 59
GQ+ G + R DG +NGLC
Sbjct: 886 GQRTGS-----TRNFRSLDGVLYNGLC 907
>gnl|CDD|176658 cd06588, PhnB_like, Escherichia coli PhnB and similar proteins;
the E. coli phnB gene is found next to an operon
involved in the cleavage of carbon-phosphorus bonds in
unactivated alkylphosphonates. The Escherichia coli
phnB gene is found next to an operon of fourteen genes
(phnC-to-phnP) related to the cleavage of
carbon-phosphorus (C-P) bonds in unactivated
alkylphosphonates, supporting bacterial growth on
alkylphosphonates as the sole phosphorus source. It was
originally considered part of that operon. PhnB appears
to play no direct catalytic role in the usage of
alkylphosphonate. Although many of the proteins in this
family have been annotated as 3-demethylubiquinone-9
3-methyltransferase enzymes by automatic annotation
programs, the experimental evidence for this assignment
is lacking. In Escherichia coli, the gene coding
3-demethylubiquinone-9 3-methyltransferase enzyme is
ubiG, which belongs to the AdoMet-MTase protein family.
PhnB-like proteins adopt a structural fold similar to
bleomycin resistance proteins, glyoxalase I, and type I
extradiol dioxygenases.
Length = 128
Score = 23.7 bits (52), Expect = 9.3
Identities = 8/29 (27%), Positives = 8/29 (27%)
Query: 1 MSQKDEEEYPGVVQHGSFKYDDGTLYIGD 29
D EE G V H L D
Sbjct: 35 GPPPDPEEPEGKVMHAELTIGGQRLMASD 63
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
0.317 0.139 0.447
Gapped
Lambda K H
0.267 0.0933 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,098,404
Number of extensions: 308692
Number of successful extensions: 221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 217
Number of HSP's successfully gapped: 30
Length of query: 79
Length of database: 10,937,602
Length adjustment: 48
Effective length of query: 31
Effective length of database: 8,808,610
Effective search space: 273066910
Effective search space used: 273066910
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 (23.8 bits)