RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3951
(132 letters)
>gnl|CDD|217504 pfam03345, DDOST_48kD, Oligosaccharyltransferase 48 kDa subunit
beta. Members of this family are involved in
asparagine-linked protein glycosylation. In particular,
dolichyl-diphosphooligosaccharide-protein
glycosyltransferase (DDOST), also known as
oligosaccharyltransferase EC:2.4.1.119, transfers the
high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a
dolichol-linked donor to an asparagine acceptor in a
consensus Asn-X-Ser/Thr motif. In most eukaryotes, the
DDOST complex is composed of three subunits, which in
humans are described as a 48kD subunit, ribophorin I,
and ribophorin II. However, the yeast DDOST appears to
consist of six subunits (alpha, beta, gamma, delta,
epsilon, zeta). The yeast beta subunit is a 45kD
polypeptide, previously discovered as the Wbp1 protein,
with known sequence similarity to the human 48kD subunit
and the other orthologues. This family includes the
48kD-like subunits from several eukaryotes; it also
includes the yeast DDOST beta subunit Wbp1.
Length = 421
Score = 183 bits (467), Expect = 1e-57
Identities = 64/136 (47%), Positives = 84/136 (61%), Gaps = 6/136 (4%)
Query: 2 DNVVFRLELERKSGNTWVPHNANDVQMEFVRIDPFVRTTLKSIAQ----GKYETVFKIPD 57
D VV+ +E+ S WVP A+D+Q+EF +DP+ R TLK + G Y T FK+PD
Sbjct: 281 DEVVYSIEISEYSNGKWVPFEADDIQLEFTMLDPYYRLTLKPSRRTSDSGVYSTSFKLPD 340
Query: 58 VYGVYQFKVIYNRIGYTGISNATQVSVRPLEHTQYER--FISSAYPYYASAFSMMFGVFV 115
V+GV+ FKV Y R G T I TQV+VR L H +Y R FI++A+PYYAS FS++ G
Sbjct: 341 VHGVFTFKVDYKRPGLTFIEEKTQVTVRHLAHDEYPRSWFITNAWPYYASIFSVIIGFLA 400
Query: 116 FSIVFLHYKDDEKSKS 131
F VFL+ K K S
Sbjct: 401 FVAVFLYSKPVGKVAS 416
>gnl|CDD|133433 cd05297, GH4_alpha_glucosidase_galactosidase, Glycoside Hydrolases
Family 4; Alpha-glucosidases and alpha-galactosidases.
Glucosidases cleave glycosidic bonds to release glucose
from oligosaccharides. Alpha-glucosidases and
alpha-galactosidases release alpha-D-glucose and
alpha-D-galactose, respectively, via the hydrolysis of
alpha-glycopyranoside bonds. Some bacteria
simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP-PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by the GH4 glycoside hydrolases such as the
alpha-glucosidases. Other organsisms (such as archaea
and Thermotoga maritima) lack the PEP-PTS system, but
have several enzymes normally associated with the
PEP-PTS operon. Alpha-glucosidases and
alpha-galactosidases are part of the NAD(P)-binding
Rossmann fold superfamily, which includes a wide variety
of protein families including the NAD(P)-binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 423
Score = 30.6 bits (70), Expect = 0.17
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 4/32 (12%)
Query: 49 YETVFKIPDVYGVYQFKVIYNR-IGYTGISNA 79
ET F+IP+ YG YQ G GI A
Sbjct: 90 TETDFEIPEKYGYYQT---VGDTSGPGGIFRA 118
>gnl|CDD|183376 PRK11909, PRK11909, cobalt transport protein CbiM; Provisional.
Length = 230
Score = 27.8 bits (62), Expect = 1.4
Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 16/83 (19%)
Query: 53 FKIPDV-YGVYQF-------KVIYNRIG-YTGISNAT-----QVSVRP-LEHTQYERFIS 97
F +P V Y VY+ +VI + IG Y GI+ A + ++P L HT +
Sbjct: 115 FVLPFVGYYVYKLLSILKVRRVIASAIGGYVGINAAALATGIEFGLQPFLFHTANGTPLY 174
Query: 98 SAYPYYASAFSMMFG-VFVFSIV 119
Y S +M+F + V IV
Sbjct: 175 CPYGLNVSIPAMLFAHLTVAGIV 197
>gnl|CDD|235593 PRK05758, PRK05758, F0F1 ATP synthase subunit delta; Validated.
Length = 177
Score = 27.4 bits (62), Expect = 1.6
Identities = 13/66 (19%), Positives = 30/66 (45%), Gaps = 6/66 (9%)
Query: 33 IDPFVRTTLKSIAQGKYETVFKIPDVYGVYQFKVIYNRIGYTGISNATQVSVRPLEHTQY 92
+ +V+ LK +A+ + +P++ QF+ + + I +A S PL Q
Sbjct: 69 LSEYVQNFLKVLAENGRLAL--LPEILE--QFEALRAE--HENIVDAEVTSAFPLSEEQL 122
Query: 93 ERFISS 98
++ ++
Sbjct: 123 DKLKAA 128
>gnl|CDD|241356 cd13202, FERM_C_MyoX, Myosin X (MyoX, Myo10) FERM domain C-lobe.
MyoX, a MyTH-FERM myosin, is a molecular motor that has
crucial functions in the transport and/or tethering of
integrins in the actin-based extensions known as
filopodia, microtubule binding, and in netrin-mediated
axon guidance. It functions as a dimer. MyoX walks on
bundles of actin, rather than single filaments, unlike
the other unconventional myosins. MyoX is present in
organisms ranging from humans to choanoflagellates, but
not in Drosophila and Caenorhabditis elegans.MyoX
consists of a N-terminal motor/head region, a neck made
of 3 IQ motifs, and a tail consisting of a coiled-coil
domain, a PEST region, 3 PH domains, a myosin tail
homology 4 (MyTH4), and a FERM domain at its very
C-terminus. The MyoX FERM domain binds to the NPXY
motif of several beta-integrins, a key family of cell
surface receptors that are involved in cell adhesion
and migration. In addition the FERM domain binds to the
cytoplasmic domains of the netrin receptors DCC
(deleted in colorectal cancer) and neogenin. The FERM
domain also forms a supramodule with its MyTH4 domain
which binds to the negatively charged E-hook region in
the tails of alpha- and beta-tubulin forming a proposed
motorized link between actin filaments and
microtubules. The FERM domain has a cloverleaf tripart
structure (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The
C-lobe/F3 within the FERM domain is part of the PH
domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a
link between the membrane and cytoskeleton and are
involved in signal transduction pathways. The FERM
domain is also found in protein tyrosine phosphatases
(PTPs) , the tyrosine kinases FAK and JAK, in addition
to other proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 111
Score = 26.1 bits (58), Expect = 3.8
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 13/65 (20%)
Query: 45 AQGKYETVFKIPDVYGVYQFKVIYNRIG------YTGISNATQVSV------RPLEHTQY 92
A KY + + YG F+V N+ G + G+S A VS+ PLE Y
Sbjct: 6 AMAKYMAIIREWPGYGSTLFEVECNKEGGFPQELWLGVS-AKGVSLYKRGEPEPLESFPY 64
Query: 93 ERFIS 97
E+ +S
Sbjct: 65 EKILS 69
>gnl|CDD|227132 COG4795, PulJ, Type II secretory pathway, component PulJ
[Intracellular trafficking and secretion].
Length = 194
Score = 26.6 bits (59), Expect = 3.9
Identities = 11/57 (19%), Positives = 23/57 (40%), Gaps = 11/57 (19%)
Query: 1 MDNVVFRLELERKSGNTWVPHNANDVQMEFVRIDPFVRTTLKSIAQGKYETVFKIPD 57
+++++ ++ SG W P + V+ TLK+ G E + +P
Sbjct: 146 LEDIISAFLVQGLSGKGWSP-----------ALPLAVKGTLKTKPYGVIERTYLVPG 191
>gnl|CDD|198235 cd10372, SH2_STAT1, Src homology 2 (SH2) domain found in signal
transducer and activator of transcription (STAT) 1
proteins. STAT1 is a member of the STAT family of
transcription factors. STAT1 is involved in
upregulating genes due to a signal by interferons.
STAT1 forms homodimers or heterodimers with STAT3 that
bind to the Interferon-Gamma Activated Sequence (GAS)
promoter element in response to IFN-gamma stimulation.
STAT1 forms a heterodimer with STAT2 that can bind
Interferon Stimulated Response Element (ISRE) promoter
element in response to either IFN-alpha or IFN-beta
stimulation. Binding in both cases leads to an
increased expression of ISG (Interferon Stimulated
Genes). STAT1 has been shown to interact with protein
kinase R, Src, IRF1, STAT3, MCM5, STAT2, CD117, Fanconi
anemia, complementation group C, CREB-binding protein,
Interleukin 27 receptor, alpha subunit, PIAS1, BRCA1,
Epidermal growth factor receptor, PTK2, Mammalian
target of rapamycin, IFNAR2, PRKCD, TRADD, C-jun,
Calcitriol receptor, ISGF3G, and GNB2L1. STAT proteins
mediate the signaling of cytokines and a number of
growth factors from the receptors of these
extracellular signaling molecules to the cell nucleus.
STATs are specifically phosphorylated by
receptor-associated Janus kinases, receptor tyrosine
kinases, or cytoplasmic tyrosine kinases. The
phosphorylated STAT molecules dimerize by reciprocal
binding of their SH2 domains to the phosphotyrosine
residues. These dimeric STATs translocate into the
nucleus, bind to specific DNA sequences, and regulate
the transcription of their target genes. However there
are a number of unphosphorylated STATs that travel
between the cytoplasm and nucleus and some STATs that
exist as dimers in unstimulated cells that can exert
biological functions independent of being activated.
There are seven mammalian STAT family members which
have been identified: STAT1, STAT2, STAT3, STAT4, STAT5
(STAT5A and STAT5B), and STAT6. There are 6 conserved
domains in STAT: N-terminal domain (NTD), coiled-coil
domain (CCD), DNA-binding domain (DBD), alpha-helical
linker domain (LD), SH2 domain, and transactivation
domain (TAD). NTD is involved in dimerization of
unphosphorylated STATs monomers and for the
tetramerization between STAT1, STAT3, STAT4 and STAT5
on promoters with two or more tandem STAT binding
sites. It also plays a role in promoting interactions
with transcriptional co-activators such as CREB binding
protein (CBP)/p300, as well as being important for
nuclear import and deactivation of STATs involving
tyrosine de-phosphorylation. CCD interacts with other
proteins, such as IFN regulatory protein 9 (IRF-9/p48)
with STAT1 and c-JUN with STAT3 and is also thought to
participate in the negative regulation of these
proteins. Distinct genes are bound to STATs via their
DBD domain. This domain is also involved in nuclear
translocation of activated STAT1 and STAT3
phosphorylated dimers upon cytokine stimulation. LD
links the DNA-binding and SH2 domains and is important
for the transcriptional activation of STAT1 in response
to IFN-gamma. It also plays a role in protein-protein
interactions and has also been implicated in the
constitutive nucleocytoplasmic shuttling of
unphosphorylated STATs in resting cells. The SH2
domain is necessary for receptor association and
tyrosine phosphodimer formation. Residues within this
domain may be particularly important for some cellular
functions mediated by the STATs as well as residues
adjacent to this domain. The TAD interacts with
several proteins, namely minichromosome maintenance
complex component 5 (MCM5), breast cancer 1 (BRCA1) and
CBP/p300. TAD also contains a modulatory
phosphorylation site that regulates STAT activity and
is necessary for maximal transcription of a number of
target genes. The conserved tyrosine residue present in
the C-terminus is crucial for dimerization via
interaction with the SH2 domain upon the interaction of
the ligand with the receptor. STAT activation by
tyrosine phosphorylation also determines nuclear import
and retention, DNA binding to specific DNA elements in
the promoters of responsive genes, and transcriptional
activation of STAT dimers. In addition to the SH2
domain there is a coiled-coil domain, a DNA binding
domain, and a transactivation domain in the STAT
proteins. In general SH2 domains are involved in signal
transduction. They typically bind pTyr-containing
ligands via two surface pockets, a pTyr and hydrophobic
binding pocket, allowing proteins with SH2 domains to
localize to tyrosine phosphorylated sites.
Length = 151
Score = 26.4 bits (58), Expect = 4.1
Identities = 7/29 (24%), Positives = 16/29 (55%)
Query: 17 TWVPHNANDVQMEFVRIDPFVRTTLKSIA 45
TWV + N + +F ++P+ + L ++
Sbjct: 59 TWVERSQNGGEPDFHAVEPYTKKELSAVT 87
>gnl|CDD|220620 pfam10183, ESSS, ESSS subunit of NADH:ubiquinone oxidoreductase
(complex I). This subunit is part of the mitochondrial
NADH:ubiquinone oxidoreductase (complex I). It carries
mitochondrial import sequences.
Length = 101
Score = 25.5 bits (56), Expect = 4.9
Identities = 12/69 (17%), Positives = 18/69 (26%), Gaps = 13/69 (18%)
Query: 69 NRIGYTGISNATQVSVRPLEHTQYERFISSAYPYY-----------ASAFSMMFGVFVFS 117
G + S EH + + + P + F V
Sbjct: 16 GGSSSGGAARRA--SAGHEEHERPNGRLFNKNPPPPGEKRKWEDWELPFYFGFFLTLVIL 73
Query: 118 IVFLHYKDD 126
V L+YK D
Sbjct: 74 GVGLNYKPD 82
>gnl|CDD|239612 cd03538, Rieske_RO_Alpha_AntDO, Rieske non-heme iron oxygenase
(RO) family, Anthranilate 1,2-dioxygenase (AntDO)
subfamily, N-terminal Rieske domain of the oxygenase
alpha subunit; ROs comprise a large class of aromatic
ring-hydroxylating dioxygenases that enable
microorganisms to tolerate and utilize aromatic
compounds for growth. The oxygenase alpha subunit
contains an N-terminal Rieske domain with an [2Fe-2S]
cluster and a C-terminal catalytic domain with a
mononuclear Fe(II) binding site. The Rieske [2Fe-2S]
cluster accepts electrons from a reductase or
ferredoxin component and transfers them to the
mononuclear iron for catalysis. AntDO converts
anthranilate to catechol, a naturally occurring
compound formed through tryptophan degradation and an
important intermediate in the metabolism of many
N-heterocyclic compounds such as indole,
o-nitrobenzoate, carbazole, and quinaldine.
Length = 146
Score = 25.5 bits (56), Expect = 7.5
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 1 MDNVVFRLELERKSGNTWV 19
D +F LE+ER GN W+
Sbjct: 6 TDPEIFALEMERLFGNAWI 24
>gnl|CDD|182229 PRK10083, PRK10083, putative oxidoreductase; Provisional.
Length = 339
Score = 25.9 bits (57), Expect = 9.1
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 2 DNVVFRLELERKSGNTWVPHNAN 24
D + RL L ++SG WV +NA
Sbjct: 193 DRIDERLALAKESGADWVINNAQ 215
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
0.323 0.137 0.405
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,644,103
Number of extensions: 569850
Number of successful extensions: 629
Number of sequences better than 10.0: 1
Number of HSP's gapped: 625
Number of HSP's successfully gapped: 28
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.1 bits)