RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9207
(125 letters)
>gnl|CDD|220553 pfam10075, PCI_Csn8, COP9 signalosome, subunit CSN8. This PCI_Csn8
domain is conserved from plants to humans. It is a
signature protein motif found in components of CSN (COP9
signalosome). It functions as a structural scaffold for
subunit-subunit interactions within the complex and is a
key regulator of photomorphogenic development.
Length = 144
Score = 81.9 bits (203), Expect = 4e-21
Identities = 33/91 (36%), Positives = 54/91 (59%), Gaps = 2/91 (2%)
Query: 2 SHPEIGQVWEVGKHLWNGNYPSIYSTLKRT-WSDDIAHIMKALQDEVQKRAISLISKAYS 60
S+PEI Q+ +G+ LW +Y + TL+ WS+D + L+D ++ +L+ KAYS
Sbjct: 37 SNPEIQQLLTLGQLLWENDYAKFWQTLRSNDWSEDYTPFIAGLEDTIRDEIAALVGKAYS 96
Query: 61 SIPNTSLSEFLGV-TEQEAAAIAQAEGWTVD 90
SI L+E LG+ +++E A+ GWT+D
Sbjct: 97 SISIDDLAELLGLSSDEELEKFAKKRGWTLD 127
>gnl|CDD|217534 pfam03399, SAC3_GANP, SAC3/GANP/Nin1/mts3/eIF-3 p25 family. This
large family includes diverse proteins involved in large
complexes. The alignment contains one highly conserved
negatively charged residue and one highly conserved
positively charged residue that are probably important
for the function of these proteins. The family includes
the yeast nuclear export factor Sac3, and mammalian
GANP/MCM3-associated proteins, which facilitate the
nuclear localisation of MCM3, a protein that associates
with chromatin in the G1 phase of the cell-cycle. The
26S protease (or 26S proteasome) is responsible for
degrading ubiquitin conjugates. It consists of 19S
regulatory complexes associated with the ends of 20S
proteasomes. The 19S regulatory complex is composed of
about 20 different polypeptides and confers
ATP-dependence and substrate specificity to the 26S
enzyme. The conserved region occurs at the C-terminal of
the Nin1-like regulatory subunit. This family includes
several eukaryotic translation initiation factor 3
subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation
factor 3 (eIF3) is a multisubunit complex that is
required for binding of mRNA to 40 S ribosomal subunits,
stabilisation of ternary complex binding to 40 S
subunits, and dissociation of 40 and 60 S subunits.
Length = 155
Score = 44.2 bits (105), Expect = 1e-06
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 1 MSHPEIGQVWEVGKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQDEVQKRAISLISKAYS 60
+ P I E+ + L GNY + LK+ A +++ D ++K A+ ISKAY
Sbjct: 85 RNDPYIQFALELEQALMEGNYHRFFRLLKKA-PYLYACLLERFLDRIRKEALKAISKAYR 143
Query: 61 SIPNTSLSEFLG 72
SIP + L+E LG
Sbjct: 144 SIPLSYLAELLG 155
>gnl|CDD|216479 pfam01399, PCI, PCI domain. This domain has also been called the
PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15).
Length = 100
Score = 32.2 bits (74), Expect = 0.017
Identities = 12/45 (26%), Positives = 29/45 (64%)
Query: 34 DDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEA 78
D +A +++ L+ ++++ + ++K YSSI + L++ LG++ E
Sbjct: 30 DGLAELLEDLRRKIRELNLRRLAKPYSSISLSDLAKLLGLSVDEV 74
>gnl|CDD|214803 smart00753, PAM, PCI/PINT associated module.
Length = 88
Score = 28.4 bits (64), Expect = 0.38
Identities = 11/39 (28%), Positives = 24/39 (61%)
Query: 40 MKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEA 78
++ LQ +++ + +S+ YSSI + L++ LG++ E
Sbjct: 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEV 41
>gnl|CDD|214509 smart00088, PINT, motif in proteasome subunits, Int-6, Nip-1 and
TRIP-15. Also called the PCI (Proteasome, COP9,
Initiation factor 3) domain. Unknown function.
Length = 88
Score = 28.4 bits (64), Expect = 0.38
Identities = 11/39 (28%), Positives = 24/39 (61%)
Query: 40 MKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEA 78
++ LQ +++ + +S+ YSSI + L++ LG++ E
Sbjct: 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEV 41
>gnl|CDD|200532 cd11271, Sema_plexin_A1, The Sema domain, a protein interacting
module, of Plexin A1. Plexin A1 is found in both the
nervous and immune systems. Its external Sema domain is
also shared by semaphorin proteins. In the nervous
system, Plexin A1 mediates Sema3A axon guidance function
by interacting with the Sema3A coreceptor neuropilin,
resulting in actin depolarization and cell repulsion. In
the immune system, Plexin A1 mediates Sema6D signaling
by binding to the Sema6D-Trem2-DAP12 complex on immune
cells and osteoclasts to promote Rac activation and
DAP12 phosphorylation. In gene profiling experiments,
Plexin A1 was identified as a CIITA (class II
transactivator) regulated gene in primary dendritic
cells (DCs). The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
ligand-recognition and -binding module.
Length = 474
Score = 28.8 bits (64), Expect = 0.77
Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 44 QDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQE 77
QD V+ R LI AY S P +L++ LG++E+E
Sbjct: 265 QDGVEYR---LIQDAYLSKPGKALAKQLGISERE 295
>gnl|CDD|225302 COG2469, COG2469, Uncharacterized conserved protein [Function
unknown].
Length = 284
Score = 28.6 bits (64), Expect = 0.90
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 45 DEVQKRAISLISKAYSSIPNTSLSEFLGVTEQE 77
E++K+ + + YS + SL FLGV E
Sbjct: 215 SEIEKQILVAL---YSGGDSASLELFLGVDTDE 244
>gnl|CDD|212671 cd10229, HSPA12_like_NBD, Nucleotide-binding domain of HSPA12A,
HSPA12B and similar proteins. Human HSPA12A (also known
as 70-kDa heat shock protein-12A) and HSPA12B (also
known as 70-kDa heat shock protein-12B, chromosome 20
open reading frame 60/C20orf60, dJ1009E24.2) belong to
the heat shock protein 70 (HSP70) family of chaperones
that assist in protein folding and assembly, and can
direct incompetent "client" proteins towards
degradation. Typically, HSP70s have a nucleotide-binding
domain (NBD) and a substrate-binding domain (SBD). The
nucleotide sits in a deep cleft formed between the two
lobes of the NBD. The two subdomains of each lobe change
conformation between ATP-bound, ADP-bound, and
nucleotide-free states. ATP binding opens up the
substrate-binding site; substrate-binding increases the
rate of ATP hydrolysis. HSP70 chaperone activity is
regulated by various co-chaperones: J-domain proteins
and nucleotide exchange factors (NEFs). No co-chaperones
have yet been identified for HSPA12A or HSPA12B. The
gene encoding HSPA12A maps to 10q26.12, a cytogenetic
region that might represent a common susceptibility
locus for both schizophrenia and bipolar affective
disorder; reduced expression of HSPA12A has been shown
in the prefrontal cortex of subjects with schizophrenia.
HSPA12A is also a candidate gene for forelimb-girdle
muscular anomaly, an autosomal recessive disorder of
Japanese black cattle. HSPA12A is predominantly
expressed in neuronal cells. It may also play a role in
the atherosclerotic process. The gene encoding HSPA12B
maps to 20p13. HSPA12B is predominantly expressed in
endothelial cells, is required for angiogenesis, and may
interact with known angiogenesis mediators. It may be
important for host defense in microglia-mediated immune
response. HSPA12B expression is up-regulated in
lipopolysaccharide (LPS)-induced inflammatory response
in the spinal cord, and mostly located in active
microglia; this induced expression may be regulated by
activation of MAPK-p38, ERK1/2 and SAPK/JNK signaling
pathways. Overexpression of HSPA12B also protects
against LPS-induced cardiac dysfunction and involves the
preserved activation of the PI3K/Akt signaling pathway.
Length = 404
Score = 26.5 bits (59), Expect = 3.8
Identities = 15/52 (28%), Positives = 19/52 (36%), Gaps = 11/52 (21%)
Query: 31 TWSDDIAHIMKALQDEVQKRAISLISKAYSSIPNTSLSEFLGVTEQEAAAIA 82
WSD M+ E +A L+S L V E EAAA+
Sbjct: 150 IWSDAAKQAMR----EAAIKAG-LVS------SREGPDRLLIVLEPEAAALY 190
>gnl|CDD|222306 pfam13670, PepSY_2, Peptidase propeptide and YPEB domain. This
region is likely to have a protease inhibitory function
(personal obs:C Yeats). The name is derived from
Peptidase & Bacillus subtilis YPEB.
Length = 83
Score = 25.3 bits (56), Expect = 4.2
Identities = 5/21 (23%), Positives = 10/21 (47%)
Query: 72 GVTEQEAAAIAQAEGWTVDKV 92
+ A +A+G+ V K+
Sbjct: 28 WQPREAVQAKLEAQGYKVKKI 48
>gnl|CDD|239959 cd04586, CBS_pair_BON_assoc, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
associated with the BON (bacterial OsmY and nodulation
domain) domain. BON is a putative phospholipid-binding
domain found in a family of osmotic shock protection
proteins. It is also found in some secretins and a
group of potential haemolysins. Its likely function is
attachment to phospholipid membranes. CBS is a small
domain originally identified in cystathionine
beta-synthase and subsequently found in a wide range of
different proteins. CBS domains usually come in tandem
repeats, which associate to form a so-called Bateman
domain or a CBS pair which is reflected in this model.
The interface between the two CBS domains forms a cleft
that is a potential ligand binding site. The CBS pair
coexists with a variety of other functional domains. It
has been proposed that the CBS domain may play a
regulatory role, although its exact function is
unknown.
Length = 135
Score = 26.0 bits (58), Expect = 4.6
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 69 EFLGVTEQEAAAIAQAEGWTVDKVYTQPV 97
+ L E+ AAA ++ G V V T+PV
Sbjct: 63 DLLAGAEELAAAFVRSHGRKVADVMTRPV 91
>gnl|CDD|133199 cd05068, PTKc_Frk_like, Catalytic domain of Fyn-related
kinase-like Protein Tyrosine Kinases. Protein Tyrosine
Kinase (PTK) family; Human Fyn-related kinase (Frk) and
similar proteins; catalytic (c) domain. The PTKc family
is part of a larger superfamily that includes the
catalytic domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. Frk and
Srk are members of the Src subfamily of proteins, which
are cytoplasmic (or non-receptor) tyr kinases. Src
kinases contain an N-terminal SH4 domain with a
myristoylation site, followed by SH3 and SH2 domains, a
tyr kinase domain, and a regulatory C-terminal region
containing a conserved tyr. They are activated by
autophosphorylation at the tyr kinase domain, but are
negatively regulated by phosphorylation at the
C-terminal tyr by Csk (C-terminal Src Kinase). Src
proteins are involved in signaling pathways that
regulate cytokine and growth factor responses,
cytoskeleton dynamics, cell proliferation, survival,
and differentiation. Frk, also known as Rak, is
specifically expressed in liver, lung, kidney,
intestine, mammary glands, and the islets of
Langerhans. Rodent homologs were previously referred to
as GTK (gastrointestinal tyr kinase), BSK (beta-cell
Src-like kinase), or IYK (intestinal tyr kinase).
Studies in mice reveal that Frk is not essential for
viability. It plays a role in the signaling that leads
to cytokine-induced beta-cell death in Type I diabetes.
It also regulates beta-cell number during embryogenesis
and early in life.
Length = 261
Score = 26.2 bits (58), Expect = 5.4
Identities = 17/43 (39%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 7 GQVWEVGKHLWNGNYPSIYSTLKRTWSDDI-----AHIMKALQ 44
GQ EV + LWN P TLK D A IMK L+
Sbjct: 17 GQFGEVWEGLWNNTTPVAVKTLKPGTMDPKDFLAEAQIMKKLR 59
>gnl|CDD|235735 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated.
Length = 309
Score = 26.3 bits (58), Expect = 5.5
Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 15/79 (18%)
Query: 4 PEIGQVWEVGKHLWNGNYPSIYSTLKRTWSDDIAHIMKALQ------DEVQKRAISLISK 57
E ++WE KH +N N + S DI+ + K L+ + ++K
Sbjct: 65 LEFDKIWEKIKHYFNNNL-----VIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAK 119
Query: 58 -AYSSIPNTSL---SEFLG 72
YS+I N L + FLG
Sbjct: 120 NFYSNIDNARLNTVNNFLG 138
>gnl|CDD|237544 PRK13887, PRK13887, conjugal transfer protein TrbF; Provisional.
Length = 250
Score = 25.9 bits (57), Expect = 7.4
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 25 YSTLKRTWSDDIAHIMKALQ 44
Y +RTW+D + ++ Q
Sbjct: 34 YLNARRTWNDHVGGVVSQRQ 53
>gnl|CDD|173626 cd05034, PTKc_Src_like, Catalytic domain of Src kinase-like
Protein Tyrosine Kinases. Protein Tyrosine Kinase
(PTK) family; Src kinase subfamily; catalytic (c)
domain. Src subfamily members include Src, Lck, Hck,
Blk, Lyn, Fgr, Fyn, Yrk, and Yes. The PTKc family is
part of a larger superfamily that includes the
catalytic domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. Src (or
c-Src) proteins are cytoplasmic (or non-receptor) tyr
kinases which are anchored to the plasma membrane. They
contain an N-terminal SH4 domain with a myristoylation
site, followed by SH3 and SH2 domains, a tyr kinase
domain, and a regulatory C-terminal region containing a
conserved tyr. They are activated by
autophosphorylation at the tyr kinase domain, but are
negatively regulated by phosphorylation at the
C-terminal tyr by Csk (C-terminal Src Kinase). Src
proteins are involved in signaling pathways that
regulate cytokine and growth factor responses,
cytoskeleton dynamics, cell proliferation, survival,
and differentiation. They were identified as the first
proto-oncogene products, and they regulate cell
adhesion, invasion, and motility in cancer cells and
tumor vasculature, contributing to cancer progression
and metastasis. Src kinases are overexpressed in a
variety of human cancers, making them attractive
targets for therapy. They are also implicated in acute
inflammatory responses and osteoclast function. Src,
Fyn, Yes, and Yrk are widely expressed, while Blk, Lck,
Hck, Fgr, and Lyn show a limited expression pattern.
Length = 261
Score = 25.7 bits (57), Expect = 8.1
Identities = 17/45 (37%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 7 GQVWEVGKHLWNGNYPSIYSTLKR-TWSDDI----AHIMKALQDE 46
GQ EV WNG TLK T S + A IMK L+ +
Sbjct: 17 GQFGEVWMGTWNGTTKVAVKTLKPGTMSPEAFLQEAQIMKKLRHD 61
>gnl|CDD|183466 PRK12354, PRK12354, carbamate kinase; Reviewed.
Length = 307
Score = 25.6 bits (57), Expect = 8.7
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 74 TEQEAAAIAQAEGWTV 89
E EA +A +GWT+
Sbjct: 128 DEAEAERLAAEKGWTI 143
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
0.312 0.128 0.378
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,395,888
Number of extensions: 536780
Number of successful extensions: 497
Number of sequences better than 10.0: 1
Number of HSP's gapped: 495
Number of HSP's successfully gapped: 33
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)