RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy369
(107 letters)
>gnl|CDD|241248 cd01212, PTB_JIP, JNK-interacting protein-like (JIP)
Phosphotyrosine-binding (PTB) domain. JIP is a
mitogen-activated protein kinase scaffold protein. JIP
consists of a C-terminal SH3 domain, followed by a PTB
domain. PTB domains have a common PH-like fold and are
found in various eukaryotic signaling molecules. This
domain was initially shown to binds peptides with a
NPXY motif with differing requirements for
phosphorylation of the tyrosine, although more recent
studies have found that some types of PTB domains can
bind to peptides lack tyrosine residues altogether. In
contrast to SH2 domains, which recognize
phosphotyrosine and adjacent carboxy-terminal residues,
PTB-domain binding specificity is conferred by residues
amino-terminal to the phosphotyrosine. PTB domains are
classified into three groups: phosphotyrosine-dependent
Shc-like, phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 149
Score = 84.6 bits (210), Expect = 2e-22
Identities = 35/64 (54%), Positives = 44/64 (68%), Gaps = 6/64 (9%)
Query: 34 KRERFLLGYLGSVETSAHKGNAVICQAVHKIRQTQHR------PHSCILEVSDEGLRMVE 87
RERFLL +LGSVE HKGN V+CQA+ KI + P SCILE+SD GL+MV+
Sbjct: 1 WRERFLLKFLGSVEVPYHKGNDVLCQAMQKIATARRLTVHLRPPASCILEISDRGLKMVD 60
Query: 88 KSRP 91
+S+P
Sbjct: 61 QSKP 64
>gnl|CDD|241315 cd13161, PTB_TK_HMTK, Tyrosine-specific kinase/HM-motif TK
(TM/HMTK) Phosphotyrosine-binding (PTB) PH-like fold.
TK kinases catalyzes the transfer of the terminal
phosphate of ATP to a specific tyrosine residue on its
target protein. TK kinases play significant roles in
development and cell division. Tyrosine-protein kinases
can be divided into two subfamilies: receptor tyrosine
kinases, which have an intracellular tyrosine kinase
domain, a transmembrane domain and an extracellular
ligand-binding domain; and non-receptor (cytoplasmic)
tyrosine kinases, which are soluble, cytoplasmic
kinases. In HMTK the conserved His-Arg-Asp sequence
within the catalytic loop is replaced by a His-Met
sequence. TM/HMTK have are 2-3 N-terminal PTB domains.
PTB domains in TKs are thought to function analogously
to the membrane targeting (PH, myristoylation) and pTyr
binding (SH2) domains of Src subgroup kinases. PTB
domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif
with differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 120
Score = 49.2 bits (118), Expect = 7e-09
Identities = 20/52 (38%), Positives = 31/52 (59%)
Query: 37 RFLLGYLGSVETSAHKGNAVICQAVHKIRQTQHRPHSCILEVSDEGLRMVEK 88
F YLGSV KGN V+ AV +++ + +P +L V+ EG+R+VE+
Sbjct: 3 VFEAKYLGSVPVKEPKGNEVVMAAVKRLKDLKLKPKKVVLVVTSEGIRVVER 54
>gnl|CDD|241298 cd01268, PTB_Numb, Numb Phosphotyrosine-binding (PTB) domain.
Numb is a membrane associated adaptor protein which
plays critical roles in cell fate determination. Numb
proteins are involved in control of asymmetric cell
division and cell fate choice, endocytosis, cell
adhesion, cell migration, ubiquitination of specific
substrates and a number of signaling pathways (Notch,
Hedgehog, p53). Mutations in Numb plays a critical role
in disease (cancer). Numb has an N-terminal PTB domain
and a C-terminal NumbF domain. PTB domains have a
common PH-like fold and are found in various eukaryotic
signaling molecules. This domain was initially shown to
binds peptides with a NPXY motif with differing
requirements for phosphorylation of the tyrosine,
although more recent studies have found that some types
of PTB domains can bind to peptides lack tyrosine
residues altogether. In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred
by residues amino-terminal to the phosphotyrosine. PTB
domains are classified into three groups:
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 135
Score = 48.1 bits (115), Expect = 2e-08
Identities = 18/52 (34%), Positives = 32/52 (61%)
Query: 38 FLLGYLGSVETSAHKGNAVICQAVHKIRQTQHRPHSCILEVSDEGLRMVEKS 89
F + YLG VE +G V +A+ K++ ++ +P +L VS +GLR+V++
Sbjct: 17 FPVKYLGCVEVGESRGMQVCEEALKKLKASRKKPVRAVLWVSGDGLRVVDEK 68
>gnl|CDD|214675 smart00462, PTB, Phosphotyrosine-binding domain,
phosphotyrosine-interaction (PI) domain. PTB/PI domain
structure similar to those of pleckstrin homology (PH)
and IRS-1-like PTB domains.
Length = 134
Score = 44.2 bits (105), Expect = 7e-07
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 37 RFLLGYLGSVETSAHKGNAVICQAVHKIR--QTQHRPH--SCILEVSDEGLRMVEKSR 90
F + YLGSVE +G V+ +A+ K+R Q + IL +S G++++++
Sbjct: 5 SFRVKYLGSVEVPEARGLQVVQEAIRKLRAAQGSEKKEPQKVILSISSRGVKLIDEDT 62
>gnl|CDD|212735 cd11801, SH3_JIP1_like, Src homology 3 domain of JNK-interacting
proteins 1 and 2, and similar domains. JNK-interacting
proteins (JIPs) function as scaffolding proteins for
c-Jun N-terminal kinase (JNK) signaling pathways. They
bind to components of Mitogen-activated protein kinase
(MAPK) pathways such as JNK, MKK, and several MAP3Ks
such as MLK and DLK. There are four JIPs (JIP1-4); all
contain a JNK binding domain. JIP1 and JIP2 also
contain SH3 and Phosphotyrosine-binding (PTB) domains.
Both are highly expressed in the brain and pancreatic
beta-cells. JIP1 functions as an adaptor linking motor
to cargo during axonal transport and also is involved
in regulating insulin secretion. JIP2 form complexes
with fibroblast growth factor homologous factors
(FHFs), which facilitates activation of the p38delta
MAPK. The SH3 domain of JIP1 homodimerizes at the
interface usually involved in proline-rich ligand
recognition, despite the lack of this motif in the
domain itself. SH3 domains are protein interaction
domains that bind to proline-rich ligands with moderate
affinity and selectivity, preferentially to PxxP
motifs. They play versatile and diverse roles in the
cell including the regulation of enzymes, changing the
subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 55
Score = 41.1 bits (97), Expect = 2e-06
Identities = 13/19 (68%), Positives = 17/19 (89%)
Query: 2 GVNLRTGRQGIFPSAYAVD 20
G NLRTG++GIFP+AY V+
Sbjct: 37 GTNLRTGQRGIFPAAYVVE 55
>gnl|CDD|241236 cd00934, PTB, Phosphotyrosine-binding (PTB) PH-like fold. PTB
domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to bind peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains.
Length = 119
Score = 36.4 bits (84), Expect = 5e-04
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 36 ERFLLGYLGSVETSAHKGNAVICQAVHKIRQTQHR----PHSCILEVSDEGLRMVEKSRP 91
F + YLGSVE + +G VI +A+ + P +LEVS EG+++++
Sbjct: 1 VSFQVKYLGSVEVGSPRGVKVIEEALKLLALLLKSSKRKPGPVLLEVSPEGVKLLDLDTK 60
Query: 92 T 92
Sbjct: 61 E 61
>gnl|CDD|241303 cd01273, PTB_CED-6, Cell death protein 6 homolog (CED-6/GULP1)
Phosphotyrosine-binding (PTB) domain. CED6 (also known
as GULP1: engulfment adaptor PTB domain containing 1)
is an adaptor protein involved in the specific
recognition and engulfment of apoptotic cells. CED6
has been shown to interact with the cytoplasmic tail of
another protein involved in the engulfment of apoptotic
cells, CED1. CED6 has a C-terminal PTB domain, which
can bind to NPXY motifs. PTB domains have a common
PH-like fold and are found in various eukaryotic
signaling molecules. This domain was initially shown to
binds peptides with a NPXY motif with differing
requirements for phosphorylation of the tyrosine,
although more recent studies have found that some types
of PTB domains can bind to peptides lack tyrosine
residues altogether. In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred
by residues amino-terminal to the phosphotyrosine. PTB
domains are classified into three groups:
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 144
Score = 36.1 bits (84), Expect = 0.001
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 38 FLLGYLGSVETSAHKGNAVICQAVHKIRQTQHRPHS 73
+L+ +LG E KG V+ +A+ K++ + S
Sbjct: 14 YLVKFLGCTEVDQPKGTEVVKEAIRKLKFARQIKKS 49
>gnl|CDD|212875 cd11942, SH3_JIP2, Src homology 3 domain of JNK-interacting
protein 2. JNK-interacting protein 2 (JIP2) is also
called Mitogen-activated protein kinase 8-interacting
protein 2 (MAPK8IP2) or Islet-brain-2 (IB2). It is
widely expressed in the brain, where it forms complexes
with fibroblast growth factor homologous factors
(FHFs), which facilitates activation of the p38delta
MAPK. JIP2 is enriched in postsynaptic densities and
may play a role in motor and cognitive function. In
addition to a JNK binding domain, JIP2 also contains
SH3 and Phosphotyrosine-binding (PTB) domains. The SH3
domain of the related protein JIP1 homodimerizes at the
interface usually involved in proline-rich ligand
recognition, despite the lack of this motif in the
domain itself. SH3 domains are protein interaction
domains that bind to proline-rich ligands with moderate
affinity and selectivity, preferentially to PxxP
motifs. They play versatile and diverse roles in the
cell including the regulation of enzymes, changing the
subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 55
Score = 31.4 bits (71), Expect = 0.014
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 2 GVNLRTGRQGIFPSAYA 18
G N+RTG +GIFP+ YA
Sbjct: 37 GYNMRTGERGIFPAFYA 53
>gnl|CDD|212718 cd11784, SH3_SH3RF2_3, Third Src Homology 3 domain of SH3 domain
containing ring finger 2. SH3RF2 is also called POSHER
(POSH-eliminating RING protein) or HEPP1 (heart protein
phosphatase 1-binding protein). It acts as an
anti-apoptotic regulator of the JNK pathway by binding
to and promoting the degradation of SH3RF1 (or POSH), a
scaffold protein that is required for pro-apoptotic JNK
activation. It may also play a role in cardiac
functions together with protein phosphatase 1. SH3RF2
contains an N-terminal RING finger domain and three SH3
domains. This model represents the third SH3 domain,
located in the middle, of SH3RF2. SH3 domains are
protein interaction domains that bind to proline-rich
ligands with moderate affinity and selectivity,
preferentially to PxxP motifs. They play versatile and
diverse roles in the cell including the regulation of
enzymes, changing the subcellular localization of
signaling pathway components, and mediating the
formation of multiprotein complex assemblies.
Length = 55
Score = 30.5 bits (69), Expect = 0.027
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 2 GVNLRTGRQGIFPSAY 17
G++L TGR GIFPS Y
Sbjct: 37 GLSLVTGRVGIFPSNY 52
>gnl|CDD|212876 cd11943, SH3_JIP1, Src homology 3 domain of JNK-interacting
protein 1. JNK-interacting protein 1 (JIP1) is also
called Islet-brain 1 (IB1) or Mitogen-activated protein
kinase 8-interacting protein 1 (MAPK8IP1). It is highly
expressed in neurons, where it functions as an adaptor
linking motor to cargo during axonal transport. It also
affects microtubule dynamics in neurons. JIP1 is also
found in pancreatic beta-cells, where it is involved in
regulating insulin secretion. In addition to a JNK
binding domain, JIP1 also contains SH3 and
Phosphotyrosine-binding (PTB) domains. Its SH3 domain
homodimerizes at the interface usually involved in
proline-rich ligand recognition, despite the lack of
this motif in the domain itself. SH3 domains are
protein interaction domains that bind to proline-rich
ligands with moderate affinity and selectivity,
preferentially to PxxP motifs. They play versatile and
diverse roles in the cell including the regulation of
enzymes, changing the subcellular localization of
signaling pathway components, and mediating the
formation of multiprotein complex assemblies.
Length = 55
Score = 30.7 bits (69), Expect = 0.027
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 2 GVNLRTGRQGIFPSAYAVD 20
N+RTG +GIFP+ YA++
Sbjct: 37 AYNMRTGARGIFPAYYAIE 55
>gnl|CDD|224088 COG1166, SpeA, Arginine decarboxylase (spermidine biosynthesis)
[Amino acid transport and metabolism].
Length = 652
Score = 31.1 bits (71), Expect = 0.081
Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 25/85 (29%)
Query: 23 YEDLQTTTPKPKRE--------------RFLLGYLGSVETSAHKGNA-----VICQAVHK 63
E ++ T + RE F LGYL + + A IC V +
Sbjct: 400 QELYESITARNLREWYHDSQDDLEDAHSLFNLGYL----SLQERAWAEQLYLAICHKVQQ 455
Query: 64 IRQTQHRPHSCILEVSDEGLRMVEK 88
+ + ++R H IL+ E R+ +K
Sbjct: 456 LLRQKNRSHRPILDELQE--RLADK 478
>gnl|CDD|212819 cd11886, SH3_BOI, Src Homology 3 domain of fungal BOI-like
proteins. This subfamily includes the Saccharomyces
cerevisiae proteins BOI1 and BOI2, and similar
proteins. They contain an N-terminal SH3 domain, a
Sterile alpha motif (SAM), and a Pleckstrin homology
(PH) domain at the C-terminus. BOI1 and BOI2 interact
with the SH3 domain of Bem1p, a protein involved in bud
formation. They promote polarized cell growth and
participates in the NoCut signaling pathway, which is
involved in the control of cytokinesis. SH3 domains
bind to proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs; they play a
role in the regulation of enzymes by intramolecular
interactions, changing the subcellular localization of
signal pathway components and mediate multiprotein
complex assemblies.
Length = 55
Score = 28.8 bits (65), Expect = 0.12
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 1 MGVNLRTGRQGIFPSAY 17
+G NLRTG G+FP +
Sbjct: 39 LGRNLRTGETGLFPVVF 55
>gnl|CDD|212713 cd11779, SH3_Irsp53_BAIAP2L, Src Homology 3 domain of Insulin
Receptor tyrosine kinase Substrate p53, Brain-specific
Angiogenesis Inhibitor 1-Associated Protein 2
(BAIAP2)-Like proteins, and similar proteins. Proteins
in this family include IRSp53, BAIAP2L1, BAIAP2L2, and
similar proteins. They all contain an
Inverse-Bin/Amphiphysin/Rvs (I-BAR) or IMD domain in
addition to the SH3 domain. IRSp53, also known as
BAIAP2, is a scaffolding protein that takes part in
many signaling pathways including Cdc42-induced
filopodia formation, Rac-mediated lamellipodia
extension, and spine morphogenesis. IRSp53 exists as
multiple splicing variants that differ mainly at the
C-termini. BAIAP2L1, also called IRTKS (Insulin
Receptor Tyrosine Kinase Substrate), serves as a
substrate for the insulin receptor and binds the small
GTPase Rac. It plays a role in regulating the actin
cytoskeleton and colocalizes with F-actin, cortactin,
VASP, and vinculin. IRSp53 and IRTKS also mediate the
recruitment of effector proteins Tir and EspFu, which
regulate host cell actin reorganization, to bacterial
attachment sites. BAIAP2L2 co-localizes with clathrin
plaques but its function has not been determined. The
SH3 domains of IRSp53 and IRTKS have been shown to bind
the proline-rich C-terminus of EspFu. SH3 domains are
protein interaction domains that bind to proline-rich
ligands with moderate affinity and selectivity,
preferentially to PxxP motifs. They play versatile and
diverse roles in the cell including the regulation of
enzymes, changing the subcellular localization of
signaling pathway components, and mediating the
formation of multiprotein complex assemblies.
Length = 57
Score = 28.8 bits (65), Expect = 0.14
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 2 GVNLRTGRQGIFPSAY 17
G N R+GR+G FP AY
Sbjct: 39 GENERSGRRGWFPIAY 54
>gnl|CDD|241316 cd13162, PTB_RGS12, Regulator of G-protein signaling 12
Phosphotyrosine-binding (PTB) PH-like fold. RGS12
functions as a GTPase-activating protein and a
transcriptional repressor. It is thought to play a
role in tumorigenesis. RGS12 specifically interacts
with guanine nucleotide-binding protein G(i), alpha-1
subunit and guanine nucleotide-binding protein G(k)
subunit alpha. RGS proteins are multi-functional,
GTPase-accelerating proteins that promote GTP
hydrolysis by the alpha subunit of heterotrimeric G
proteins, thereby inactivating the G protein and
rapidly switching off G protein-coupled receptor
signalling pathways. Upon activation by GPCRs,
heterotrimeric G proteins exchange GDP for GTP, are
released from the receptor, and dissociate into free,
active GTP-bound alpha subunit and beta-gamma dimer,
both of which activate downstream effectors. The
response is terminated upon GTP hydrolysis by the alpha
subunit, which can then bind the beta-gamma dimer and
the receptor. RGS proteins markedly reduce the lifespan
of GTP-bound alpha subunits by stabilizing the G
protein transition state. PTB domains have a common
PH-like fold and are found in various eukaryotic
signaling molecules. This domain was initially shown to
binds peptides with a NPXY motif with differing
requirements for phosphorylation of the tyrosine,
although more recent studies have found that some types
of PTB domains can bind to peptides lack tyrosine
residues altogether. In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred
by residues amino-terminal to the phosphotyrosine. PTB
domains are classified into three groups:
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 130
Score = 28.5 bits (64), Expect = 0.48
Identities = 17/59 (28%), Positives = 35/59 (59%), Gaps = 7/59 (11%)
Query: 37 RFLLGYLGSVE---TSAHKGNA--VICQAVHKIRQTQHRPHSCIL-EVSDEGLRMVEKS 89
R ++GYLGS+E TS+++ ++ I V ++R Q + HS +L +V + +++ +
Sbjct: 2 RMIVGYLGSIELPSTSSNESDSLQAIRGCVRRLRAEQ-KIHSLVLMKVMHDSVQLCDDR 59
>gnl|CDD|212726 cd11792, SH3_Fut8, Src homology 3 domain of
Alpha1,6-fucosyltransferase (Fut8). Fut8 catalyzes the
alpha1,6-linkage of a fucose residue from a donor
substrate to N-linked oligosaccharides on glycoproteins
in a process called core fucosylation, which is crucial
for growth factor receptor-mediated biological
functions. Fut8-deficient mice show severe growth
retardation, early death, and a pulmonary
emphysema-like phenotype. Fut8 is also implicated to
play roles in aging and cancer metastasis. It contains
an N-terminal coiled-coil domain, a catalytic domain,
and a C-terminal SH3 domain. The SH3 domain of Fut8 is
located in the lumen and its role in glycosyl transfer
is unclear. SH3 domains are protein interaction domains
that bind to proline-rich ligands with moderate
affinity and selectivity, preferentially to PxxP
motifs. They play versatile and diverse roles in the
cell including the regulation of enzymes, changing the
subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 55
Score = 26.4 bits (59), Expect = 0.85
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 2 GVNLRTGRQGIFPS 15
G N RTG+ G++PS
Sbjct: 37 GRNRRTGKTGLYPS 50
>gnl|CDD|212697 cd11763, SH3_SNX9_like, Src Homology 3 domain of Sorting Nexin 9
and similar proteins. Sorting nexins (SNXs) are Phox
homology (PX) domain containing proteins that are
involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. This subfamily consists of SH3 domain
containing SNXs including SNX9, SNX18, SNX33, and
similar proteins. SNX9 is localized to plasma membrane
endocytic sites and acts primarily in clathrin-mediated
endocytosis, while SNX18 is localized to peripheral
endosomal structures, and acts in a trafficking pathway
that is clathrin-independent but relies on AP-1 and
PACS1. SH3 domains are protein interaction domains that
bind to proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 55
Score = 26.1 bits (58), Expect = 1.2
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 4/22 (18%)
Query: 2 GVNLRTGRQGIFPSAYAVDVEY 23
G N R G G+FPS+Y VE
Sbjct: 38 GRNSR-GEVGLFPSSY---VEI 55
>gnl|CDD|212723 cd11789, SH3_Nebulin_family_C, C-terminal Src Homology 3 domain
of the Nebulin family of proteins. Nebulin family
proteins contain multiple nebulin repeats, and may
contain an N-terminal LIM domain and/or a C-terminal
SH3 domain. They have molecular weights ranging from 34
to 900 kD, depending on the number of nebulin repeats,
and they all bind actin. They are involved in the
regulation of actin filament architecture and function
as stabilizers and scaffolds for cytoskeletal
structures with which they associate, such as long
actin filaments or focal adhesions. Nebulin family
proteins that contain a C-terminal SH3 domain include
the giant filamentous protein nebulin, nebulette,
Lasp1, and Lasp2. Lasp2, also called LIM-nebulette, is
an alternatively spliced variant of nebulette. SH3
domains are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 55
Score = 26.1 bits (58), Expect = 1.2
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 2 GVNLRTGRQGIFPSAY 17
G RTG+ G+ P+ Y
Sbjct: 37 GTVQRTGQSGMLPANY 52
>gnl|CDD|144292 pfam00640, PID, Phosphotyrosine interaction domain (PTB/PID).
Length = 133
Score = 27.3 bits (61), Expect = 1.2
Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 12/56 (21%)
Query: 42 YLGSVETSAHKGNAVICQAVHKIRQT-----------QHRPHSCILEVSDEGLRMV 86
YLGSVE + V +A+ +++ + S L +S +GL+++
Sbjct: 5 YLGSVEVPEERM-DVANEAISRLKMAKNAKRAGLTGHRQPGTSIDLSISTDGLKLL 59
>gnl|CDD|212895 cd11962, SH3_Abp1_fungi_C1, First C-terminal Src homology 3
domain of Fungal Actin-binding protein 1. Abp1 is an
adaptor protein that functions in receptor-mediated
endocytosis and vesicle trafficking. It contains an
N-terminal actin-binding module, the
actin-depolymerizing factor (ADF) homology domain, a
central proline-rich region, and a C-terminal SH3
domain (many yeast Abp1 proteins contain two C-terminal
SH3 domains). Yeast Abp1 also contains two acidic
domains that bind directly to the Arp2/3 complex, which
is required to initiate actin polymerization. The SH3
domain of yeast Abp1 binds and localizes the kinases,
Ark1p and Prk1p, which facilitate actin patch
disassembly following vesicle internalization. It also
mediates the localization to the actin patch of the
synaptojanin-like protein, Sjl2p, which plays a key
role in endocytosis. SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles
in the cell including the regulation of enzymes,
changing the subcellular localization of signaling
pathway components, and mediating the formation of
multiprotein complex assemblies.
Length = 54
Score = 25.9 bits (57), Expect = 1.2
Identities = 9/17 (52%), Positives = 11/17 (64%), Gaps = 1/17 (5%)
Query: 1 MGVNLRTGRQGIFPSAY 17
MG N + G G+FPS Y
Sbjct: 36 MGTNSK-GESGLFPSNY 51
>gnl|CDD|212822 cd11889, SH3_Cyk3p-like, Src Homology 3 domain of Cytokinesis
protein 3 and similar proteins. Cytokinesis protein 3
(Cyk3 or Cyk3p) is a component of the actomyosin ring
independent cytokinesis pathway in yeast. It interacts
with Inn1 and facilitates its recruitment to the bud
neck, thereby promoting cytokinesis. Cyk3p contains an
N-terminal SH3 domain and a C-terminal
transglutaminase-like domain. The Cyk3p SH3 domain
binds to the C-terminal proline-rich region of Inn1.
SH3 domains bind to proline-rich ligands with moderate
affinity and selectivity, preferentially to PxxP
motifs; they play a role in the regulation of enzymes
by intramolecular interactions, changing the
subcellular localization of signal pathway components
and mediate multiprotein complex assemblies.
Length = 53
Score = 25.9 bits (57), Expect = 1.5
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 1 MGVNLRTGRQGIFPSAY 17
G R G +GIFPS +
Sbjct: 36 SGKLRRNGAEGIFPSNF 52
>gnl|CDD|212717 cd11783, SH3_SH3RF_3, Third Src Homology 3 domain of SH3 domain
containing ring finger 1 (SH3RF1), SH3RF3, and similar
domains. SH3RF1 (or POSH) and SH3RF3 (or POSH2) are
scaffold proteins that function as E3 ubiquitin-protein
ligases. They contain an N-terminal RING finger domain
and four SH3 domains. This model represents the third
SH3 domain, located in the middle of SH3RF1 and SH3RF3,
and similar domains. SH3RF1 plays a role in calcium
homeostasis through the control of the ubiquitin domain
protein Herp. It may also have a role in regulating
death receptor mediated and JNK mediated apoptosis.
SH3RF3 interacts with p21-activated kinase 2 (PAK2) and
GTP-loaded Rac1. It may play a role in regulating JNK
mediated apoptosis in certain conditions. SH3 domains
are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 55
Score = 25.8 bits (57), Expect = 1.7
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 2 GVNLRTGRQGIFPSAY 17
G +LRTG+ G+FP Y
Sbjct: 37 GTSLRTGQSGVFPGNY 52
>gnl|CDD|212857 cd11924, SH3_Vinexin_2, Second Src Homology 3 domain of Vinexin,
also called Sorbin and SH3 domain containing 3
(Sorbs3). Vinexin is also called Sorbs3, SH3P3, and
SH3-containing adapter molecule 1 (SCAM-1). It is an
adaptor protein containing one sorbin homology (SoHo)
and three SH3 domains. Vinexin was first identified as
a vinculin binding protein; it is co-localized with
vinculin at cell-ECM and cell-cell adhesion sites.
There are several splice variants of vinexin: alpha,
which contains the SoHo and three SH3 domains and
displays tissue-specific expression; and beta, which
contains only the three SH3 domains and is widely
expressed. Vinexin alpha stimulates the accumulation of
F-actin at focal contact sites. Vinexin also promotes
keratinocyte migration and wound healing. The SH3
domains of vinexin have been reported to bind a number
of ligands including vinculin, WAVE2, DLG5, Abl, and
Cbl. SH3 domains are protein interaction domains that
bind to proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 56
Score = 25.7 bits (56), Expect = 1.8
Identities = 9/11 (81%), Positives = 11/11 (100%)
Query: 7 TGRQGIFPSAY 17
TGRQGIFP++Y
Sbjct: 43 TGRQGIFPASY 53
>gnl|CDD|212858 cd11925, SH3_SH3RF3_3, Third Src Homology 3 domain of SH3 domain
containing ring finger 3, an E3 ubiquitin-protein
ligase. SH3RF3 is also called POSH2 (Plenty of SH3s 2)
or SH3MD4 (SH3 multiple domains protein 4). It is a
scaffold protein with E3 ubiquitin-protein ligase
activity. It was identified in the screen for
interacting partners of p21-activated kinase 2 (PAK2).
It may play a role in regulating JNK mediated apoptosis
in certain conditions. It also interacts with
GTP-loaded Rac1. SH3RF3 is highly homologous to SH3RF1;
it also contains an N-terminal RING finger domain and
four SH3 domains. This model represents the third SH3
domain, located in the middle, of SH3RF3. SH3 domains
are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 57
Score = 25.7 bits (56), Expect = 2.0
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 2 GVNLRTGRQGIFPSAYAVDV 21
G +LRTG G+FP Y V
Sbjct: 38 GTSLRTGVSGVFPGNYVTPV 57
>gnl|CDD|212690 cd00174, SH3, Src Homology 3 domain superfamily. Src Homology 3
(SH3) domains are protein interaction domains that bind
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. Thus, they
are referred to as proline-recognition domains (PRDs).
SH3 domains are less selective and show more diverse
specificity compared to other PRDs. They have been
shown to bind peptide sequences that lack the PxxP
motif; examples include the PxxDY motif of Eps8 and the
RKxxYxxY sequence in SKAP55. SH3 domain containing
proteins play versatile and diverse roles in the cell,
including the regulation of enzymes, changing the
subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies, among others. Many members of this
superfamily are adaptor proteins that associate with a
number of protein partners, facilitating complex
formation and signal transduction.
Length = 51
Score = 25.1 bits (56), Expect = 2.2
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 5 LRTGRQGIFPSAY 17
L GR+G+FP+ Y
Sbjct: 39 LNGGREGLFPANY 51
>gnl|CDD|212714 cd11780, SH3_Sorbs_3, Third (or C-terminal) Src Homology 3 domain
of Sorbin and SH3 domain containing (Sorbs) proteins
and similar domains. This family, also called the
vinexin family, is composed predominantly of adaptor
proteins containing one sorbin homology (SoHo) and
three SH3 domains. Members include the third SH3
domains of Sorbs1 (or ponsin), Sorbs2 (or ArgBP2),
Vinexin (or Sorbs3), and similar domains. They are
involved in the regulation of cytoskeletal
organization, cell adhesion, and growth factor
signaling. Members of this family bind multiple
partners including signaling molecules like c-Abl,
c-Arg, Sos, and c-Cbl, as well as cytoskeletal
molecules such as vinculin and afadin. They may have
overlapping functions. SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles
in the cell including the regulation of enzymes,
changing the subcellular localization of signaling
pathway components, and mediating the formation of
multiprotein complex assemblies.
Length = 55
Score = 25.3 bits (56), Expect = 2.7
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 2 GVNLRTGRQGIFPSAY 17
G + RTG G FP Y
Sbjct: 37 GTSERTGLFGTFPGNY 52
>gnl|CDD|241249 cd01213, PTB_tensin, Tensin Phosphotyrosine-binding (PTB) domain.
Tensin is a a focal adhesion protein, which contains a
C-terminal SH2 domain followed by a PTB domain. PTB
domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif
with differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 136
Score = 25.7 bits (57), Expect = 4.5
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 10/65 (15%)
Query: 42 YLGSVETSAHKGNAVICQAVHKIRQTQHRPHSCI--LEVSDEGLRMVEKSR--------P 91
YLGSV+T + G + +AV + + P + +VS++G+ + + R P
Sbjct: 8 YLGSVDTESLTGPQAVRKAVSETLERDPLPTPTVVHFKVSEQGITLTDNQRKLFFRRHYP 67
Query: 92 TSSVS 96
++VS
Sbjct: 68 VNTVS 72
>gnl|CDD|185362 PRK15465, pabB, aminodeoxychorismate synthase subunit I;
Provisional.
Length = 453
Score = 26.0 bits (57), Expect = 4.9
Identities = 16/59 (27%), Positives = 21/59 (35%), Gaps = 8/59 (13%)
Query: 15 SAYAVDVEYEDLQTTTPKPKRERFLLGYLGSVETSAHKGNAVICQAVHKIRQTQHRPHS 73
S V+ L++ +E F L TS + N Q K RQ Q HS
Sbjct: 156 SHNDVNARRAWLESQQF-SPQEDFTL-------TSDWQSNMTREQYGEKFRQVQEYLHS 206
>gnl|CDD|233367 TIGR01349, PDHac_trf_mito, pyruvate dehydrogenase complex
dihydrolipoamide acetyltransferase, long form. This
model represents one of several closely related clades
of the dihydrolipoamide acetyltransferase subunit of the
pyruvate dehydrogenase complex. It includes sequences
from mitochondria and from alpha and beta branches of
the proteobacteria, as well as from some other bacteria.
Sequences from Gram-positive bacteria are not included.
The non-enzymatic homolog protein X, which serves as an
E3 component binding protein, falls within the clade
phylogenetically but is rejected by its low score
[Energy metabolism, Pyruvate dehydrogenase].
Length = 436
Score = 25.5 bits (56), Expect = 6.5
Identities = 9/38 (23%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 71 PHSCILEVSDEGLRMVEKSRPTS--SVSGTVQITITSD 106
P +CIL V V + +V+ + +T++ D
Sbjct: 371 PQACILAVGAVEDVAVVDNDEEKGFAVASIMSVTLSCD 408
>gnl|CDD|241250 cd01214, PTB_FAM43A, Family with sequence similarity 43, member A
(FAM43A) Phosphotyrosine-binding (PTB) domain. The
function of FAM43A is currently unknown. Human FAM43A
is located on chromosome 3 at location 3q29. It
encodes a 3182 base pair mRNA which possesses one
Pleckstrin homology-like domain. The mRNA translates
into LOC131583, a hydrophilic protein that is predicted
to localize in the nucleus. The FAM43A gene is
conserved through a broad range of vertebrates. It is
highly conserved from chimpanzees to zebrafish. PTB
domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif
with differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains.
Length = 125
Score = 24.9 bits (55), Expect = 7.1
Identities = 15/54 (27%), Positives = 20/54 (37%), Gaps = 4/54 (7%)
Query: 42 YLGSVETSAHKGNAVICQAVHKI--RQTQHRPHSCI--LEVSDEGLRMVEKSRP 91
YLG+V T KG + + I TQ L V+ GL+ K
Sbjct: 12 YLGNVLTLWAKGEGCTEKPLATIWRNYTQGSKPDVKMKLTVTPSGLKATTKQHG 65
>gnl|CDD|235592 PRK05756, PRK05756, pyridoxamine kinase; Validated.
Length = 286
Score = 25.2 bits (56), Expect = 7.4
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 5/28 (17%)
Query: 39 LLGYLGSVETSAHKGNAVICQAVHKIRQ 66
L GYLGS E I AV +++
Sbjct: 79 LSGYLGSAEQGEA-----ILDAVRRVKA 101
>gnl|CDD|238305 cd00545, MCH, Methenyltetrahydromethanopterin (methenyl-H4MPT)
cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that
has been identified in methanogenic archaea, sulfate-
reducing archaea, and methylotrophic bacteria. It
catalyzes the reversible formation of N(5),
N(10)-methenyltetrahydromethanopterin (methenyl-H4MPT+)
from N(5)-formyltetrahydromethanopterin (formyl- H4MPT),
in the third step of the reaction to reduce CO2 to CH4.
The protein functions as a homodimer or homotrimer,
depending on the organism.
Length = 312
Score = 25.0 bits (55), Expect = 9.1
Identities = 7/11 (63%), Positives = 11/11 (100%)
Query: 91 PTSSVSGTVQI 101
PT+S++G+VQI
Sbjct: 168 PTASLAGSVQI 178
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
0.315 0.130 0.368
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,061,096
Number of extensions: 396923
Number of successful extensions: 331
Number of sequences better than 10.0: 1
Number of HSP's gapped: 328
Number of HSP's successfully gapped: 34
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
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 (24.2 bits)