RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15745
(170 letters)
>gnl|CDD|241338 cd13184, FERM_C_4_1_family, Protein 4.1 family FERM domain C-lobe.
The protein 4.1 family includes four well-defined
members: erythroid protein 4.1 (4.1R), the bestknown and
characterized member, 4.1G (general), 4.1N (neuronal),
and 4.1 B (brain). The less well understood 4.1O/FRMD3
is not a true member of this family and is not included
in this hierarchy. Besides three highly conserved
domains, FERM, SAB (spectrin and actin binding domain)
and CTD (C-terminal domain), the proteins from this
family contain several unique domains: U1, U2 and U3.
FERM domains like other members of the FERM domain
superfamily have a cloverleaf architecture with three
distinct lobes (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 brain is a particularly rich source of protein 4.1
isoforms. The various 4.1R, 4.1G, 4.1N, and 4.1B mRNAs
are all expressed in distinct patterns within the brain.
It is likely that 4.1 proteins play important functional
roles in the brain including motor coordination and
spatial learning, postmitotic differentiation, and
synaptic architecture and function. In addition they are
found in nonerythroid, nonneuronal cells where they may
play a general structural role in nuclear architecture
and/or may interact with splicing factors. The FERM C
domain is the third structural domain within the FERM
domain. 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 = 113
Score = 103 bits (258), Expect = 4e-29
Identities = 41/48 (85%), Positives = 46/48 (95%)
Query: 121 GQTPAEAELNYLDNAKKLSMYGVVLHPAKDSEGVDIMLGVCASGILVY 168
GQTPAEAEL++L+NAKKL++YGV LHPAKDSEGVDIMLGVCA GILVY
Sbjct: 1 GQTPAEAELHFLENAKKLALYGVDLHPAKDSEGVDIMLGVCAGGILVY 48
>gnl|CDD|214604 smart00295, B41, Band 4.1 homologues. Also known as
ezrin/radixin/moesin (ERM) protein domains. Present in
myosins, ezrin, radixin, moesin, protein tyrosine
phosphatases. Plasma membrane-binding domain. These
proteins play structural and regulatory roles in the
assembly and stabilization of specialized plasmamembrane
domains. Some PDZ domain containing proteins bind one or
more of this family. Now includes JAKs.
Length = 201
Score = 88.5 bits (220), Expect = 2e-22
Identities = 37/95 (38%), Positives = 50/95 (52%), Gaps = 7/95 (7%)
Query: 58 THKLPCSYVTYALLGSYLVQSELGDYDQEEHKGNPDYLREFKFAPNQT------PELEQR 111
+LPC LL + +Q+E GDYD+E H L +F P Q E +R
Sbjct: 108 EGRLPCPEEEALLLAALALQAEFGDYDEELHDL-RGELSLKRFLPKQLLDSRKLKEWRER 166
Query: 112 VMELHKTHKGQTPAEAELNYLDNAKKLSMYGVVLH 146
++ELHK G +P EA+L YL+ A+KL YGV L
Sbjct: 167 IVELHKELIGLSPEEAKLKYLELARKLPTYGVELF 201
Score = 53.8 bits (130), Expect = 2e-09
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 7/66 (10%)
Query: 1 LPCSYVTYALLGSYLVQSELGDYDQEEHKGNPDYLREFKFAPNQT------PELEQRVME 54
LPC LL + +Q+E GDYD+E H L +F P Q E +R++E
Sbjct: 111 LPCPEEEALLLAALALQAEFGDYDEELHDL-RGELSLKRFLPKQLLDSRKLKEWRERIVE 169
Query: 55 LHKTHK 60
LHK
Sbjct: 170 LHKELI 175
>gnl|CDD|215882 pfam00373, FERM_M, FERM central domain. This domain is the central
structural domain of the FERM domain.
Length = 113
Score = 85.0 bits (211), Expect = 5e-22
Identities = 36/95 (37%), Positives = 54/95 (56%), Gaps = 9/95 (9%)
Query: 59 HKLPCSYVTYALLGSYLVQSELGDYDQEEHKGNPDYLREFKFAP-------NQTPELEQR 111
+LPCS LL + +Q+E GDY+ E+H YL+E ++ ++ ELE+R
Sbjct: 21 GRLPCSEEEALLLAALALQAEFGDYNPEKHS--SSYLKELEYFLPSRLIKKEKSKELEKR 78
Query: 112 VMELHKTHKGQTPAEAELNYLDNAKKLSMYGVVLH 146
++E HK +G +PAEA+L YL A+ L YGV
Sbjct: 79 ILEAHKNLRGLSPAEAKLKYLQIAQSLPTYGVTFF 113
>gnl|CDD|241343 cd13189, FERM_C_PTPN4_PTPN3_like, Protein tyrosine phosphatase
non-receptor proteins 3 and 4 (PTPN4 and PTPN3) FERM
domain C-lobe. PTPN4 (also called PTPMEG, protein
tyrosine phosphatase, megakaryocyte) is a cytoplasmic
protein-tyrosine phosphatase (PTP) thought to play a
role in cerebellar function. PTPMEG-knockout mice have
impaired memory formation and cerebellar long-term
depression. PTPN3/PTPH1 is a membrane-associated PTP
that is implicated in regulating tyrosine
phosphorylation of growth factor receptors, p97 VCP
(valosin-containing protein, or Cdc48 in Saccharomyces
cerevisiae), and HBV (Hepatitis B Virus) gene
expression; it is mutated in a subset of colon cancers.
PTPMEG and PTPN3/PTPH1 contains a N-terminal FERM
domain, a middle PDZ domain, and a C-terminal
phosphatase domain. PTP1/Tyrosine-protein phosphatase 1
from nematodes and a FERM_C repeat 1 from Tetraodon
nigroviridis also included in this cd. 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 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 = 123
Score = 80.8 bits (200), Expect = 2e-20
Identities = 24/48 (50%), Positives = 37/48 (77%)
Query: 121 GQTPAEAELNYLDNAKKLSMYGVVLHPAKDSEGVDIMLGVCASGILVY 168
GQ+PAEAE N+L+ A+ L +YGV LH A+D+ +++ +GV + GILV+
Sbjct: 1 GQSPAEAEFNFLNTARTLELYGVELHSARDASNLELQVGVTSGGILVF 48
>gnl|CDD|241340 cd13186, FERM_C_NBL4_NBL5, Novel band 4.1-like protein 4 and 5 FERM
(NBL4 and 5) domain C-lobe. NBL4 (also called
Erythrocyte protein band 4.1-like 4; Epb4 1l4) plays a
role the beta-catenin/Tcf signaling pathway and is
thought to be involved in establishing the cell polarity
or proliferation. NBL4 may be also involved in adhesion,
in cell motility and/or in cell-to-cell communication.
No role for NBL5 has been proposed to date. Both NBL4
and NBL5 contain a N-terminal FERM domain which 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).
A single FERM_C repeat 2 from Tetraodon nigroviridis
also included in this cdThe C-lobe is a member of the PH
superfamily. 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 = 64.2 bits (157), Expect = 5e-14
Identities = 29/46 (63%), Positives = 34/46 (73%)
Query: 123 TPAEAELNYLDNAKKLSMYGVVLHPAKDSEGVDIMLGVCASGILVY 168
TPAEAELNYL+ AK L MYGV LHP K +G + LG+ +GILVY
Sbjct: 1 TPAEAELNYLNKAKWLEMYGVDLHPVKGEDGNEYFLGLTPTGILVY 46
>gnl|CDD|241347 cd13193, FERM_C_FARP1-like, FERM, RhoGEF and pleckstrin
domain-containing protein 1 and related proteins FERM
domain. Members here include FARP1 (also called
Chondrocyte-derived ezrin-like protein; PH
domain-containing family C member 2), FARP2 (also called
FIR/FERM domain including RhoGEF; FGD1-related
Cdc42-GEF/FRG), and FRMD7(FERM domain containing 7).
FARP1 and FARP2 are members of the Dbl family guanine
nucleotide exchange factors (GEFs) which are upstream
positive regulators of Rho GTPases. FARP1 has increased
expression in differentiated chondrocytes. FARP2 is
thought to regulate neurite remodeling by mediating the
signaling pathways from membrane proteins to Rac. It is
found in brain, lung, and testis, as well as embryonic
hippocampal and cortical neurons. These members are
composed of a N-terminal FERM domain, a proline-rich
(PR) domain, Dbl-homology (DH), and two C-terminal PH
domains. Other members in this family do not contain
the DH domains such as the Human FERM domain containing
protein 7 and Caenorhabditis elegans CFRM3, both of
which have unknown functions. They contain an N-terminal
FERM domain, a PH domain, followed by a FA (FERM
adjacent) domain. 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 = 122
Score = 56.2 bits (136), Expect = 9e-11
Identities = 20/36 (55%), Positives = 26/36 (72%)
Query: 133 DNAKKLSMYGVVLHPAKDSEGVDIMLGVCASGILVY 168
D A++ +YG+ LHPAKD EGVD+ L V GILV+
Sbjct: 1 DIARRCELYGIRLHPAKDREGVDLNLAVAHMGILVF 36
>gnl|CDD|241342 cd13188, FERM_C_PTPN14_PTPN21, Protein tyrosine phosphatase
non-receptor proteins 14 and 21 (PTPN14 and 21) FERM
domain. This CD contains PTP members: pez/PTPN14 and
PTPN21. A number of mutations in Pez have been shown to
be associated with breast and colorectal cancer. The
PTPN protein family belong to larger family of PTPs.
PTPs are known to be signaling molecules that regulate a
variety of cellular processes including cell growth,
differentiation, mitotic cycle, and oncogenic
transformation. The members are composed of a N-terminal
FERM domain and a C-terminal PTP catalytic domain. 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. Like most other ERM
members they have a phosphoinositide-binding site in
their FERM domain. The FERM C domain is the third
structural domain within the FERM domain. 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 = 50.4 bits (121), Expect = 1e-08
Identities = 22/47 (46%), Positives = 30/47 (63%)
Query: 121 GQTPAEAELNYLDNAKKLSMYGVVLHPAKDSEGVDIMLGVCASGILV 167
G +PAEAEL Y+ ++L YG +PAKD++G DI +G GI V
Sbjct: 1 GLSPAEAELLYIQEVEQLDGYGEESYPAKDNQGNDIFIGASFEGIFV 47
>gnl|CDD|241341 cd13187, FERM_C_PTPH13, Protein tyrosine phosphatase non-receptor
13 (PTPH13) FERM domain C-lobe. There are many
functions of PTPN13 (also called PTPL1, PTP-BAS, hPTP1E,
FAP1, or PTPL1). Mice lacking PTPN13 activity have
abnormal regulation of signal transducer and activator
of transcription signaling in their T cells, mild
impairment of motor nerve repair, and a significant
reduction in the growth of retinal glia cultures. It
also plays a role in adipocyte differentiation. PTPN13
contains a kinase non-catalytic C-lobe domain (KIND), a
FERM domain with two potential phosphatidylinositol
4,5-biphosphate [PtdIns(4,5)P2]-binding motifs, 5 PDZ
domains, and a carboxy-terminal catalytic domain. There
is an nteraction between the FERM domain of PTPL1 and
PtdIns(4,5)P2 which is thought to regulate the membrane
localization of PTPN13. PDZ are protein/protein
interaction domains so there is the potential for
numerous partners that can actively participate in the
regulation of its phosphatase activity or can permit
direct or indirect recruitment of tyrosine
phosphorylated PTPL1 substrates. 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 = 124
Score = 48.5 bits (116), Expect = 6e-08
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 121 GQTPAEAELNYLDNAKKLSMYGVVLH---PAKDSEGVDIMLGVCASGILVYSE 170
G + EAEL +L +KL YGV H K S I LG+C+ GI++Y
Sbjct: 1 GLSEEEAELEFLKVCQKLPEYGVHFHRVYREKKSSTGGIWLGICSRGIIIYEV 53
>gnl|CDD|241346 cd13192, FERM_C_FRMD3_FRMD5, FERM domain-containing protein 3 and 5
FERM (FRMD3 and 5) domain C-lobe. FRMD3 (also called
Band 4.1-like protein 4O/4.1O though it is not a true
member of that family) is a novel putative tumor
suppressor gene that is implicated in the origin and
progression of lung cancer. In humans there are 5
isoforms that are produced by alternative splicing. Less
is known about FRMD5, though there are 2 isoforms of the
human protein are produced by alternative splicing. Both
FRMD3 and FRMD5 contain a N-terminal FERM domain,
followed by a FERM adjacent (FA) domain, and 4.1 protein
C-terminal domain (CTD). 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 = 105
Score = 47.8 bits (114), Expect = 9e-08
Identities = 19/42 (45%), Positives = 25/42 (59%)
Query: 127 AELNYLDNAKKLSMYGVVLHPAKDSEGVDIMLGVCASGILVY 168
AELN+L A L YGV HP KD G + LG +G++V+
Sbjct: 1 AELNFLRKAHTLETYGVDPHPVKDHYGTQLYLGFTHTGVVVF 42
>gnl|CDD|241349 cd13195, FERM_C_MYLIP_IDOL, The E3 ubiquitin ligase myosin
regulatory light chain-interacting protein (MYLIP; also
called inducible degrader of the LDL receptor, IDOL)
FERM domain C-lobe. MYLIP/IDOL is a regulator of the
LDL receptor (LDLR) pathway via the nuclear receptor
liver X receptor (LXR). In response to cellular
cholesterol loading, the activation of LXR leads to the
induction of MYLIP expression. MYLIP stimulates
ubiquitination of the LDLR on its cytoplasmic tail,
directing its degradation. The LXR-MYLIP-LDLR pathway
provides a complementary pathway to sterol regulatory
element-binding proteins for the feedback inhibition of
cholesterol uptake. MYLIP has an N-terminal FERM domain
and in some cases a C-terminal RING domain. 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 = 131
Score = 47.6 bits (114), Expect = 2e-07
Identities = 15/50 (30%), Positives = 26/50 (52%)
Query: 121 GQTPAEAELNYLDNAKKLSMYGVVLHPAKDSEGVDIMLGVCASGILVYSE 170
G +P+ AE +L +L YGV + EG +++GV GI + ++
Sbjct: 1 GMSPSTAEYLFLKEVSELENYGVETFHVRTIEGQKLVIGVGPDGIRICND 50
>gnl|CDD|220216 pfam09380, FERM_C, FERM C-terminal PH-like domain.
Length = 90
Score = 38.8 bits (91), Expect = 1e-04
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 150 DSEGVDIMLGVCASGILVY 168
D +G D+ LGV A GILVY
Sbjct: 1 DKKGTDLWLGVSAKGILVY 19
>gnl|CDD|241233 cd00836, FERM_C-lobe, FERM domain C-lobe. 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 = 91
Score = 37.7 bits (88), Expect = 3e-04
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 142 GVVLHPAKDSE-GVDIMLGVCASGILVYSE 170
GV KD G +++LGV GI V +
Sbjct: 1 GVEFFDVKDKSGGSELILGVSLEGISVLDD 30
>gnl|CDD|241348 cd13194, FERM_C_ERM, ERM family FERM domain C-lobe/F3. The ERM
family includes ezrin, radixin, moesin and merlin. They
are composed of a N-terminal FERM (ERM) domain (also
called N-ERMAD (N-terminal ERM association domain)), a
coiled coil region (CRR), and a C-terminal domain CERMAD
(C-terminal ERM association domain) which has an
F-actin-binding site (ABD). Two actin-binding sites have
been identified in the middle and N-terminal domains.
Merlin is structurally similar to the ERM proteins, but
instead of an actin-binding domain (ABD), it contains a
C-terminal domain (CTD), just like the proteins from the
4.1 family. Activated ezrin, radixin and moesin are
thought to be involved in the linking of actin filaments
to CD43, CD44, ICAM1-3 cell adhesion molecules, various
membrane channels and receptors, such as the Na+/H+
exchanger-3 (NHE3), cystic fibrosis transmembrane
conductance regulator (CFTR), and the beta2-adrenergic
receptor. The ERM proteins exist in two states, a
dormant state in which the FERM domain binds to its own
C-terminal tail and thereby precludes binding of some
partner proteins, and an activated state, in which the
FERM domain binds to one of many membrane binding
proteins and the C-terminal tail binds to F-actin. 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
of ERM 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 = 97
Score = 31.4 bits (72), Expect = 0.057
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 140 MYGVVLHPAKDSEGVDIMLGVCASGILVY 168
MYGV K+ +G D+ LGV A G+ +Y
Sbjct: 1 MYGVNYFEIKNKKGTDLWLGVDALGLNIY 29
>gnl|CDD|132987 cd06656, STKc_PAK3, Catalytic domain of the Protein
Serine/Threonine Kinase, p21-activated kinase 3.
Serine/threonine kinases (STKs), p21-activated kinase
(PAK) 3, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The PAK
subfamily is part of a larger superfamily that includes
the catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. PAKs are Rho family GTPase-regulated kinases
that serve as important mediators in the function of
Cdc42 (cell division cycle 42) and Rac. PAKs from higher
eukaryotes are classified into two groups (I and II),
according to their biochemical and structural features.
PAK3 belongs to group I. Group I PAKs contain a PBD
(p21-binding domain) overlapping with an AID
(autoinhibitory domain), a C-terminal catalytic domain,
SH3 binding sites and a non-classical SH3 binding site
for PIX (PAK-interacting exchange factor). PAK3 is
highly expressed in the brain. It is implicated in
neuronal plasticity, synapse formation, dendritic spine
morphogenesis, cell cycle progression, neuronal
migration, and apoptosis. Inactivating mutations in the
PAK3 gene cause X-linked non-syndromic mental
retardation, the severity of which depends on the site
of the mutation.
Length = 297
Score = 30.8 bits (69), Expect = 0.29
Identities = 34/136 (25%), Positives = 52/136 (38%), Gaps = 19/136 (13%)
Query: 35 LREFKFAPNQTPELEQRVMELHKTHKLPCSYVTYALLGSYLVQSELGDYDQEEHKGNPDY 94
L +F F TPE +R + + + VT G + LG E +G P Y
Sbjct: 156 LTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMVEGEPPY 215
Query: 95 LRE------FKFAPNQTPELE-------------QRVMELHKTHKGQTPAEAELNYLDNA 135
L E + A N TPEL+ R +E+ +G + +L A
Sbjct: 216 LNENPLRALYLIATNGTPELQNPERLSAVFRDFLNRCLEMDVDRRGSAKELLQHPFLKLA 275
Query: 136 KKLSMYGVVLHPAKDS 151
K LS ++ AK++
Sbjct: 276 KPLSSLTPLIIAAKEA 291
>gnl|CDD|132986 cd06655, STKc_PAK2, Catalytic domain of the Protein
Serine/Threonine Kinase, p21-activated kinase 2.
Serine/threonine kinases (STKs), p21-activated kinase
(PAK) 2, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The PAK
subfamily is part of a larger superfamily that includes
the catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. PAKs are Rho family GTPase-regulated kinases
that serve as important mediators in the function of
Cdc42 (cell division cycle 42) and Rac. PAKs from higher
eukaryotes are classified into two groups (I and II),
according to their biochemical and structural features.
PAK2 belongs to group I. Group I PAKs contain a PBD
(p21-binding domain) overlapping with an AID
(autoinhibitory domain), a C-terminal catalytic domain,
SH3 binding sites and a non-classical SH3 binding site
for PIX (PAK-interacting exchange factor). PAK2 plays a
role in pro-apoptotic signaling. It is cleaved and
activated by caspases leading to morphological changes
during apoptosis. PAK2 is also activated in response to
a variety of stresses including DNA damage,
hyperosmolarity, serum starvation, and contact
inhibition, and may play a role in coordinating the
stress response. PAK2 also contributes to cancer cell
invasion through a mechanism distinct from that of PAK1.
Length = 296
Score = 30.5 bits (68), Expect = 0.38
Identities = 34/136 (25%), Positives = 52/136 (38%), Gaps = 19/136 (13%)
Query: 35 LREFKFAPNQTPELEQRVMELHKTHKLPCSYVTYALLGSYLVQSELGDYDQEEHKGNPDY 94
L +F F TPE +R + + + VT G + LG E +G P Y
Sbjct: 156 LTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMVEGEPPY 215
Query: 95 LRE------FKFAPNQTPELE-------------QRVMELHKTHKGQTPAEAELNYLDNA 135
L E + A N TPEL+ R +E+ +G + +L A
Sbjct: 216 LNENPLRALYLIATNGTPELQNPEKLSPIFRDFLNRCLEMDVEKRGSAKELLQHPFLKLA 275
Query: 136 KKLSMYGVVLHPAKDS 151
K LS ++ AK++
Sbjct: 276 KPLSSLTPLILAAKEA 291
>gnl|CDD|132985 cd06654, STKc_PAK1, Catalytic domain of the Protein
Serine/Threonine Kinase, p21-activated kinase 1.
Serine/threonine kinases (STKs), p21-activated kinase
(PAK) 1, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The PAK
subfamily is part of a larger superfamily that includes
the catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. PAKs are Rho family GTPase-regulated kinases
that serve as important mediators in the function of
Cdc42 (cell division cycle 42) and Rac. PAKs from higher
eukaryotes are classified into two groups (I and II),
according to their biochemical and structural features.
PAK1 belongs to group I. Group I PAKs contain a PBD
(p21-binding domain) overlapping with an AID
(autoinhibitory domain), a C-terminal catalytic domain,
SH3 binding sites and a non-classical SH3 binding site
for PIX (PAK-interacting exchange factor). PAK1 is
important in the regulation of many cellular processes
including cytoskeletal dynamics, cell motility, growth,
and proliferation. Although PAK1 has been regarded
mainly as a cytosolic protein, recent reports indicate
that PAK1 also exists in significant amounts in the
nucleus, where it is involved in transcription
modulation and in cell cycle regulatory events. PAK1 is
also involved in transformation and tumorigenesis. Its
overexpression, hyperactivation and increased nuclear
accumulation is correlated to breast cancer invasiveness
and progression. Nuclear accumulation is also linked to
tamoxifen resistance in breast cancer cells.
Length = 296
Score = 30.1 bits (67), Expect = 0.54
Identities = 33/136 (24%), Positives = 52/136 (38%), Gaps = 19/136 (13%)
Query: 35 LREFKFAPNQTPELEQRVMELHKTHKLPCSYVTYALLGSYLVQSELGDYDQEEHKGNPDY 94
L +F F TPE +R + + + VT G + LG E +G P Y
Sbjct: 157 LTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPY 216
Query: 95 LRE------FKFAPNQTPELE-------------QRVMELHKTHKGQTPAEAELNYLDNA 135
L E + A N TPEL+ R +++ +G + +L A
Sbjct: 217 LNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQHQFLKIA 276
Query: 136 KKLSMYGVVLHPAKDS 151
K LS ++ AK++
Sbjct: 277 KPLSSLTPLIAAAKEA 292
>gnl|CDD|197309 cd09075, DNase1-like, Deoxyribonuclease 1 and related proteins.
This family includes Deoxyribonuclease 1 (DNase1, EC
3.1.21.1) and related proteins. DNase1, also known as
DNase I, is a Ca2+, Mg2+/Mn2+-dependent secretory
endonuclease, first isolated from bovine pancreas
extracts. It cleaves DNA preferentially at
phosphodiester linkages next to a pyrimidine nucleotide,
producing 5'-phosphate terminated polynucleotides with a
free hydroxyl group on position 3'. It generally
produces tetranucleotides. DNase1 substrates include
single-stranded DNA, double-stranded DNA, and chromatin.
This enzyme may be responsible for apoptotic DNA
fragmentation. Other deoxyribonucleases in this
subfamily include human DNL1L (human DNase I
lysosomal-like, also known as DNASE1L1, Xib and DNase X
), human DNASE1L2 (also known as DNAS1L2), and DNASE1L3
(also known as DNAS1L3, nhDNase, LS-DNase, DNase Y, and
DNase gamma). DNASE1L3 is also implicated in apoptotic
DNA fragmentation. DNase1 is also a cytoskeletal protein
which binds actin. A recombinant form of human DNase1 is
used as a mucoactive therapy in patients with cystic
fibrosis; it hydrolyzes the extracellular DNA in sputum
and reduces its viscosity. Mutations in the gene
encoding DNase1 have been associated with Systemic Lupus
Erythematosus, a multifactorial autoimmune disease. This
family also includes a subfamily of mostly
uncharacterized proteins, which includes Mycoplasma
pulmonis MnuA, a membrane-associated nuclease. The in
vivo role of MnuA is as yet undetermined. This family
belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 258
Score = 29.3 bits (65), Expect = 0.92
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 11/72 (15%)
Query: 84 DQEEHKGNPDYLRE---FKFAPNQTPELEQRVMELHKTHKGQTPAEAELNYLDNAKKLSM 140
D + GN + RE KF+ + T E ++ L H + A AE+N L +
Sbjct: 98 DGCKSCGNDSFSREPAVVKFSSHSTKVKEFAIVAL---HSAPSDAVAEINSLY-----DV 149
Query: 141 YGVVLHPAKDSE 152
Y V ++
Sbjct: 150 YLDVQQKWHLND 161
>gnl|CDD|148950 pfam07614, DUF1577, Protein of unknown function (DUF1577). A
family of hypothetical proteins in Leptospira
interrogans.
Length = 256
Score = 28.6 bits (64), Expect = 1.4
Identities = 18/90 (20%), Positives = 32/90 (35%), Gaps = 12/90 (13%)
Query: 15 LVQSELGDYDQEEHKGNPDYLREFKFAPNQTPELE-----QRVMELHKTHKLPCSYVTYA 69
LV+ DY ++ + PD F + + E ++ + + T SY
Sbjct: 127 LVKVNFNDYKRKLKQKYPDLRLVDIFGSDLDKKFELVKKTKKPLYIENTSD-EESYKGNN 185
Query: 70 LLGSYLVQSELGDYDQEEHKGNPDYLREFK 99
+ ELG+ D +RE+K
Sbjct: 186 SENRIDYEKELGEDDL------DSRIREYK 209
>gnl|CDD|241353 cd13199, FERM_C2_MyoVII, Myosin VII (MyoVII, Myo7) FERM domain
C-lobe, repeat 2. MyoVII, a MyTH-FERM myosin, is an
actin-based motor protein essential for a variety of
biological processes in the actin cytoskeleton function.
Mutations in MyoVII leads to problems in sensory
perception: deafness and blindness in humans (Usher
Syndrome), retinal defects and deafness in mice (shaker
1), and aberrant auditory and vestibular function in
zebrafish. Myosin VIIAs have plus (barbed) end-directed
motor activity on actin filaments and a characteristic
actin-activated ATPase activity. MyoVII consists of a
conserved spectrin-like, SH3 subdomain N-terminal
region, a motor/head region, a neck made of 4-5 IQ
motifs, and a tail consisting of a coiled-coil domain,
followed by a tandem repeat of myosin tail homology 4
(MyTH4) domains and partial FERM domains that are
separated by an SH3 subdomain and are thought to mediate
dimerization and binding to other proteins or cargo.
Members include: MyoVIIa, MyoVIIb, and MyoVII members
that do not have distinct myosin VIIA and myosin VIIB
genes. 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 = 176
Score = 27.2 bits (61), Expect = 3.5
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 5/78 (6%)
Query: 69 ALLGSYLVQSELGDYDQEEHKGNPDYLREF---KFAPNQTP-ELEQRVMELHKTHKGQTP 124
L + + + GD D+ + + P L+E Q+P E ++ ++ + H G +
Sbjct: 5 IQLAALIYRVRFGD-DKSQFQSIPKMLKELIPADLIKLQSPDEWKKLIIAAYNKHAGMSS 63
Query: 125 AEAELNYLDNAKKLSMYG 142
EA+L +L + +G
Sbjct: 64 EEAKLAFLKIIYRWPTFG 81
>gnl|CDD|212571 cd11698, DHR2_DOCK9, Dock Homology Region 2, a GEF domain, of Class
D Dedicator of Cytokinesis 9. Dock9, also called
Zizimin1, 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. It plays
important roles in spine formation and dendritic growth.
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 Dock9, which
contains the catalytic GEF activity for Cdc42. Class D
DOCKs also contain a Pleckstrin homology (PH) domain at
the N-terminus.
Length = 415
Score = 26.9 bits (59), Expect = 6.4
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 70 LLGSYLVQSELGDYDQEEHKGNPDYLREFKFAPNQTPELEQRVMELHKTHKGQ 122
LLG+Y + G E+ G +E K P E+ QR+++L+ G
Sbjct: 144 LLGTYFRVAFFGQGFFEDEDGKEYIYKEPKLTP--LSEISQRLLKLYSDKFGS 194
>gnl|CDD|185076 PRK15121, PRK15121, right oriC-binding transcriptional activator;
Provisional.
Length = 289
Score = 26.5 bits (59), Expect = 6.9
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 3/59 (5%)
Query: 42 PNQTPELEQRVMELHKTHKLPCSYVTYALLGSYLVQSELGDYDQEEHKGNPDYLREFKF 100
P+Q + EQ V T L + + V + G+Y ++G L+EF
Sbjct: 186 PSQEKDDEQEVF---YTTALEPDQADGYVQTGHPVMLQGGEYVMFTYEGLGTGLQEFIL 241
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
0.314 0.134 0.394
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,669,312
Number of extensions: 783718
Number of successful extensions: 521
Number of sequences better than 10.0: 1
Number of HSP's gapped: 516
Number of HSP's successfully gapped: 35
Length of query: 170
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 80
Effective length of database: 6,945,742
Effective search space: 555659360
Effective search space used: 555659360
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: 42 (21.9 bits)
S2: 55 (24.9 bits)