RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10562
(135 letters)
>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 = 231 bits (592), Expect = 3e-80
Identities = 88/122 (72%), Positives = 103/122 (84%)
Query: 13 ETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKINTFSWAKIRKISFKRKRF 72
+ ARRCELYG++LHPAKD + + LNL+VAHMGILVFQ TKINTFSWAKIRK+SFKRKRF
Sbjct: 1 DIARRCELYGIRLHPAKDREGVDLNLAVAHMGILVFQGFTKINTFSWAKIRKLSFKRKRF 60
Query: 73 LIKLHPEGYGYYKDIVEFLFDNRNDCKNFWKKCVENHGFFRCSAVKNTPRQRTRVLSRGS 132
LIKLHPE YGYYKD VEF F++RN+CK+FWKKC+E+H FFR S V P + R+ SRGS
Sbjct: 61 LIKLHPEAYGYYKDTVEFSFESRNECKSFWKKCIEHHAFFRLSEVPKPPSPKPRLFSRGS 120
Query: 133 SF 134
SF
Sbjct: 121 SF 122
>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 = 146 bits (370), Expect = 1e-46
Identities = 62/113 (54%), Positives = 74/113 (65%)
Query: 1 GQSPAAADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKINTFSWA 60
GQSPA A+ N L TAR ELYGV+LH A+D N+ L + V GILVFQN +INTF W+
Sbjct: 1 GQSPAEAEFNFLNTARTLELYGVELHSARDASNLELQVGVTSGGILVFQNGIRINTFPWS 60
Query: 61 KIRKISFKRKRFLIKLHPEGYGYYKDIVEFLFDNRNDCKNFWKKCVENHGFFR 113
KI KISFKRK+F I+L E I+ F + CKN WK CVE+H FFR
Sbjct: 61 KIVKISFKRKQFFIQLRREPSESRDTILGFNMLSYRACKNLWKSCVEHHTFFR 113
>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 = 127 bits (321), Expect = 3e-39
Identities = 53/113 (46%), Positives = 72/113 (63%)
Query: 1 GQSPAAADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKINTFSWA 60
GQ+PA A+L+ LE A++ LYGV LHPAKD + + + L V GILV++++ +IN F+W
Sbjct: 1 GQTPAEAELHFLENAKKLALYGVDLHPAKDSEGVDIMLGVCAGGILVYRDRLRINRFAWP 60
Query: 61 KIRKISFKRKRFLIKLHPEGYGYYKDIVEFLFDNRNDCKNFWKKCVENHGFFR 113
KI KIS+KR F IKL P + + + F N K WK CVE+H FFR
Sbjct: 61 KILKISYKRNNFYIKLRPGEFEQSETTIGFKLPNHRAAKRLWKVCVEHHTFFR 113
>gnl|CDD|220216 pfam09380, FERM_C, FERM C-terminal PH-like domain.
Length = 90
Score = 112 bits (282), Expect = 2e-33
Identities = 41/85 (48%), Positives = 51/85 (60%), Gaps = 1/85 (1%)
Query: 30 DHDNILLNLSVAHMGILVFQNQTKINTFSWAKIRKISFKRKRFLIKLHPEGYGYYKDIVE 89
D L L V+ GILV+++ KINTF W++IRKISFKRK+FLIKL E + +
Sbjct: 1 DKKGTDLWLGVSAKGILVYEDNNKINTFPWSEIRKISFKRKKFLIKLRDE-DESKETTLT 59
Query: 90 FLFDNRNDCKNFWKKCVENHGFFRC 114
F + CK WK CVE H FFR
Sbjct: 60 FYTPSPRACKYLWKLCVEQHAFFRL 84
>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 = 106 bits (266), Expect = 7e-31
Identities = 45/111 (40%), Positives = 62/111 (55%)
Query: 3 SPAAADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKINTFSWAKI 62
+PA A+LN L A+ E+YGV LHP K D L + GILV++N+TKI F W KI
Sbjct: 1 TPAEAELNYLNKAKWLEMYGVDLHPVKGEDGNEYFLGLTPTGILVYENKTKIGLFFWPKI 60
Query: 63 RKISFKRKRFLIKLHPEGYGYYKDIVEFLFDNRNDCKNFWKKCVENHGFFR 113
K+ FK K+ + + + + F N+ CK+ WK VE+H FFR
Sbjct: 61 TKLDFKGKKLKLVVVEKDEQEQEHTFVFRLPNKKACKHLWKCAVEHHAFFR 111
>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 = 81.7 bits (202), Expect = 2e-21
Identities = 37/107 (34%), Positives = 53/107 (49%), Gaps = 2/107 (1%)
Query: 7 ADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKINTFSWAKIRKIS 66
A+LN L A E YGV HP KDH L L H G++VFQ +++ F W I K +
Sbjct: 1 AELNFLRKAHTLETYGVDPHPVKDHYGTQLYLGFTHTGVVVFQGGKRVHHFKWDDISKFN 60
Query: 67 FKRKRFLIKLHPEGYGYYKDIVEFLFDNRNDCKNFWKKCVENHGFFR 113
++ K F++ + K + F CK+ WK VEN F++
Sbjct: 61 YEGKTFILHVMQNEEK--KHTLGFKCPTPAACKHLWKCAVENQAFYK 105
>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 = 71.3 bits (175), Expect = 2e-17
Identities = 31/95 (32%), Positives = 46/95 (48%), Gaps = 7/95 (7%)
Query: 22 GVKLHPAKDHD-NILLNLSVAHMGILVFQNQT--KINTFSWAKIRKISFKRKRFLIKLHP 78
GV+ KD L L V+ GI V + T + F W +IRKISF +K F I++
Sbjct: 1 GVEFFDVKDKSGGSELILGVSLEGISVLDDNTGNPLTLFRWPEIRKISFSKKTFTIEIRG 60
Query: 79 EGYGYYKDIVEFLFDNRNDCKNFWKKCVENHGFFR 113
+ ++ + F + + K WK CV H F+R
Sbjct: 61 DK----EEKLAFQTSSPREAKYIWKLCVGYHRFYR 91
>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 = 57.6 bits (140), Expect = 1e-11
Identities = 28/138 (20%), Positives = 51/138 (36%), Gaps = 13/138 (9%)
Query: 1 GQSPAAADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILVF-QNQTKINTFSW 59
G SP+ A+ L+ E YGV+ + + L + V GI + + I +
Sbjct: 1 GMSPSTAEYLFLKEVSELENYGVETFHVRTIEGQKLVIGVGPDGIRICNDDGELIQRIPY 60
Query: 60 AKIRKISFKRKRFLIKLHPEGYGYYKD-----IVEFLFDNRNDCKNFWKKCVENHGFFRC 114
I+ + K F + Y D +EF + ++ E H F+RC
Sbjct: 61 TAIQMATSSGKVFTLT-------YLSDDGDVTKLEFKLPSTRAASALYRAITEKHAFYRC 113
Query: 115 SAVKNTPRQRTRVLSRGS 132
V++ + +G+
Sbjct: 114 ETVRSAVTDQFSRDLKGT 131
>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 = 53.8 bits (130), Expect = 2e-10
Identities = 31/114 (27%), Positives = 54/114 (47%), Gaps = 6/114 (5%)
Query: 1 GQSPAAADLNLLETARRCELYGVKLHPAKDHDNILLNLSVAHMGILV-FQNQTKINTFSW 59
G SPA A+L ++ + + YG + +PAKD+ + + + GI V +N F W
Sbjct: 1 GLSPAEAELLYIQEVEQLDGYGEESYPAKDNQGNDIFIGASFEGIFVKHKNGRPPVVFKW 60
Query: 60 AKIRKISFKRKRFLIKLHPEGYGYYKDIVEFLFDNRNDCKNFWKKCVENHGFFR 113
I IS + F ++L + + ++F ++ K W+ CV H F+R
Sbjct: 61 NDIGNISHNKSFFSVELINKE-----ETIQFQMEDAETAKYVWRMCVARHKFYR 109
>gnl|CDD|241339 cd13185, FERM_C_FRMD1_FRMD6, FERM domain containing 1 and 6
proteins FERM domain C-lobe. FRMD6 (also called willin
and hEx/human expanded) is localized throughout the
cytoplasm or along the plasma membrane The Drosophilla
protein Ex is a regulator of the Hippo/SWH
(Sav/Wts/Hpo) signaling pathway, a signaling pathway
that plays a pivotal role in organ size control and is
tumor suppression by restricting proliferation and
promoting apoptosis. Surprisingly, hEx is thought to
function independently of the Hippo pathway. Instead it
is hypothesized that hEx inhibits progression through
the S phase of the cell cycle by upregulating p21(Cip1)
and downregulating Cyclin A. It is also implicated in
the progression of Alzheimer disease. Not much is known
about FRMD1 to date. Both FRMD1 and FRMD6 contains a
single 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). The 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 = 109
Score = 43.1 bits (102), Expect = 2e-06
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 18 CELYGVKLHPAKDHDNILLNLSVAHMGILVFQN----QTKINTFSWAKIRKISFKRKRFL 73
LY ++ + ++LL + GI ++Q + + TF W+ I K+SF RK+F
Sbjct: 5 AHLYRLRKSKKETTGSVLL--GITAKGIQIYQESDGEKQLLRTFPWSNIGKLSFDRKKFE 62
Query: 74 I 74
I
Sbjct: 63 I 63
>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 = 42.3 bits (100), Expect = 6e-06
Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 7/88 (7%)
Query: 1 GQSPAAADLNLLETARRCELYGVKLH---PAKDHDNILLNLSVAHMGILVF--QNQTKIN 55
G S A+L L+ ++ YGV H K + L + GI+++ N +
Sbjct: 1 GLSEEEAELEFLKVCQKLPEYGVHFHRVYREKKSSTGGIWLGICSRGIIIYEVHNGARTP 60
Query: 56 T--FSWAKIRKISFKRKRFLIKLHPEGY 81
F W + +KISF RK+F+I+
Sbjct: 61 VLRFPWRETKKISFDRKKFIIENRGGSG 88
>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 = 40.7 bits (96), Expect = 1e-05
Identities = 27/95 (28%), Positives = 42/95 (44%), Gaps = 7/95 (7%)
Query: 21 YGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKIN---TFSWAKIRKISFKRKRFLIKLH 77
YGV K+ L L V +G+ +++ + K+ F W++IR ISF K+F+IK
Sbjct: 2 YGVNYFEIKNKKGTDLWLGVDALGLNIYELENKLTPKIGFPWSEIRNISFNDKKFVIKPI 61
Query: 78 PEGYGYYKDIVEFLFDNRNDCKNFWKKCVENHGFF 112
+ D V F K C+ NH +
Sbjct: 62 DKK---APDFV-FYSPRLRINKRILDLCMGNHELY 92
>gnl|CDD|241345 cd13191, FERM_C_FRMD4A_FRMD4B, FERM domain-containing protein 4A
and 4B (FRMD4A and 4B) FERM domain C-lobe. FRMD4A is
part of the Par-3/FRMD4A/cytohesin-1 complex that
activates Arf6, a central player in actin cytoskeleton
dynamics and membrane trafficking, during junctional
remodeling and epithelial polarization. The
Par-3/Par-6/aPKC/Cdc42 complex regulates the conversion
of primordial adherens junctions (AJs) into belt-like
AJs and the formation of linear actin cables. When
primordial AJs are formed, Par-3 recruits scaffolding
protein FRMD4A which connects Par-3 and the Arf6
guanine-nucleotide exchange factor (GEF), cytohesin-1.
FRMD4B (also called GRP1-binding protein, GRSP1) is a
novel member of GRP1 signaling complexes that are
recruited to plasma membrane ruffles in response to
insulin receptor signaling. The GRSP1/FRMD4B protein
contains a FERM protein domain as well as two coiled
coil domains and may function as a scaffolding protein.
GRP1 and GRSP1 interact through the coiled coil domains
in the two proteins. 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 = 115
Score = 33.9 bits (78), Expect = 0.007
Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 21 YGVKLHPAKDHDNILLNLSVAHMGILVFQNQTKIN---TFSWAKIRKISFKRKRFLIKLH 77
YGV + KD + I L +++ GI + Q K+ F W ++ + F+ ++F I++H
Sbjct: 3 YGVHYYEVKDKNGIPWWLGLSYKGIGQYDLQDKVKPRKLFQWKQLENLYFRDRKFSIEVH 62
>gnl|CDD|215882 pfam00373, FERM_M, FERM central domain. This domain is the central
structural domain of the FERM domain.
Length = 113
Score = 32.6 bits (75), Expect = 0.020
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 1 GQSPAAADLNLLETARRCELYGVKLH 26
G SPA A L L+ A+ YGV
Sbjct: 88 GLSPAEAKLKYLQIAQSLPTYGVTFF 113
>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 = 32.7 bits (75), Expect = 0.031
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 1 GQSPAAADLNLLETARRCELYGVKLH 26
G SP A L LE AR+ YGV+L
Sbjct: 176 GLSPEEAKLKYLELARKLPTYGVELF 201
>gnl|CDD|184966 PRK15004, PRK15004, alpha-ribazole phosphatase; Provisional.
Length = 199
Score = 29.2 bits (66), Expect = 0.49
Identities = 9/32 (28%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 15 ARRCELYGVKLHPAKDHDNILLNLSVAHMGIL 46
++R E + +L + + N+L+ V+H G+L
Sbjct: 125 SQRVERFIARLSAFQHYQNLLI---VSHQGVL 153
>gnl|CDD|223768 COG0696, GpmI, Phosphoglyceromutase [Carbohydrate transport and
metabolism].
Length = 509
Score = 29.2 bits (66), Expect = 0.57
Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 8/55 (14%)
Query: 37 NLSVAHM----GILVFQNQTKINTFSWAKIRKISFKRKRFLIKLHPEGYGYYKDI 87
N V H+ G +V+Q+ T+I+ I SF L+ E +
Sbjct: 61 NSEVGHLNIGAGRIVYQDLTRID----KAIEDGSFFENPALLNAIDEVKANGSAL 111
>gnl|CDD|143527 cd06969, NR_DBD_NGFI-B, DNA-binding domain of the orphan nuclear
receptor, nerve growth factor-induced-B. DNA-binding
domain (DBD) of the orphan nuclear receptor, nerve
growth factor-induced-B (NGFI-B) is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which co-ordinates a single zinc
atom. NGFI-B interacts with specific DNA sites upstream
of the target gene and modulates the rate of
transcriptional initiation. NGFI-B is a member of the
nuclear-steroid receptor superfamily. NGFI-B is
classified as an orphan receptor because no ligand has
yet been identified. NGFI-B is an early immediate gene
product of embryo development that is rapidly produced
in response to a variety of cellular signals including
nerve growth factor. It is involved in T-cell-mediated
apoptosis, as well as neuronal differentiation and
function. NGFI-B regulates transcription by binding to a
specific DNA target upstream of its target genes and
regulating the rate of transcriptional initiation.
NGFI-B binds to the NGFI-B response element (NBRE)
5'-(A/T)AAAGGTCA as a monomer. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, NGFI-B has a central
well-conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 75
Score = 26.3 bits (58), Expect = 2.1
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 98 CKNFWKKCVENHGFFRCSAVKNTP---RQRTR 126
CK F+K+ V+ + + C A KN P R+R R
Sbjct: 23 CKGFFKRTVQKNAKYVCLANKNCPVDKRRRNR 54
>gnl|CDD|179379 PRK02155, ppnK, NAD(+)/NADH kinase family protein; Provisional.
Length = 291
Score = 26.8 bits (60), Expect = 3.2
Identities = 10/19 (52%), Positives = 10/19 (52%), Gaps = 3/19 (15%)
Query: 66 SFKRKRFLIKLHPEGYGYY 84
S RFL HP GY YY
Sbjct: 262 SPHTVRFL---HPVGYSYY 277
>gnl|CDD|211799 TIGR03247, glucar-dehydr, glucarate dehydratase. Glucarate
dehydratase converts D-glucarate (and L-idarate, a
stereoisomer) to 5-dehydro-4-deoxyglucarate which is
subsequently acted on by GarL, tartronate semialdehyde
reductase and glycerate kinase (, GenProp0716). The E.
coli enzyme has been well-characterized.
Length = 441
Score = 27.1 bits (60), Expect = 3.3
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 23 VKLHPAKDHDNILLNLSVAH 42
+++ P HD++LLNLS AH
Sbjct: 9 MRVIPVAGHDSMLLNLSGAH 28
>gnl|CDD|221631 pfam12543, DUF3738, Protein of unknown function (DUF3738). This
family of proteins is found in bacteria. Proteins in
this family are typically between 251 and 457 amino
acids in length.
Length = 182
Score = 26.5 bits (59), Expect = 3.9
Identities = 10/31 (32%), Positives = 12/31 (38%)
Query: 22 GVKLHPAKDHDNILLNLSVAHMGILVFQNQT 52
G KL +K D A G L +N T
Sbjct: 77 GPKLKESKPDDGGSTAGGPAGNGRLKAKNTT 107
>gnl|CDD|227933 COG5646, COG5646, Uncharacterized conserved protein [Function
unknown].
Length = 126
Score = 25.9 bits (57), Expect = 5.6
Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 8/83 (9%)
Query: 29 KDHDNILLNLSVA--HMGILVFQNQTKINTFSWAKIRKISFKRKRFLIKLHPEG---YGY 83
+ N L++ SVA H+G V+ I+ F+ ++++ + + I+ + Y
Sbjct: 46 TNQGNFLIHFSVAKKHLG--VYPEVAGIDAFA-DELKEAGYDYTKGTIRFPWKAPVDYDL 102
Query: 84 YKDIVEFLFDNRNDCKNFWKKCV 106
K ++EF + FW+K V
Sbjct: 103 LKKMIEFNLADNAGYSAFWRKLV 125
>gnl|CDD|99827 cd05784, DNA_polB_II_exo, DEDDy 3'-5' exonuclease domain of
Escherichia coli DNA polymerase II and similar bacterial
family-B DNA polymerases. The 3'-5' exonuclease domain
of Escherichia coli DNA polymerase II (Pol II) and
similar bacterial proteins. Pol II is a family-B DNA
polymerase. Family-B DNA polymerases contain an
N-terminal DEDDy DnaQ-like exonuclease domain in the
same polypeptide chain as the polymerase domain, similar
to family-A DNA polymerases. This exonuclease domain
contains three sequence motifs termed ExoI, ExoII and
ExoIII, with a specific YX(3)D pattern at ExoIII. These
motifs are clustered around the active site and are
involved in metal binding and catalysis. The exonuclease
domain has a fundamental role in the proofreading
activity of polII. It contains a beta hairpin structure
that plays an important role in active site switching in
the event of a nucleotide misincorporation. Pol II is
involved in a variety of cellular activities, such as
the repair of DNA damaged by UV irradiation or
oxidation. It plays a pivotal role in
replication-restart, a process that bypasses DNA damage
in an error-free manner. Pol II is also involved in
lagging strand synthesis.
Length = 193
Score = 25.6 bits (57), Expect = 8.5
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 8 DLNLLETARRCELYGVKLHPAKDHDNI 34
DL LL RR E +G+ L + +
Sbjct: 79 DLRLL--QRRAEAHGLPLRLGRGGSPL 103
>gnl|CDD|165216 PHA02889, PHA02889, hypothetical protein; Provisional.
Length = 241
Score = 25.8 bits (56), Expect = 8.8
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 61 KIRKISFKRKRFLIKLHPEGYGYYKDIVEFLFDNRND 97
KI KI LIKLHP+ + DI E D+ ++
Sbjct: 205 KIDKIDDIEDFILIKLHPDKEPLFHDIDEIDVDSDDE 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
0.325 0.139 0.435
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: 6,810,516
Number of extensions: 597433
Number of successful extensions: 675
Number of sequences better than 10.0: 1
Number of HSP's gapped: 665
Number of HSP's successfully gapped: 34
Length of query: 135
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 48
Effective length of database: 7,078,804
Effective search space: 339782592
Effective search space used: 339782592
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)