RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9052
(356 letters)
>gnl|CDD|215882 pfam00373, FERM_M, FERM central domain. This domain is the central
structural domain of the FERM domain.
Length = 113
Score = 104 bits (261), Expect = 1e-27
Identities = 45/116 (38%), Positives = 69/116 (59%), Gaps = 4/116 (3%)
Query: 10 ITDEMTRYHCFLQLKNDIIEGRIQCNLDDAVVLASYCMQAEFGNYNSERHTLEYLKDF-A 68
+ DE+TR +LQLK DI+EGR+ C+ ++A++LA+ +QAEFG+YN E+H+ YLK+
Sbjct: 1 LQDEVTRELLYLQLKRDILEGRLPCSEEEALLLAALALQAEFGDYNPEKHSSSYLKELEY 60
Query: 69 LFPKDLVENGHNGLLERLTDAVIQQHSALVGLSQGTAEEYYILAAQQLDGYGQETF 124
P L++ + L +++ H L GLS A+ Y+ AQ L YG F
Sbjct: 61 FLPSRLIKKEK---SKELEKRILEAHKNLRGLSPAEAKLKYLQIAQSLPTYGVTFF 113
>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 = 102 bits (256), Expect = 7e-27
Identities = 45/109 (41%), Positives = 64/109 (58%), Gaps = 3/109 (2%)
Query: 99 GLSQGTAEEYYILAAQQLDGYGQETFLVKDEHGLETILGVTLKGIIVSGTN--SSKFYKW 156
GLS AE YI +QLDGYG+E++ KD G + +G + +GI V N +KW
Sbjct: 1 GLSPAEAELLYIQEVEQLDGYGEESYPAKDNQGNDIFIGASFEGIFVKHKNGRPPVVFKW 60
Query: 157 AEIANVLNHKKNFGIETSNADDHIVNFVFPDVESAKYVFRMCVHQHTFY 205
+I N+ ++K F +E N ++ I F D E+AKYV+RMCV +H FY
Sbjct: 61 NDIGNISHNKSFFSVELINKEETIQ-FQMEDAETAKYVWRMCVARHKFY 108
>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 = 92.0 bits (229), Expect = 5e-22
Identities = 41/125 (32%), Positives = 72/125 (57%), Gaps = 5/125 (4%)
Query: 2 YYVSGISLITDEMTRY-HCFLQLKNDIIEGRIQCNLDDAVVLASYCMQAEFGNYNSERH- 59
+Y + + ++ TR +LQ++NDI+EGR+ C ++A++LA+ +QAEFG+Y+ E H
Sbjct: 80 FYPPDPNQLKEDPTRLNLLYLQVRNDILEGRLPCPEEEALLLAALALQAEFGDYDEELHD 139
Query: 60 TLEYLKDFALFPKDLVENGHNGLLERLTDAVIQQHSALVGLSQGTAEEYYILAAQQLDGY 119
L PK L+++ L+ + +++ H L+GLS A+ Y+ A++L Y
Sbjct: 140 LRGELSLKRFLPKQLLDSRK---LKEWRERIVELHKELIGLSPEEAKLKYLELARKLPTY 196
Query: 120 GQETF 124
G E F
Sbjct: 197 GVELF 201
>gnl|CDD|220216 pfam09380, FERM_C, FERM C-terminal PH-like domain.
Length = 90
Score = 79.6 bits (197), Expect = 1e-18
Identities = 26/86 (30%), Positives = 44/86 (51%), Gaps = 4/86 (4%)
Query: 128 DEHGLETILGVTLKGIIV-SGTNSSKFYKWAEIANVLNHKKNFGIETSNAD---DHIVNF 183
D+ G + LGV+ KGI+V N + W+EI + +K F I+ + D + + F
Sbjct: 1 DKKGTDLWLGVSAKGILVYEDNNKINTFPWSEIRKISFKRKKFLIKLRDEDESKETTLTF 60
Query: 184 VFPDVESAKYVFRMCVHQHTFYMTYE 209
P + KY++++CV QH F+
Sbjct: 61 YTPSPRACKYLWKLCVEQHAFFRLRR 86
>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 = 75.9 bits (187), Expect = 2e-17
Identities = 34/91 (37%), Positives = 47/91 (51%), Gaps = 4/91 (4%)
Query: 120 GQETFLVKDE-HGLETILGVTLKGIIVSGTNSSK---FYKWAEIANVLNHKKNFGIETSN 175
G E F VKD+ G E ILGV+L+GI V N+ ++W EI + KK F IE
Sbjct: 1 GVEFFDVKDKSGGSELILGVSLEGISVLDDNTGNPLTLFRWPEIRKISFSKKTFTIEIRG 60
Query: 176 ADDHIVNFVFPDVESAKYVFRMCVHQHTFYM 206
+ + F AKY++++CV H FY
Sbjct: 61 DKEEKLAFQTSSPREAKYIWKLCVGYHRFYR 91
>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 = 70.8 bits (174), Expect = 4e-15
Identities = 35/113 (30%), Positives = 56/113 (49%), Gaps = 7/113 (6%)
Query: 99 GLSQGTAEEYYILAAQQLDGYGQETFLVKDEHGLETILGVTLKGIIV--SGTNSSKFYKW 156
G S AE ++ A+ L+ YG E +D LE +GVT GI+V +G + + W
Sbjct: 1 GQSPAEAEFNFLNTARTLELYGVELHSARDASNLELQVGVTSGGILVFQNGIRIN-TFPW 59
Query: 157 AEIANVLNHKKNFGI----ETSNADDHIVNFVFPDVESAKYVFRMCVHQHTFY 205
++I + +K F I E S + D I+ F + K +++ CV HTF+
Sbjct: 60 SKIVKISFKRKQFFIQLRREPSESRDTILGFNMLSYRACKNLWKSCVEHHTFF 112
>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 = 61.1 bits (149), Expect = 1e-11
Identities = 28/111 (25%), Positives = 50/111 (45%), Gaps = 4/111 (3%)
Query: 99 GLSQGTAEEYYILAAQQLDGYGQETFLVKDEHGLETILGVTLKGIIVSGTNSS--KFYKW 156
G+S TAE ++ +L+ YG ETF V+ G + ++GV GI + + + +
Sbjct: 1 GMSPSTAEYLFLKEVSELENYGVETFHVRTIEGQKLVIGVGPDGIRICNDDGELIQRIPY 60
Query: 157 AEIANVLNHKKNFGIETSNADDHI--VNFVFPDVESAKYVFRMCVHQHTFY 205
I + K F + + D + + F P +A ++R +H FY
Sbjct: 61 TAIQMATSSGKVFTLTYLSDDGDVTKLEFKLPSTRAASALYRAITEKHAFY 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 = 57.8 bits (140), Expect = 1e-10
Identities = 28/104 (26%), Positives = 48/104 (46%), Gaps = 3/104 (2%)
Query: 105 AEEYYILAAQQLDGYGQETFLVKDEHGLETILGVTLKGIIV-SGTNSSKFYKWAEIANVL 163
AE ++ A L+ YG + VKD +G + LG T G++V G +KW +I+
Sbjct: 1 AELNFLRKAHTLETYGVDPHPVKDHYGTQLYLGFTHTGVVVFQGGKRVHHFKWDDISKFN 60
Query: 164 NHKKNFGIETSNADD--HIVNFVFPDVESAKYVFRMCVHQHTFY 205
K F + ++ H + F P + K++++ V FY
Sbjct: 61 YEGKTFILHVMQNEEKKHTLGFKCPTPAACKHLWKCAVENQAFY 104
>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 = 56.1 bits (136), Expect = 4e-10
Identities = 31/108 (28%), Positives = 51/108 (47%), Gaps = 7/108 (6%)
Query: 104 TAEEYYILAAQQLDGYGQETFLVKDEHGLETILGVTLKGIIVSGTNSSK--FYKWAEIAN 161
AE Y+ A+ L+ YG + VK E G E LG+T GI+V N +K + W +I
Sbjct: 4 EAELNYLNKAKWLEMYGVDLHPVKGEDGNEYFLGLTPTGILVY-ENKTKIGLFFWPKITK 62
Query: 162 VLNHKKNFGIETSNADD----HIVNFVFPDVESAKYVFRMCVHQHTFY 205
+ K + D+ H F P+ ++ K++++ V H F+
Sbjct: 63 LDFKGKKLKLVVVEKDEQEQEHTFVFRLPNKKACKHLWKCAVEHHAFF 110
>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 = 54.6 bits (132), Expect = 2e-09
Identities = 31/118 (26%), Positives = 49/118 (41%), Gaps = 10/118 (8%)
Query: 99 GLSQGTAEEYYILAAQQLDGYG---QETFLVKDEHGLETILGVTLKGIIV------SGTN 149
GLS+ AE ++ Q+L YG + K LG+ +GII+ + T
Sbjct: 1 GLSEEEAELEFLKVCQKLPEYGVHFHRVYREKKSSTGGIWLGICSRGIIIYEVHNGARTP 60
Query: 150 SSKFYKWAEIANVLNHKKNFGIETSNADDHIVNFVFPDVESAKYVFRMCVHQHTFYMT 207
+F W E + +K F IE F + ++Y+ R+C QH F+M
Sbjct: 61 VLRF-PWRETKKISFDRKKFIIENRGGSGIKHTFYTDSYKKSQYLLRLCSSQHKFHMK 117
>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 = 49.9 bits (120), Expect = 5e-08
Identities = 23/92 (25%), Positives = 40/92 (43%), Gaps = 4/92 (4%)
Query: 119 YGQETFLVKDEHGLETILGVTLKGIIVSGTNS----SKFYKWAEIANVLNHKKNFGIETS 174
YG F +K++ G + LGV G+ + + + W+EI N+ + K F I+
Sbjct: 2 YGVNYFEIKNKKGTDLWLGVDALGLNIYELENKLTPKIGFPWSEIRNISFNDKKFVIKPI 61
Query: 175 NADDHIVNFVFPDVESAKYVFRMCVHQHTFYM 206
+ F P + K + +C+ H YM
Sbjct: 62 DKKAPDFVFYSPRLRINKRILDLCMGNHELYM 93
>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 = 49.2 bits (118), Expect = 1e-07
Identities = 31/113 (27%), Positives = 57/113 (50%), Gaps = 7/113 (6%)
Query: 99 GLSQGTAEEYYILAAQQLDGYGQETFLVKDEHGLETILGVTLKGIIV--SGTNSSKFYKW 156
G + AE +++ A++L YG + KD G++ +LGV GI+V ++F W
Sbjct: 1 GQTPAEAELHFLENAKKLALYGVDLHPAKDSEGVDIMLGVCAGGILVYRDRLRINRFA-W 59
Query: 157 AEIANVLNHKKNFGIE----TSNADDHIVNFVFPDVESAKYVFRMCVHQHTFY 205
+I + + NF I+ + + F P+ +AK ++++CV HTF+
Sbjct: 60 PKILKISYKRNNFYIKLRPGEFEQSETTIGFKLPNHRAAKRLWKVCVEHHTFF 112
>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 = 37.3 bits (87), Expect = 0.002
Identities = 26/105 (24%), Positives = 44/105 (41%), Gaps = 17/105 (16%)
Query: 119 YGQETFLVKDEHGLETILGVTLKGIIVSGTNS----SKFYKWAEIANVLNHKKNFGIETS 174
YG + VKD++G+ LG++ KGI K ++W ++ N+ + F IE
Sbjct: 3 YGVHYYEVKDKNGIPWWLGLSYKGIGQYDLQDKVKPRKLFQWKQLENLYFRDRKFSIEVH 62
Query: 175 NADDHIV---NFVFPDV-------ESA---KYVFRMCVHQHTFYM 206
+ V F V + K ++ M + QH FY+
Sbjct: 63 DPRRISVSRRTFGQSGVAVHVWYGNTPSLIKSIWSMAISQHQFYL 107
>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 = 35.4 bits (82), Expect = 0.010
Identities = 27/100 (27%), Positives = 41/100 (41%), Gaps = 7/100 (7%)
Query: 112 AAQQLDGYGQETFLVKDEHGLETILGVTLKGIIV--SGTNSSKFYKWAEIANVLNHKKNF 169
A++ + YG KD G++ L V GI+V T + F WA+I + +K F
Sbjct: 2 IARRCELYGIRLHPAKDREGVDLNLAVAHMGILVFQGFTKINTF-SWAKIRKLSFKRKRF 60
Query: 170 GI----ETSNADDHIVNFVFPDVESAKYVFRMCVHQHTFY 205
I E V F F K ++ C+ H F+
Sbjct: 61 LIKLHPEAYGYYKDTVEFSFESRNECKSFWKKCIEHHAFF 100
>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 = 34.6 bits (80), Expect = 0.017
Identities = 21/88 (23%), Positives = 32/88 (36%), Gaps = 8/88 (9%)
Query: 127 KDEHGLETILGVTLKGI----IVSGTNSSKF-YKWAEIANVLNHKKNFGIETSNADDH-- 179
K E +LG+T KGI G + W+ I + +K F I
Sbjct: 14 KKETTGSVLLGITAKGIQIYQESDGEKQLLRTFPWSNIGKLSFDRKKFEIRPEGLPSLRK 73
Query: 180 IVNFVFPDVESAKYVFRMCVHQHTFYMT 207
+ + E +KY+ +C H F M
Sbjct: 74 LT-YYTGSDEKSKYLLALCRETHQFSMA 100
>gnl|CDD|215507 PLN02939, PLN02939, transferase, transferring glycosyl groups.
Length = 977
Score = 34.1 bits (78), Expect = 0.11
Identities = 27/111 (24%), Positives = 55/111 (49%), Gaps = 11/111 (9%)
Query: 234 QNIDTALLSSREELDEVTSPSMRNVMSNSREELGDLNERTTSNLD---LVDGNHQD---- 286
+ +++ + ++E++ ++ SP + E L DL +R T+ ++ LV +QD
Sbjct: 274 RELESKFIVAQEDVSKL-SPLQYDCWWEKVENLQDLLDRATNQVEKAALVLDQNQDLRDK 332
Query: 287 IDKLRSLLPS---YRPAPDYETAIQQKYNASEQQMYSSQPEIHSFPDVTQH 334
+DKL + L + + +QQK E+++ +S EIHS+ + Q
Sbjct: 333 VDKLEASLKEANVSKFSSYKVELLQQKLKLLEERLQASDHEIHSYIQLYQE 383
>gnl|CDD|233200 TIGR00940, 2a6301s01, Tmonovalent cation:proton antiporter. This
family of proteins constists of bacterial multicomponent
K+:H+ and Na+:H+ antiporters. The best characterized
systems are the PhaABCDEFG system of Rhizobium meliloti
which functions in pH adaptation and as a K+ efflux
system and the MnhABCDEFG system of Staphylococcus
aureus which functions as a Na+:H+ antiporter [Transport
and binding proteins, Cations and iron carrying
compounds].
Length = 793
Score = 32.9 bits (75), Expect = 0.29
Identities = 8/53 (15%), Positives = 18/53 (33%), Gaps = 3/53 (5%)
Query: 96 ALVGLSQGTAEEYYILAAQQL-DGYGQETFLVKDEHGLETILGVTLKGIIVSG 147
+ ++Y L G ++ D G++T+ ++ GI
Sbjct: 728 GNRHF--ESISKFYQEHVYDLAHGKNMVNVILVDFRGMDTLFESSVLGIAGLA 778
>gnl|CDD|222675 pfam14317, YcxB, YcxB-like protein. The YcxB-like protein family
includes the B. subtilis YcxB protein, which is a
functionally uncharacterized transmembrane protein. This
family of proteins is found in bacteria, and is
approximately 60 amino acids in length.
Length = 62
Score = 27.6 bits (62), Expect = 2.0
Identities = 11/41 (26%), Positives = 17/41 (41%)
Query: 141 KGIIVSGTNSSKFYKWAEIANVLNHKKNFGIETSNADDHIV 181
GI+V S KW++I V+ K + S I+
Sbjct: 4 DGIVVESGEGSSEIKWSDIKKVVETKDYILLYLSKNQAIII 44
>gnl|CDD|222856 PHA02530, pseT, polynucleotide kinase; Provisional.
Length = 300
Score = 29.6 bits (67), Expect = 2.5
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 141 KGIIVSGTNSSKFY--KWAEIANVLNHK 166
K +I+S TN + KW E+A L +
Sbjct: 76 KSVIISDTNLNPERRRKWKELAKELGAE 103
>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 = 29.1 bits (66), Expect = 2.6
Identities = 33/140 (23%), Positives = 64/140 (45%), Gaps = 27/140 (19%)
Query: 37 DDAVVLASYCMQAEFGNYNSERHTL-EYLKDFALFPKDLVENGHNGLLERLTDAVIQQHS 95
+DA+ LA+ + FG+ S+ ++ + LK+ L P DL++ ++ +I ++
Sbjct: 2 EDAIQLAALIYRVRFGDDKSQFQSIPKMLKE--LIPADLIKLQSPDEWKK---LIIAAYN 56
Query: 96 ALVGLSQGTAEEYYILAAQQLDGYGQETFLVK---DEHGLETIL------GVTL-----K 141
G+S A+ ++ + +G F VK D + E +L GV+L K
Sbjct: 57 KHAGMSSEEAKLAFLKIIYRWPTFGSAFFEVKQTTDPNLPEILLIAINKNGVSLIDPKTK 116
Query: 142 GIIVSGTNSSKFYKWAEIAN 161
I+V+ Y + +I+N
Sbjct: 117 EILVT-------YPFTKISN 129
>gnl|CDD|151621 pfam11179, DUF2967, Protein of unknown function (DUF2967). This
family of proteins with unknown function appears to be
restricted to Drosophila.
Length = 284
Score = 29.2 bits (64), Expect = 3.6
Identities = 29/117 (24%), Positives = 44/117 (37%), Gaps = 18/117 (15%)
Query: 209 EATEEDNEGEVQN--------PRSSGGGNGRLFQNIDTALLSSREELDEVTSPSMRNVMS 260
EA + E + N R GN N + SSR + SPS N S
Sbjct: 85 EAADAQEEDAIANRNKKLRARERDPMAGNANANANANGGSNSSRNHISPSVSPSHSNRAS 144
Query: 261 NSREELGDLNERTTSNLDLVDGNHQDIDKLRSLLPSYRPAPDYETAIQQKYNASEQQ 317
RE+ +RTT + I K+ S P+ + A + ++ +QK S+
Sbjct: 145 PKREK-----KRTTPIA-----STGAIAKINSAPPTMKDANFFGSSGKQKQRPSQNI 191
>gnl|CDD|215223 PLN02398, PLN02398, hydroxyacylglutathione hydrolase.
Length = 329
Score = 29.0 bits (65), Expect = 3.7
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 316 QQMYSSQPEIHSFPDVTQHY-GHRNVL 341
+QM SS +I S PD T Y GH L
Sbjct: 222 EQMLSSLQKIISLPDDTNIYCGHEYTL 248
>gnl|CDD|130163 TIGR01091, upp, uracil phosphoribosyltransferase. A fairly deep
split in phylogenetic and UPGMA trees separates this
mostly prokaryotic set of uracil
phosphoribosyltransferases from a mostly eukaryotic set
that includes uracil phosphoribosyltransferase, uridine
kinases, and other, uncharacterized proteins [Purines,
pyrimidines, nucleosides, and nucleotides, Salvage of
nucleosides and nucleotides].
Length = 207
Score = 28.7 bits (65), Expect = 3.9
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 195 FRMCVHQHTFYMTYEATE--EDNEGEVQNP 222
FR + + + YEAT E E EV+ P
Sbjct: 27 FRELLRELGRLLAYEATRDLELEEVEVETP 56
>gnl|CDD|233937 TIGR02580, cas_RAMP_Cmr4, CRISPR type III-B/RAMP module RAMP
protein Cmr4. This model represents a CRISPR-associated
protein from the family that includes TM1792 of
Thermotoga maritima. This family is part of the broad
RAMP superfamily (pfam03787) collection of
CRISPR-associated proteins. It is the fourth of a
recurring set of six proteins, four of are in the RAMP
superfamily, that we designate the CRISPR RAMP module
[Mobile and extrachromosomal element functions, Other].
Length = 280
Score = 29.0 bits (65), Expect = 4.1
Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 5/64 (7%)
Query: 125 LVKDEH-GLETILGVTLKGIIVSGTNSSKFYKWAEIANVLNHKKNFGIETSNADDHIVNF 183
+ ++ H G I G +LKG + S + + + + FG A++
Sbjct: 27 IQRERHTGYPIIYGSSLKGALRSYFIR----QISRDKDESKVECVFGNPKEEAEESAGKV 82
Query: 184 VFPD 187
VF D
Sbjct: 83 VFSD 86
>gnl|CDD|217761 pfam03850, Tfb4, Transcription factor Tfb4. This family appears to
be distantly related to the VWA domain.
Length = 270
Score = 28.8 bits (65), Expect = 4.3
Identities = 10/56 (17%), Positives = 17/56 (30%)
Query: 199 VHQHTFYMTYEATEEDNEGEVQNPRSSGGGNGRLFQNIDTALLSSREELDEVTSPS 254
H Y + + G R F+N++ +L +L TS
Sbjct: 52 SHSQGAKYLYPSPLSASNDGDVEMSGVGDNKYRQFRNVEETVLEELRKLLSSTSKD 107
>gnl|CDD|217090 pfam02536, mTERF, mTERF. This family contains one sequence of
known function Human mitochondrial transcription
termination factor (mTERF) the rest of the family
consists of hypothetical proteins none of which have any
functional information. mTERF is a multizipper protein
possessing three putative leucine zippers one of which
is bipartite. The protein binds DNA as a monomer. The
leucine zippers are not implicated in a dimerisation
role as in other leucine zippers.
Length = 345
Score = 27.8 bits (62), Expect = 8.7
Identities = 12/50 (24%), Positives = 22/50 (44%)
Query: 26 DIIEGRIQCNLDDAVVLASYCMQAEFGNYNSERHTLEYLKDFALFPKDLV 75
D ++ I +LD + L Y GN ++ + L++ + PK L
Sbjct: 74 DFLKKIIVADLDKSSKLEKYPESLPQGNNGNKIRNVSVLRELGVPPKLLF 123
>gnl|CDD|187813 cd09682, Cmr4_III-B, CRISPR/Cas system-associated RAMP superfamily
protein Cmr4. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein; This protein is a subunit of
Cmr complex.
Length = 242
Score = 27.7 bits (62), Expect = 9.4
Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 10/76 (13%)
Query: 118 GYGQETFLV-----KDEH-GLETILGVTLKGIIVSGTNSSKFYKWAEIANVLNHKKNFGI 171
G GQ +V ++ H G I G +LKG + S S++ + + V + FG
Sbjct: 14 GAGQGIGVVDLPIQRERHTGYPIIYGSSLKGALRSYF-SAQIVDDKDESKV---ECVFGG 69
Query: 172 ETSNADDHIVNFVFPD 187
A++ VF D
Sbjct: 70 PKEEAEESAGKVVFSD 85
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 0.133 0.381
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: 18,049,241
Number of extensions: 1727770
Number of successful extensions: 1361
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1341
Number of HSP's successfully gapped: 35
Length of query: 356
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 258
Effective length of database: 6,590,910
Effective search space: 1700454780
Effective search space used: 1700454780
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: 60 (26.9 bits)