RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5417
(265 letters)
>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 = 107 bits (269), Expect = 1e-29
Identities = 36/57 (63%), Positives = 44/57 (77%)
Query: 205 TPSQAELNYLDRVKNLPLYGVDLHPVLGEDSIEYFLGLTPAGIVVLRNKIKVASYLW 261
TP++AELNYL++ K L +YGVDLHPV GED EYFLGLTP GI+V NK K+ + W
Sbjct: 1 TPAEAELNYLNKAKWLEMYGVDLHPVKGEDGNEYFLGLTPTGILVYENKTKIGLFFW 57
Score = 66.5 bits (163), Expect = 4e-14
Identities = 19/41 (46%), Positives = 30/41 (73%), Gaps = 2/41 (4%)
Query: 1 MIRVCDKTDE--ENTYGFETPSRSACKHLYKCCVDHHSFFR 39
+ V +K ++ E+T+ F P++ ACKHL+KC V+HH+FFR
Sbjct: 71 KLVVVEKDEQEQEHTFVFRLPNKKACKHLWKCAVEHHAFFR 111
Score = 50.0 bits (120), Expect = 5e-08
Identities = 15/36 (41%), Positives = 23/36 (63%), Gaps = 5/36 (13%)
Query: 94 TLAVTDE-----ENTYGFETPSRSACKHLYKCCVDH 124
L V ++ E+T+ F P++ ACKHL+KC V+H
Sbjct: 71 KLVVVEKDEQEQEHTFVFRLPNKKACKHLWKCAVEH 106
>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 = 71.9 bits (177), Expect = 4e-16
Identities = 25/59 (42%), Positives = 41/59 (69%)
Query: 203 GQTPSQAELNYLDRVKNLPLYGVDLHPVLGEDSIEYFLGLTPAGIVVLRNKIKVASYLW 261
GQTP++AEL++L+ K L LYGVDLHP + ++ LG+ GI+V R+++++ + W
Sbjct: 1 GQTPAEAELHFLENAKKLALYGVDLHPAKDSEGVDIMLGVCAGGILVYRDRLRINRFAW 59
Score = 48.8 bits (117), Expect = 1e-07
Identities = 18/41 (43%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 1 MIRVCDKTDE--ENTYGFETPSRSACKHLYKCCVDHHSFFR 39
I++ E E T GF+ P+ A K L+K CV+HH+FFR
Sbjct: 73 YIKLRPGEFEQSETTIGFKLPNHRAAKRLWKVCVEHHTFFR 113
Score = 34.9 bits (81), Expect = 0.008
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 101 ENTYGFETPSRSACKHLYKCCVDH 124
E T GF+ P+ A K L+K CV+H
Sbjct: 85 ETTIGFKLPNHRAAKRLWKVCVEH 108
>gnl|CDD|215882 pfam00373, FERM_M, FERM central domain. This domain is the central
structural domain of the FERM domain.
Length = 113
Score = 70.8 bits (174), Expect = 1e-15
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 7/74 (9%)
Query: 162 AELGDYDPRRHSPGYVSEFRFT-------SHQSAALESRVAELHRDLSGQTPSQAELNYL 214
AE GDY+P +HS Y+ E + +S LE R+ E H++L G +P++A+L YL
Sbjct: 40 AEFGDYNPEKHSSSYLKELEYFLPSRLIKKEKSKELEKRILEAHKNLRGLSPAEAKLKYL 99
Query: 215 DRVKNLPLYGVDLH 228
++LP YGV
Sbjct: 100 QIAQSLPTYGVTFF 113
Score = 51.9 bits (125), Expect = 9e-09
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 54 SRFRYQFFLQIKQDILQGRLPVSFELSAELGAYVVQ 89
R +LQ+K+DIL+GRLP S E + L A +Q
Sbjct: 4 EVTRELLYLQLKRDILEGRLPCSEEEALLLAALALQ 39
>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 = 66.5 bits (163), Expect = 5e-14
Identities = 23/59 (38%), Positives = 40/59 (67%)
Query: 203 GQTPSQAELNYLDRVKNLPLYGVDLHPVLGEDSIEYFLGLTPAGIVVLRNKIKVASYLW 261
GQ+P++AE N+L+ + L LYGV+LH ++E +G+T GI+V +N I++ ++ W
Sbjct: 1 GQSPAEAEFNFLNTARTLELYGVELHSARDASNLELQVGVTSGGILVFQNGIRINTFPW 59
Score = 52.7 bits (127), Expect = 5e-09
Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 10 EENTYGFETPSRSACKHLYKCCVDHHSFFRLVQVSSNPPP 49
+ GF S ACK+L+K CV+HH+FFRL PPP
Sbjct: 84 RDTILGFNMLSYRACKNLWKSCVEHHTFFRL--KRPLPPP 121
Score = 37.3 bits (87), Expect = 0.002
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 93 KTLAVTDEENTYGFETPSRSACKHLYKCCVDH 124
+ + GF S ACK+L+K CV+H
Sbjct: 77 RREPSESRDTILGFNMLSYRACKNLWKSCVEH 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 = 58.5 bits (142), Expect = 2e-10
Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 7/74 (9%)
Query: 162 AELGDYDPRRHS-PGYVSEFRF------TSHQSAALESRVAELHRDLSGQTPSQAELNYL 214
AE GDYD H G +S RF S + R+ ELH++L G +P +A+L YL
Sbjct: 128 AEFGDYDEELHDLRGELSLKRFLPKQLLDSRKLKEWRERIVELHKELIGLSPEEAKLKYL 187
Query: 215 DRVKNLPLYGVDLH 228
+ + LP YGV+L
Sbjct: 188 ELARKLPTYGVELF 201
Score = 47.3 bits (113), Expect = 1e-06
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 59 QFFLQIKQDILQGRLPVSFELSAELGAYVVQCKYK 93
+LQ++ DIL+GRLP E + L A +Q ++
Sbjct: 97 LLYLQVRNDILEGRLPCPEEEALLLAALALQAEFG 131
>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 = 53.2 bits (128), Expect = 2e-09
Identities = 21/55 (38%), Positives = 30/55 (54%)
Query: 209 AELNYLDRVKNLPLYGVDLHPVLGEDSIEYFLGLTPAGIVVLRNKIKVASYLWKE 263
AELN+L + L YGVD HPV + +LG T G+VV + +V + W +
Sbjct: 1 AELNFLRKAHTLETYGVDPHPVKDHYGTQLYLGFTHTGVVVFQGGKRVHHFKWDD 55
Score = 45.1 bits (107), Expect = 2e-06
Identities = 14/38 (36%), Positives = 28/38 (73%)
Query: 2 IRVCDKTDEENTYGFETPSRSACKHLYKCCVDHHSFFR 39
+ V ++++T GF+ P+ +ACKHL+KC V++ +F++
Sbjct: 68 LHVMQNEEKKHTLGFKCPTPAACKHLWKCAVENQAFYK 105
Score = 38.1 bits (89), Expect = 5e-04
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 7/47 (14%)
Query: 87 VVQCKY--KTL---AVTDEE--NTYGFETPSRSACKHLYKCCVDHVA 126
+ + Y KT + +EE +T GF+ P+ +ACKHL+KC V++ A
Sbjct: 56 ISKFNYEGKTFILHVMQNEEKKHTLGFKCPTPAACKHLWKCAVENQA 102
>gnl|CDD|220216 pfam09380, FERM_C, FERM C-terminal PH-like domain.
Length = 90
Score = 51.5 bits (124), Expect = 7e-09
Identities = 18/32 (56%), Positives = 23/32 (71%)
Query: 11 ENTYGFETPSRSACKHLYKCCVDHHSFFRLVQ 42
E T F TPS ACK+L+K CV+ H+FFRL +
Sbjct: 55 ETTLTFYTPSPRACKYLWKLCVEQHAFFRLRR 86
Score = 36.1 bits (84), Expect = 0.002
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 101 ENTYGFETPSRSACKHLYKCCVDH 124
E T F TPS ACK+L+K CV+
Sbjct: 55 ETTLTFYTPSPRACKYLWKLCVEQ 78
Score = 31.5 bits (72), Expect = 0.098
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 236 IEYFLGLTPAGIVVLRNKIKVASYLWKE 263
+ +LG++ GI+V + K+ ++ W E
Sbjct: 5 TDLWLGVSAKGILVYEDNNKINTFPWSE 32
>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 = 45.8 bits (109), Expect = 2e-06
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 10 EENTYGFET-----PSRSACKHLYKCCVDHHSFFRLVQVSSNPPP 49
E Y +T SR+ CK +K C++HH+FFRL +V P P
Sbjct: 67 EAYGYYKDTVEFSFESRNECKSFWKKCIEHHAFFRLSEVPKPPSP 111
Score = 32.3 bits (74), Expect = 0.091
Identities = 13/47 (27%), Positives = 24/47 (51%)
Query: 215 DRVKNLPLYGVDLHPVLGEDSIEYFLGLTPAGIVVLRNKIKVASYLW 261
D + LYG+ LHP + ++ L + GI+V + K+ ++ W
Sbjct: 1 DIARRCELYGIRLHPAKDREGVDLNLAVAHMGILVFQGFTKINTFSW 47
Score = 27.7 bits (62), Expect = 3.5
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 5/30 (16%)
Query: 100 EENTYGFET-----PSRSACKHLYKCCVDH 124
E Y +T SR+ CK +K C++H
Sbjct: 67 EAYGYYKDTVEFSFESRNECKSFWKKCIEH 96
>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 = 38.5 bits (90), Expect = 3e-04
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 9 DEENTYGFETPSRSACKHLYKCCVDHHSFFR 39
D+E F+T S K+++K CV +H F+R
Sbjct: 61 DKEEKLAFQTSSPREAKYIWKLCVGYHRFYR 91
Score = 30.0 bits (68), Expect = 0.29
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 99 DEENTYGFETPSRSACKHLYKCCV 122
D+E F+T S K+++K CV
Sbjct: 61 DKEEKLAFQTSSPREAKYIWKLCV 84
Score = 27.3 bits (61), Expect = 2.7
Identities = 12/43 (27%), Positives = 17/43 (39%), Gaps = 3/43 (6%)
Query: 224 GVDLHPV-LGEDSIEYFLGLTPAGIVVL--RNKIKVASYLWKE 263
GV+ V E LG++ GI VL + + W E
Sbjct: 1 GVEFFDVKDKSGGSELILGVSLEGISVLDDNTGNPLTLFRWPE 43
>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 = 37.3 bits (87), Expect = 0.002
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 203 GQTPSQAELNYLDRVKNLPLYGVDLHPVLGED---SIEYFLGLTPAGIVVLR----NKIK 255
G + +AEL +L + LP YGV H V E + +LG+ GI++ +
Sbjct: 1 GLSEEEAELEFLKVCQKLPEYGVHFHRVYREKKSSTGGIWLGICSRGIIIYEVHNGARTP 60
Query: 256 VASYLWKE 263
V + W+E
Sbjct: 61 VLRFPWRE 68
>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 = 35.7 bits (83), Expect = 0.006
Identities = 16/49 (32%), Positives = 24/49 (48%)
Query: 203 GQTPSQAELNYLDRVKNLPLYGVDLHPVLGEDSIEYFLGLTPAGIVVLR 251
G +PS AE +L V L YGV+ V + + +G+ P GI +
Sbjct: 1 GMSPSTAEYLFLKEVSELENYGVETFHVRTIEGQKLVIGVGPDGIRICN 49
Score = 29.1 bits (66), Expect = 1.2
Identities = 11/42 (26%), Positives = 17/42 (40%)
Query: 4 VCDKTDEENTYGFETPSRSACKHLYKCCVDHHSFFRLVQVSS 45
+ F+ PS A LY+ + H+F+R V S
Sbjct: 77 YLSDDGDVTKLEFKLPSTRAASALYRAITEKHAFYRCETVRS 118
>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 = 35.0 bits (81), Expect = 0.009
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 203 GQTPSQAELNYLDRVKNLPLYGVDLHPVLGEDSIEYFLGLTPAGIVV 249
G +P++AEL Y+ V+ L YG + +P + F+G + GI V
Sbjct: 1 GLSPAEAELLYIQEVEQLDGYGEESYPAKDNQGNDIFIGASFEGIFV 47
>gnl|CDD|217157 pfam02635, DrsE, DsrE/DsrF-like family. DsrE is a small soluble
protein involved in intracellular sulfur reduction. This
family also includes DsrF.
Length = 120
Score = 32.0 bits (73), Expect = 0.094
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 201 LSGQTPSQAELNYLDRVKNLPLYGVDLHPV---------LGEDSIEYFLGLTPAGIVVLR 251
L Q P E N + +K L YGV+L+ V + ED + +G+ P+G+ L
Sbjct: 50 LKDQAPPIDEKNLQELLKALAEYGVELY-VCGNSLKARGIDEDDLLLGVGVVPSGLGELA 108
Query: 252 NKIK 255
+
Sbjct: 109 ELQQ 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 = 28.5 bits (64), Expect = 1.7
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 221 PLYGVDLHPVLGEDSIEYFLGLTPAGIVV--LRNKIK-VASYLWK 262
P YGV + V ++ I ++LGL+ GI L++K+K + WK
Sbjct: 1 PTYGVHYYEVKDKNGIPWWLGLSYKGIGQYDLQDKVKPRKLFQWK 45
>gnl|CDD|153418 cd07377, WHTH_GntR, Winged helix-turn-helix (WHTH) DNA-binding
domain of the GntR family of transcriptional
regulators. This CD represents the winged HTH
DNA-binding domain of the GntR (named after the
gluconate operon repressor in Bacillus subtilis) family
of bacterial transcriptional regulators and their
putative homologs found in eukaryota and archaea. The
GntR family has over 6000 members distributed among
almost all bacterial species, which is comprised of
FadR, HutC, MocR, YtrA, AraR, PlmA, and other
subfamilies for the regulation of the most varied
biological process. The monomeric proteins of the GntR
family are characterized by two function domains: a
small highly conserved winged helix-turn-helix
prokaryotic DNA binding domain in the N-terminus, and a
very diverse regulatory ligand-binding domain in the
C-terminus for effector-binding/oligomerization, which
provides the basis for the subfamily classifications.
Binding of the effector to GntR-like transcriptional
regulators is presumed to result in a conformational
change that regulates the DNA-binding affinity of the
repressor. The GntR-like proteins bind as dimers, where
each monomer recognizes a half-site of 2-fold symmetric
DNA sequences.
Length = 66
Score = 27.0 bits (61), Expect = 2.1
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 6/33 (18%)
Query: 58 YQFFLQIKQDILQG------RLPVSFELSAELG 84
Q Q+++ IL G RLP EL+ ELG
Sbjct: 4 EQIADQLREAILSGELKPGDRLPSERELAEELG 36
>gnl|CDD|235552 PRK05670, PRK05670, anthranilate synthase component II;
Provisional.
Length = 189
Score = 28.6 bits (65), Expect = 2.3
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 9/42 (21%)
Query: 216 RVKNLPLYGVDLHPVLGEDSIEYFLGLTPAGIVVLRNKIKVA 257
R K LP+YGV HP +SI LT G +L N +++A
Sbjct: 156 RHKELPIYGVQFHP----ESI-----LTEHGHKLLENFLELA 188
>gnl|CDD|183918 PRK13252, PRK13252, betaine aldehyde dehydrogenase; Provisional.
Length = 488
Score = 29.1 bits (66), Expect = 2.7
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 225 VDLHPVLGEDSIEYFLGLTPA 245
VD V G D +EY+ GL PA
Sbjct: 104 VD--IVTGADVLEYYAGLAPA 122
>gnl|CDD|223586 COG0512, PabA, Anthranilate/para-aminobenzoate synthases component
II [Amino acid transport and metabolism / Coenzyme
metabolism].
Length = 191
Score = 28.3 bits (64), Expect = 2.9
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 9/37 (24%)
Query: 216 RVKNLPLYGVDLHPVLGEDSIEYFLGLTPAGIVVLRN 252
R K LP+YGV HP +SI LT G +L N
Sbjct: 159 RHKKLPIYGVQFHP----ESI-----LTEYGHRILEN 186
>gnl|CDD|227642 COG5337, CotH, Spore coat assembly protein [Cell envelope
biogenesis, outer membrane].
Length = 473
Score = 28.4 bits (63), Expect = 4.3
Identities = 5/33 (15%), Positives = 14/33 (42%)
Query: 72 RLPVSFELSAELGAYVVQCKYKTLAVTDEENTY 104
R ++ + +ELG + + + + D+
Sbjct: 153 REKLALDFFSELGTVSPKASFAFVKMNDKNEGV 185
>gnl|CDD|215558 PLN03073, PLN03073, ABC transporter F family; Provisional.
Length = 718
Score = 28.7 bits (64), Expect = 4.4
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 11/54 (20%)
Query: 170 RRHSPGYVSEFRFTSHQSAALESRVAELHRDLSGQTPSQAELNYLDRVKNLPLY 223
R H ++ +FR+ + +++ ++SR+ L R L ++D V N P Y
Sbjct: 451 RSHMQAFIDKFRYNAKRASLVQSRIKALDR-----------LGHVDAVVNDPDY 493
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 27.9 bits (63), Expect = 5.2
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 228 HPVLGEDSIEYFLGLTPA---GIVVLRNKIK 255
+ GED E FL L + GI V+RNKIK
Sbjct: 60 RELYGEDWRENFLELNASDERGIDVIRNKIK 90
>gnl|CDD|184753 PRK14581, hmsF, outer membrane N-deacetylase; Provisional.
Length = 672
Score = 28.0 bits (62), Expect = 5.4
Identities = 16/82 (19%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 137 KIHSRCTLGLSSMLWILASCLKKSLAELGDYDPRRHSPGY-VSEFRFTSHQSAALESRVA 195
++ SR + + + + +LA + SL + DP+ ++R S + + R+
Sbjct: 388 QLASRPDVEVYAWMPVLAFDMDPSLPRITRIDPKTGKTSIDPDQYRRLSPFNPEVRQRII 447
Query: 196 ELHRDLSGQTPSQAELNYLDRV 217
+++RD++ P + + D V
Sbjct: 448 DIYRDMAYSAPIDGIIYHDDAV 469
>gnl|CDD|223660 COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication,
recombination, and repair].
Length = 1139
Score = 28.0 bits (63), Expect = 5.8
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 82 ELGAYVVQCKYKTLAVTDEENTYG 105
EL + LA+TD N YG
Sbjct: 24 ELVKKAKELGMPALALTDHNNLYG 47
>gnl|CDD|213986 cd07431, PHP_PolIIIA, Polymerase and Histidinol Phosphatase domain
of alpha-subunit of bacterial polymerase III. PolIIIAs
that contain an N-terminal PHP domain have been
classified into four basic groups based on genome
composition, phylogenetic, and domain structural
analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also
called histidinol phosphatase-2/HIS2) domain is
associated with several types of DNA polymerases, such
as PolIIIA and family X DNA polymerases, stand alone
histidinol phosphate phosphatases (HisPPases), and a
number of uncharacterized protein families. DNA
polymerase III holoenzyme is one of the five eubacterial
DNA polymerases that is responsible for the replication
of the DNA duplex. The alpha subunit of DNA polymerase
III core enzyme catalyzes the reaction for polymerizing
both DNA strands. The PolIIIA PHP domain has four
conserved sequence motifs and contains an invariant
histidine that is involved in metal ion coordination,
and like other PHP structures, exhibits a distorted
(beta/alpha) 7 barrel and coordinates up to 3 metals.
Initially, it was proposed that PHP region might be
involved in pyrophosphate hydrolysis, but such activity
has not been found. It has been shown that the PHP
domain of PolIIIA has a trinuclear metal complex and is
capable of proofreading activity.
Length = 179
Score = 27.2 bits (61), Expect = 8.1
Identities = 13/44 (29%), Positives = 14/44 (31%), Gaps = 15/44 (34%)
Query: 81 AELGAYVVQCKYKTLAVTDEENTYGFETPSRSACKHLYKCCVDH 124
ELG Y LA+TD YG YK C
Sbjct: 26 KELG-------YSALALTDRNVLYGAV--------RFYKACKKA 54
>gnl|CDD|240521 cd13394, Syo1_like, Fungal symportin 1 (syo1) and similar proteins.
This family of eukaryotic proteins includes
Saccharomyces cerevisiae Ydl063c and Chaetomium
thermophilum Syo1, which mediate the co-import of two
ribosomal proteins, Rpl5 and Rpl11 (which both interact
with 5S rRNA) into the nucleus. Import precedes their
association with rRNA and subsequent ribosome assembly
in the nucleolus. The primary structure of syo1 is a
mixture of Armadillo- (ARM, N-terminal part of syo1) and
HEAT-repeats (C-terminal part of syo1).
Length = 597
Score = 27.7 bits (62), Expect = 8.1
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 123 DHVACPMITTYAYGKIHSRCTLGLSSMLWILASC 156
P + +HSR L+++LW+ S
Sbjct: 370 TIEELPPPLSKLLLSLHSRALECLNNLLWLFLSL 403
>gnl|CDD|153214 cd01743, GATase1_Anthranilate_Synthase, Type 1 glutamine
amidotransferase (GATase1) domain found in Anthranilate
synthase. Type 1 glutamine amidotransferase (GATase1)
domain found in Anthranilate synthase (ASase). This
group contains proteins similar to para-aminobenzoate
(PABA) synthase and ASase. These enzymes catalyze
similar reactions and produce similar products, PABA and
ortho-aminobenzoate (anthranilate). Each enzyme is
composed of non-identical subunits: a glutamine
amidotransferase subunit (component II) and a subunit
that produces an aminobenzoate products (component I).
ASase catalyses the synthesis of anthranilate from
chorismate and glutamine and is a tetrameric protein
comprising two copies each of components I and II.
Component II of ASase belongs to the family of triad
GTases which hydrolyze glutamine and transfer nascent
ammonia between the active sites. In some bacteria, such
as Escherichia coli, component II can be much larger
than in other organisms, due to the presence of
phosphoribosyl-anthranilate transferase (PRTase)
activity. PRTase catalyses the second step in tryptophan
biosynthesis and results in the addition of
5-phosphoribosyl-1-pyrophosphate to anthranilate to
create N-5'-phosphoribosyl-anthranilate. In E.coli, the
first step in the conversion of chorismate to PABA
involves two proteins: PabA and PabB which co-operate to
transfer the amide nitrogen of glutamine to chorismate
forming 4-amino-4 deoxychorismate (ADC). PabA acts as a
glutamine amidotransferase, supplying an amino group to
PabB, which carries out the amination reaction. A third
protein PabC then mediates elimination of pyruvate and
aromatization to give PABA. Several organisms have
bipartite proteins containing fused domains homologous
to PabA and PabB commonly called PABA synthases. These
hybrid PABA synthases may produce ADC and not PABA.
Length = 184
Score = 27.1 bits (61), Expect = 8.2
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 9/37 (24%)
Query: 216 RVKNLPLYGVDLHPVLGEDSIEYFLGLTPAGIVVLRN 252
R ++LP+YGV HP E SI LT G+ +L N
Sbjct: 155 RHRDLPIYGVQFHP---E-SI-----LTEYGLRLLEN 182
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
0.322 0.136 0.420
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: 13,315,125
Number of extensions: 1224338
Number of successful extensions: 944
Number of sequences better than 10.0: 1
Number of HSP's gapped: 942
Number of HSP's successfully gapped: 47
Length of query: 265
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 170
Effective length of database: 6,723,972
Effective search space: 1143075240
Effective search space used: 1143075240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.1 bits)