RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8450
(525 letters)
>gnl|CDD|241355 cd13201, FERM_C_MyoXV, Myosin XV (MyoXV/Myo15) FERM domain C-lobe.
MyoXV, a MyTH-FERM myosin, are actin-based motor
proteins essential for a variety of biological processes
in actin cytoskeleton function. Specifically MyoXV
functions in the actin organization in hair cells of the
organ of Corti. Mutations in Human MyoXVa causes
non-syndromic deafness, DFNB3 and the mouse shaker-2
mutation. MyoXV consists of a N-terminal motor/head
region, a neck made of 1-3 IQ motifs, and a tail that
consists of either a myosin tail homology 4 (MyTH4)
domains, followed by an SH3 domain, and a MyTH-FERM
domains as in rat Myo15 or two MyTH-FERM domains
separated by a SH3 domain as in human Myo15A. The
MyTH-FERM domains are thought to mediate dimerization
and binding to other proteins or cargo. 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 = 173 bits (442), Expect = 2e-52
Identities = 64/129 (49%), Positives = 88/129 (68%), Gaps = 6/129 (4%)
Query: 398 VQSHWTQTAPLHSIQAKAQLLEILSKWPLFGSSFFAIKR-----NGDQQILALNKHGVHF 452
VQ H Q PL QA+AQ LEILSK PLFGS+FF ++R +LA+N+ G+HF
Sbjct: 1 VQQHLQQVQPLSPHQARAQFLEILSKLPLFGSNFFYVQRVSDPRIPGPCLLAVNREGLHF 60
Query: 453 LNLLTHETISSVPYGDVISTRKVRA-ESGTLYLEMKCGNLFQQRVARIQTDQAHEIARLI 511
L+ THET+ ++P ++ STRK+R E GT +L++K GNL QQ+ R++TDQAHEI+RLI
Sbjct: 61 LDPNTHETLLTIPLKEIQSTRKLRPLEDGTPFLDIKYGNLMQQKTTRLETDQAHEISRLI 120
Query: 512 RQYMSLDRQ 520
QY+ +
Sbjct: 121 AQYIEEQSE 129
>gnl|CDD|214535 smart00139, MyTH4, Domain in Myosin and Kinesin Tails. Domain
present twice in myosin-VIIa, and also present in 3
other myosins.
Length = 152
Score = 137 bits (348), Expect = 1e-38
Identities = 62/153 (40%), Positives = 87/153 (56%), Gaps = 4/153 (2%)
Query: 64 FTCVPISEPLLKLE-PPLAEIAVECFECIMRFMGDLPTTPDLTEVKCVYTILMHCHTHEP 122
+T PI LLKLE L + AV+ F+ I++FMGD+P + + V IL H
Sbjct: 1 YTKDPIKTSLLKLESDELQKEAVKIFKAILKFMGDIPLPRPDSHLDLVQFILQKGLDHPE 60
Query: 123 LRDEVYCQLMKQTTSN-KTESCQRGWRLLSIVAAYFTCSDTLRPFLLKYLETAAYDKRRA 181
LRDE+YCQL+KQ T N +S +RGW+LL + + F S+ L P+LL++L A +
Sbjct: 61 LRDEIYCQLIKQLTDNPSRQSEERGWQLLYLCTSLFPPSERLLPYLLQFLSRRADP--GS 118
Query: 182 FHGTASVCLQNLRKTLRYGGRKNVPSVEEVTAV 214
G A CL L +TL+ G RK PS E+ A+
Sbjct: 119 EQGLAKYCLYRLERTLKNGARKQPPSRLELEAI 151
>gnl|CDD|216118 pfam00784, MyTH4, MyTH4 domain. Domain in myosin and kinesin
tails, present twice in myosin-VIIa, and also present in
3 other myosins.
Length = 106
Score = 95.9 bits (239), Expect = 6e-24
Identities = 39/102 (38%), Positives = 56/102 (54%), Gaps = 8/102 (7%)
Query: 113 ILMHCHTHEPLRDEVYCQLMKQTTSN-KTESCQRGWRLLSIVAAYFTCSDTLRPFLLKYL 171
IL LRDE+YCQ++KQTT N +S RGW LL + F S+ + +L ++L
Sbjct: 10 ILQQGIKRPELRDEIYCQIIKQTTKNPSKQSALRGWELLYLCTGTFPPSEEILKYLSQFL 69
Query: 172 ETAAYDKRRAFHGTASVCLQNLRKTLRYGGRKNVPSVEEVTA 213
+RA HG A+ C + L++T + G RK PS E+ A
Sbjct: 70 ------HKRA-HGLAAYCQERLKRTFKNGTRKQPPSRLEIEA 104
>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 = 88.8 bits (221), Expect = 1e-20
Identities = 48/175 (27%), Positives = 90/175 (51%), Gaps = 16/175 (9%)
Query: 352 DVAKLAALLHRA---ADMSHPPAMKET-KFLLPKPALTQRDIKPAQWVQMVQSHWTQTAP 407
D +LAAL++R D S ++ + K L+P + + P +W +++ + + + A
Sbjct: 3 DAIQLAALIYRVRFGDDKSQFQSIPKMLKELIPADLIKLQ--SPDEWKKLIIAAYNKHAG 60
Query: 408 LHSIQAKAQLLEILSKWPLFGSSFFAIKRNGDQQ-----ILALNKHGVHFLNLLTHETIS 462
+ S +AK L+I+ +WP FGS+FF +K+ D ++A+NK+GV ++ T E +
Sbjct: 61 MSSEEAKLAFLKIIYRWPTFGSAFFEVKQTTDPNLPEILLIAINKNGVSLIDPKTKEILV 120
Query: 463 SVPYGDVISTRKVRAESGTLYLEMKCGNLFQQRVARIQTDQAHEIARLIRQYMSL 517
+ P+ + + SG Y M GNL + +T +++ L+ Y+SL
Sbjct: 121 TYPFTKISNW-----SSGNTYFHMTIGNLVRGSKLLCETSLGYKMDDLLTSYISL 170
>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 = 64.2 bits (157), Expect = 7e-12
Identities = 45/215 (20%), Positives = 71/215 (33%), Gaps = 26/215 (12%)
Query: 226 RLPGGSETVINTKSTTVVEDICIEMCQLINVNNDLEMEEFSLYCIVEGDAFTMPLAKEEY 285
L G+ S+T E++ +C+ + + E E F L + L +
Sbjct: 5 YLLDGTTLEFEVDSSTTAEELLETVCRKLGI---RESEYFGLQFEDPDEDLRHWLDPAKT 61
Query: 286 ILDVTTELHKNQQVFYLIFCRSVWYFP----LRLDCQLYVQVLFNQIAPDYLEGLLLVLP 341
+LD + F + F Y P L+ D L+ Q+ D LEG L
Sbjct: 62 LLDQDVKSEPLTLYFRVKF-----YPPDPNQLKEDPTRLNL-LYLQVRNDILEGRLPCPE 115
Query: 342 NEQIPQDIVYDVAKLAALL--HRAADMSHPPAMKETKFLLPK--PALTQRDIKPAQWVQM 397
E LAAL D + L + P K +W +
Sbjct: 116 EE---------ALLLAALALQAEFGDYDEELHDLRGELSLKRFLPKQLLDSRKLKEWRER 166
Query: 398 VQSHWTQTAPLHSIQAKAQLLEILSKWPLFGSSFF 432
+ + L +AK + LE+ K P +G F
Sbjct: 167 IVELHKELIGLSPEEAKLKYLELARKLPTYGVELF 201
>gnl|CDD|241358 cd13204, FERM_C2_myosin_like, Myosin-like FERM domain C-lobe,
repeat 2. These myosin-like proteins are unidentified
though they are sequence similar to myosin 1/myo1,
myosin 7/myoVII, and myosin 10/myoX. These myosin-like
proteins contain an N-terminal motor/head region and a
C-terminal tail consisting of two myosin tail homology 4
(MyTH4) and twos FERM domains. In myoX the FERM domain
forms a supramodule with its MyTH4 domain which binds to
the negatively charged E-hook region in the tails of
alpha- and beta-tubulin forming a proposed motorized
link between actin filaments and microtubules and a
similar thing might happen in these myosins. 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 second FERM_N repeat is present
in this hierarchy. 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 = 113
Score = 45.9 bits (109), Expect = 3e-06
Identities = 33/109 (30%), Positives = 53/109 (48%), Gaps = 12/109 (11%)
Query: 412 QAKAQLLEILSKWPLFGSSFFAIKRNGDQQI-----LALNKHGVHFLNLLTHETISSVPY 466
+ K L I+ WPL+GS+ F + ++ + LA+N+ G+H L E + S Y
Sbjct: 5 ECKRAFLNIVQSWPLYGSTIFDVMQSYTSNLPKTLWLAINQSGLHILERREKEPLISYSY 64
Query: 467 GDVISTRKVRAESGTLY-LEMKCGNLFQQRVARIQTDQAHEIARLIRQY 514
++S S +L L + G+L + T+QA +IA LIR Y
Sbjct: 65 SSIVSY------SPSLNSLMIVTGSLTRGTKFIFNTNQAFQIAHLIRDY 107
>gnl|CDD|241354 cd13200, FERM_C_KCBP, kinesin-like calmodulin binding protein FERM
domain C-lobe. KCBPs (also called KIPK/Kinesin-like
Calmodulin-Binding Protein-Interacting Protein Kinase),
a member of the Kinesin-14 family, is a C-terminal
microtubule motor with three unique domains including a
myosin tail homology region 4 (MyTH4), a talin-like
domain, and a calmodulin-binding domain (CBD). Binding
of the Ca2+-activated calmodulin to KCBP causes the
motor to dissociate from microtubules. The microtubule
binding of KCBP is controlled by the calcium binding
protein KIC containing a single EF-hand motif. KCBPs
are unique to land plants and green algae. The MyTH4
and talin-like domains are not found in other kinesins,
while the CBD domain is also only found in
Strongylocentrotus purpuratus kinesin-C (SpKinC). 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 = 189
Score = 45.5 bits (108), Expect = 1e-05
Identities = 27/81 (33%), Positives = 38/81 (46%), Gaps = 9/81 (11%)
Query: 379 LPKPALTQRDIKPAQWVQMVQSHWTQTAPLHSIQAKAQLLEILSKWPLFGSSFFAIKRNG 438
LPK L R + +W + + + L A+ QLL IL P S FF+++R
Sbjct: 34 LPKQVLITRPRE--EWDADIVARYRALEQLSKDDARQQLLRILRSLPYGNSIFFSVRRIE 91
Query: 439 D-------QQILALNKHGVHF 452
D + IL +NK GVHF
Sbjct: 92 DPIGLLPGKIILGINKRGVHF 112
>gnl|CDD|241357 cd13203, FERM_C1_myosin_like, Myosin-like FERM domain C-lobe,
repeat 1. These myosin-like proteins are unidentified
though they are sequence similar to myosin 1/myo1,
myosin 7/myoVII, and myosin 10/myoX. These myosin-like
proteins contain an N-terminal motor/head region and a
C-terminal tail consisting of two myosin tail homology 4
(MyTH4) and twos FERM domains. In myoX the FERM domain
forms a supramodule with its MyTH4 domain which binds to
the negatively charged E-hook region in the tails of
alpha- and beta-tubulin forming a proposed motorized
link between actin filaments and microtubules and a
similar thing might happen in these myosins. 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 first FERM_N repeat is present
in this hierarchy. 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 = 117
Score = 43.9 bits (104), Expect = 2e-05
Identities = 29/109 (26%), Positives = 49/109 (44%), Gaps = 6/109 (5%)
Query: 411 IQAKAQLLEILSKWPLFGSSFFAIKRNG-----DQQILALNKHGVHFLNLLTHETISSVP 465
+QAK L + ++PL+G++ F + G + IL ++ G F+N T ++
Sbjct: 4 LQAKVLYLTCVMQYPLYGTTLFDVTYKGFWSYPNNLILGVHCDGFKFVNPKTKAILAEYR 63
Query: 466 YGDVISTRKVRAESGTLYLEMKCGNLFQQRVARIQTDQAHEIARLIRQY 514
Y D+ S +V L L + + + +T Q EIA LI Y
Sbjct: 64 YSDLESI-EVDPSDDVLTLTLSQSVPDEHKCFMFETPQKEEIASLIASY 111
>gnl|CDD|215882 pfam00373, FERM_M, FERM central domain. This domain is the central
structural domain of the FERM domain.
Length = 113
Score = 43.0 bits (102), Expect = 3e-05
Identities = 27/119 (22%), Positives = 43/119 (36%), Gaps = 18/119 (15%)
Query: 318 QLYVQVLFNQIAPDYLEGLLLVLPNEQIPQDIVYDVAKLAALLHRAADMSHPPAMKETKF 377
LY+Q+ D LEG L E LAAL +A + P + +
Sbjct: 9 LLYLQLK-----RDILEGRLPCSEEE---------ALLLAALALQAEFGDYNPEKHSSSY 54
Query: 378 LLPK----PALTQRDIKPAQWVQMVQSHWTQTAPLHSIQAKAQLLEILSKWPLFGSSFF 432
L P+ + K + + + L +AK + L+I P +G +FF
Sbjct: 55 LKELEYFLPSRLIKKEKSKELEKRILEAHKNLRGLSPAEAKLKYLQIAQSLPTYGVTFF 113
>gnl|CDD|241356 cd13202, FERM_C_MyoX, Myosin X (MyoX, Myo10) FERM domain C-lobe.
MyoX, a MyTH-FERM myosin, is a molecular motor that has
crucial functions in the transport and/or tethering of
integrins in the actin-based extensions known as
filopodia, microtubule binding, and in netrin-mediated
axon guidance. It functions as a dimer. MyoX walks on
bundles of actin, rather than single filaments, unlike
the other unconventional myosins. MyoX is present in
organisms ranging from humans to choanoflagellates, but
not in Drosophila and Caenorhabditis elegans.MyoX
consists of a N-terminal motor/head region, a neck made
of 3 IQ motifs, and a tail consisting of a coiled-coil
domain, a PEST region, 3 PH domains, a myosin tail
homology 4 (MyTH4), and a FERM domain at its very
C-terminus. The MyoX FERM domain binds to the NPXY motif
of several beta-integrins, a key family of cell surface
receptors that are involved in cell adhesion and
migration. In addition the FERM domain binds to the
cytoplasmic domains of the netrin receptors DCC (deleted
in colorectal cancer) and neogenin. The FERM domain also
forms a supramodule with its MyTH4 domain which binds to
the negatively charged E-hook region in the tails of
alpha- and beta-tubulin forming a proposed motorized
link between actin filaments and microtubules. 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 = 111
Score = 36.2 bits (84), Expect = 0.007
Identities = 28/119 (23%), Positives = 49/119 (41%), Gaps = 30/119 (25%)
Query: 412 QAKAQLLEILSKWPLFGSSFFAIKRNGDQQI-----LALNKHGVHF--------LNLLTH 458
A A+ + I+ +WP +GS+ F ++ N + L ++ GV L +
Sbjct: 5 DAMAKYMAIIREWPGYGSTLFEVECNKEGGFPQELWLGVSAKGVSLYKRGEPEPLESFPY 64
Query: 459 ETISSVPYG-DVISTRKVRAESGTLYLEMKCGNLFQQRVARIQTDQAHEIARLIRQYMS 516
E I S +G +T K+ E R +T Q EIA+L++ Y++
Sbjct: 65 EKILS--FGAPQANTYKIVVEG--------------DRELLFETTQVVEIAKLMKAYIN 107
>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 = 34.3 bits (79), Expect = 0.019
Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 11/95 (11%)
Query: 428 GSSFFAIKRNGDQQ--ILALNKHGVHFLNLLTHETISSVPYGDVISTRKVRAESGTLYLE 485
G FF +K IL ++ G+ L+ T ++ + ++ RK+ T +E
Sbjct: 1 GVEFFDVKDKSGGSELILGVSLEGISVLDDNTGNPLTLFRWPEI---RKISFSKKTFTIE 57
Query: 486 MKCGNLFQQRVARIQTDQAHE---IARLIRQYMSL 517
+ ++ QT E I +L Y
Sbjct: 58 I---RGDKEEKLAFQTSSPREAKYIWKLCVGYHRF 89
>gnl|CDD|241352 cd13198, FERM_C1_MyoVII, Myosin VII (MyoVII/Myo7) FERM domain
C-lobe, repeat 1. 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 = 140
Score = 31.4 bits (72), Expect = 0.47
Identities = 28/130 (21%), Positives = 53/130 (40%), Gaps = 21/130 (16%)
Query: 399 QSHWTQTAPLHSIQAKAQLLEILS-KWPLFGSSFFAIKR------NGDQQILALNKHGVH 451
++ + Q S + K +++ KWPL S FF + ++ I+A+N G++
Sbjct: 2 KAEYVQNRV-SSQRVKEDIVDYARLKWPLLFSRFFEATKFSGPSLPKNEVIIAVNWTGIY 60
Query: 452 FLN-----LLTHETISSVPYGDVISTRKVRAESGTLYLEMKCGNLFQQRVARIQTDQAHE 506
F++ LL +S V S R R + L G + ++ A +
Sbjct: 61 FVDEQEQVLL---ELSFPEISGVSSVRGKRDGGQSFTLSTIQGEEYV----FQSSN-AED 112
Query: 507 IARLIRQYMS 516
IA L+ ++
Sbjct: 113 IAELVNYFLE 122
>gnl|CDD|236196 PRK08241, PRK08241, RNA polymerase factor sigma-70; Validated.
Length = 339
Score = 29.9 bits (68), Expect = 3.7
Identities = 11/20 (55%), Positives = 11/20 (55%)
Query: 351 YDVAKLAALLHRAADMSHPP 370
YDV L ALL A S PP
Sbjct: 230 YDVDALVALLTEDATWSMPP 249
>gnl|CDD|216306 pfam01117, Aerolysin, Aerolysin toxin. This family represents the
pore forming lobe of aerolysin.
Length = 359
Score = 29.3 bits (66), Expect = 4.5
Identities = 20/87 (22%), Positives = 32/87 (36%), Gaps = 17/87 (19%)
Query: 432 FAIKRNGDQQILALNKHG------------VHFLNLLTHETISSVPYGDV-ISTRKVRAE 478
I RNGD ++ N +G + N S +GD +S R+
Sbjct: 45 MEITRNGDSWVIKGNNNGNCSGYRCDERLKMTVSNFKFVLNPDSFKHGDPTVSDREPVKT 104
Query: 479 -SGTLYLEMKCGNLFQQRVARIQTDQA 504
SG + + QQ V ++ DQ+
Sbjct: 105 ISGYAIND---SDTPQQIVVTLRYDQS 128
>gnl|CDD|188577 TIGR04062, dnd_assoc_4, dnd system-associated protein 4. A DNA
sulfur modification system, dnd (degradation during
electrophoresis), is sparsely and sporadically
distributed among the bacteria. Members of this protein
fam ily are strictly limited to species with the dnd
operon, and are found close to the dnd operon on the
chromosomes of species such as Nostoc sp. PCC 7120,
Geobacter uraniireducens Rf4, and Roseobacter
denitrificans OCh 114 [DNA metabolism,
Restriction/modification].
Length = 151
Score = 28.5 bits (64), Expect = 5.1
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 329 APDYLEGLLLVLPNEQIPQDIVYDVAKLAALL 360
A DY E LLL++ +E+ ++ + L+ L
Sbjct: 120 AVDYSERLLLLIISERFDEEQPDEEFDLSKFL 151
>gnl|CDD|240427 PTZ00470, PTZ00470, glycoside hydrolase family 47 protein;
Provisional.
Length = 522
Score = 28.5 bits (64), Expect = 8.8
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 83 IAVECFECIMRFMGDLPTTPDLT 105
+ V FE +R +G L + DLT
Sbjct: 149 LGVSVFETTIRVLGGLLSAYDLT 171
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
0.323 0.136 0.411
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: 26,150,406
Number of extensions: 2488233
Number of successful extensions: 1841
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1827
Number of HSP's successfully gapped: 21
Length of query: 525
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 424
Effective length of database: 6,457,848
Effective search space: 2738127552
Effective search space used: 2738127552
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 (22.0 bits)
S2: 61 (27.3 bits)