RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14197
(178 letters)
>gnl|CDD|241359 cd13205, FERM_C_fermitin, Fermitin family FERM domain C-lobe.
Fermitin functions as a mediator of integrin inside-out
signalling. The recruitment of Fermitin proteins and
Talin to the membrane mediates the terminal event of
integrin signalling, via interaction with integrin beta
subunits. Fermatin has FERM domain interrupted with a
pleckstrin homology (PH) domain. Fermitin family
homologs (Fermt1, 2, and 3, also known as Kindlins) are
each encoded by a different gene. In mammalian studies,
Fermt1 is generally expressed in epithelial cells,
Fermt2 is expressed inmuscle tissues, and Fermt3 is
expressed in hematopoietic lineages. Specifically Fermt2
is expressed in smooth and striated muscle tissues in
mice and in the somites (a trunk muscle precursor) and
neural crest in Xenopus embryos. As such it has been
proposed that Fermt2 plays a role in cardiomyocyte and
neural crest differentiation. Expression of mammalian
Fermt3 is associated with hematopoietic lineages: the
anterior ventral blood islands, vitelline veins, and
early myeloid cells. In Xenopus embryos this expression,
also include the notochord and cement gland. 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). This cd is not included in the
C-lobe hierarchy based on its position in the tree. One
thing to note is that unlike the other members of the
C-lobe hierarchy it contains 2 FERM M domains which
might also reflect a difference in its evolutionary
history. 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 = 89
Score = 157 bits (398), Expect = 1e-50
Identities = 54/89 (60%), Positives = 72/89 (80%)
Query: 69 GLTLFVIKPMGHKKEELLGVTPSRLMRMELSSGDHVRTWRYDTVKAWNVNWEIKHMMLQL 128
G+T F+++ G KK+ELLGV +RL+RM+L +GD ++TWRY T+KAWNVNWEI+ +++Q
Sbjct: 1 GITYFIVRFRGSKKDELLGVAYNRLIRMDLHTGDVLKTWRYSTMKAWNVNWEIREVIIQF 60
Query: 129 TDGNFIFECQSADCKVVHEFIGGYIFLSM 157
D + F C SADCK+VHEFIGGYIFLSM
Sbjct: 61 EDESIAFACLSADCKIVHEFIGGYIFLSM 89
>gnl|CDD|215882 pfam00373, FERM_M, FERM central domain. This domain is the central
structural domain of the FERM domain.
Length = 113
Score = 59.2 bits (144), Expect = 6e-12
Identities = 32/68 (47%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 7 TPAISPASLDICAEDYVSSRYIKKLRSK-LSQRILEAHANVKDLGLTEAKLSYIRAWQSL 65
P +S E ++ SR IKK +SK L +RILEAH N++ L EAKL Y++ QSL
Sbjct: 46 NPEKHSSSYLKELEYFLPSRLIKKEKSKELEKRILEAHKNLRGLSPAEAKLKYLQIAQSL 105
Query: 66 PDYGLTLF 73
P YG+T F
Sbjct: 106 PTYGVTFF 113
>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 = 40.8 bits (96), Expect = 2e-05
Identities = 14/93 (15%), Positives = 38/93 (40%), Gaps = 6/93 (6%)
Query: 69 GLTLFVIKPMGHKKEELLGVTPSRLMRMELSSGDHVRTWRYDTVKAWNVNWEIKHMMLQL 128
G+ F +K E +LGV+ + ++ ++G+ + +R+ ++ + + K +++
Sbjct: 1 GVEFFDVKDKSGGSELILGVSLEGISVLDDNTGNPLTLFRWPEIRKISFSK--KTFTIEI 58
Query: 129 TDGN---FIFEC-QSADCKVVHEFIGGYIFLSM 157
F+ + K + + GY
Sbjct: 59 RGDKEEKLAFQTSSPREAKYIWKLCVGYHRFYR 91
>gnl|CDD|241305 cd10569, FERM_C_Talin, Talin FERM domain C-lobe/F3. Talin (also
called filopodin) plays an important role in initiating
actin filament growth in motile cell protrusions. It is
responsible for linking the cytoplasmic domains of
integrins to the actin-based cytoskeleton, and is
involved in vinculin, integrin and actin interactions.
At the leading edge of motile cells, talin colocalises
with the hyaluronan receptor layilin in transient
adhesions, some of which become more stable focal
adhesions (FA). During this maturation process, layilin
is replaced with integrins, where localized production
of PI(4,5)P(2) by type 1 phosphatidyl inositol phosphate
kinase type 1gamma (PIPK1gamma) is thought to play a
role in FA assembly. Talins are composed of a N-terminal
region FERM domain which us made up of 3 subdomains (N,
alpha-, and C-lobe-or- A-lobe, B-lobe, C-lobe -or- F1,
F2, F3) connected by short linkers, a talin rod which
binds vinculin, and a conserved C-terminal with actin-
and integrin-binding sites. There are 2 additional
actin-binding domains, one in the talin rod and the
other in the FERM domain. Both the F2 and F3 FERM
subdomains contribute to F-actin binding. Subdomain F3
of the FERM domain contains overlapping binding sites
for integrin cytoplasmic domains and for the type 1
gamma isoform of PIP-kinase (phosphatidylinositol
4-phosphate 5-kinase). The FERM domain has a cloverleaf
tripart structure . 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 = 92
Score = 33.5 bits (77), Expect = 0.011
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 69 GLTLFVIK--PMGHKKEE--LLGVTPSRLMRMELSSGDHVRTWRYDTVKAW 115
G+T F++K G K LLG+T ++R++ + + ++ W T+K W
Sbjct: 1 GVTFFLVKEKMKGKNKLVPRLLGITKESVLRVDEETKEVLKVWPLTTIKRW 51
>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 = 34.2 bits (79), Expect = 0.017
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 20 EDYVSSRYIKKLRSKLSQRILEAHANVKDLGLTEAKLSYIRAWQSLPDYGLTLF 73
+ + SR +K+ R +RI+E H + L EAKL Y+ + LP YG+ LF
Sbjct: 152 KQLLDSRKLKEWR----ERIVELHKELIGLSPEEAKLKYLELARKLPTYGVELF 201
>gnl|CDD|225936 COG3401, COG3401, Fibronectin type 3 domain-containing protein
[General function prediction only].
Length = 343
Score = 31.0 bits (70), Expect = 0.27
Identities = 18/109 (16%), Positives = 37/109 (33%), Gaps = 7/109 (6%)
Query: 27 YIKKLRSKLSQRILEAHANVKDLGLTEAKLSYIRAWQSLPDYGLTLFVIKPMGHKKEELL 86
Y K KL + +K+ T + +S P Y + + + E +L
Sbjct: 11 YRTKKDLKLKRI-----GTIKNKYQTHYYDEGLEGEESYP-YQEGTTKVDKISYDSERIL 64
Query: 87 GVTPSRLMRMELSSGDHVRTWRYDTVKAWNVNWEIKHMMLQLTDGNFIF 135
T S + R+ R + + + + ++Q +G+ F
Sbjct: 65 VKT-SFIERVRSVFASLERPKSVKVFWSPHPDVSVGKYIIQRQNGDGKF 112
>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 = 29.5 bits (67), Expect = 0.60
Identities = 10/40 (25%), Positives = 20/40 (50%)
Query: 37 QRILEAHANVKDLGLTEAKLSYIRAWQSLPDYGLTLFVIK 76
+ I+ A+ + EAKL++++ P +G F +K
Sbjct: 49 KLIIAAYNKHAGMSSEEAKLAFLKIIYRWPTFGSAFFEVK 88
>gnl|CDD|214870 smart00867, YceI, YceI-like domain. E. coli YceI is a base-induced
periplasmic protein. The recent structure of a member of
this family shows that it binds to polyisoprenoid. The
structure consists of an extended, eight-stranded,
antiparallel beta-barrel that resembles the lipocalin
fold.
Length = 166
Score = 29.3 bits (66), Expect = 0.69
Identities = 7/28 (25%), Positives = 13/28 (46%)
Query: 106 TWRYDTVKAWNVNWEIKHMMLQLTDGNF 133
T+ D +V + +KH+ + G F
Sbjct: 1 TYTLDPASHSSVGFTVKHLGVSTVTGRF 28
>gnl|CDD|225228 COG2353, COG2353, Uncharacterized conserved protein [Function
unknown].
Length = 192
Score = 27.7 bits (62), Expect = 2.5
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 95 RMELSSGDHVRTWRYDTVKAWNVNWEIKHMMLQLTDGNF 133
LSS T+ D + ++ +EI H+ + G+F
Sbjct: 13 AASLSSAAAAATYTLDPAHS-SIVFEIDHLGVSKVRGSF 50
>gnl|CDD|218101 pfam04467, DUF483, Protein of unknown function (DUF483). Family
of uncharacterized prokaryotic proteins.
Length = 127
Score = 27.1 bits (60), Expect = 2.7
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 20 EDYVSSRYIKKLRSKLSQRILEAHAN 45
+ ++ RY K+R + I H
Sbjct: 4 QIFIKRRYKPKVRPAIDPMISVGHTE 29
>gnl|CDD|177855 PLN02205, PLN02205, alpha,alpha-trehalose-phosphate synthase
[UDP-forming].
Length = 854
Score = 28.1 bits (62), Expect = 2.9
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 108 RYDTVKAWNVNWEIKHMMLQLTDG 131
+ D K W +W+ ++LQL DG
Sbjct: 76 KSDGSKGWIFSWDENSLLLQLKDG 99
>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 = 27.4 bits (61), Expect = 3.2
Identities = 17/85 (20%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
Query: 11 SPASLDICAEDYVSSRY-IKKLRSKLSQRILEAHANVKDLGLTEAKLSYIRAWQSLPDYG 69
P L E Y+ + I + R + I+ + ++ L +A+ +R +SLP
Sbjct: 22 PPEELGQLLERYLPKQVLITRPREEWDADIVARYRALEQLSKDDARQQLLRILRSLPYGN 81
Query: 70 LTLFVIKPMGHKKEELLGVTPSRLM 94
F ++ + E+ +G+ P +++
Sbjct: 82 SIFFSVR----RIEDPIGLLPGKII 102
>gnl|CDD|236018 PRK07431, PRK07431, aspartate kinase; Provisional.
Length = 587
Score = 27.6 bits (62), Expect = 4.4
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 7/38 (18%)
Query: 74 VIKPMGHKKEELLGVT-------PSRLMRMELSSGDHV 104
V+ MG +EL+ + P R M M LS+G+ V
Sbjct: 39 VVSAMGKTTDELVKLAKEISSNPPRREMDMLLSTGEQV 76
>gnl|CDD|132846 cd07207, Pat_ExoU_VipD_like, ExoU and VipD-like proteins; homologus
to patatin, cPLA2, and iPLA2. ExoU, a 74-kDa enzyme, is
a potent virulence factor of Pseudomonas aeruginosa. One
of the pathogenic mechanisms of P. aeruginosa is to
induce cytotoxicity by the injection of effector
proteins (e.g. ExoU) using the type III secretion (T3S)
system. ExoU is homologus to patatin and also has the
conserved catalytic residues of mammalian
calcium-independent (iPLA2) and cytosolic (cPLA2) PLA2.
In vitro, ExoU cytotoxity is blocked by the inhibitor of
cytosolic and Ca2-independent phospholipase A2 (cPLA2
and iPLA2) enzymes, suggesting that phospholipase A2
inhibitors may represent a novel mode of treatment for
acute P. aeruginosa infections. ExoU requires eukaryotic
superoxide dismutase as a cofactor and cleaves
phosphatidylcholine and phosphatidylethanolamine in
vitro. VipD, a 69-kDa cytosolic protein, belongs to the
members of Legionella pneumophila family and is
homologus to ExoU from Pseudomonas. Even though VipD
shows high sequence similarity with several functional
regions of ExoU (e.g. oxyanion hole, active site serine,
active site aspartate), it has been shown to have no
phospholipase activity. This family includes ExoU from
Pseudomonas aeruginosa and VipD of Legionella
pneumophila.
Length = 194
Score = 26.9 bits (60), Expect = 4.6
Identities = 12/60 (20%), Positives = 19/60 (31%)
Query: 75 IKPMGHKKEELLGVTPSRLMRMELSSGDHVRTWRYDTVKAWNVNWEIKHMMLQLTDGNFI 134
+ LL + PS L GD + W + +K N ++ L D
Sbjct: 62 FAKLLDSPVGLLFLLPSLFKEGGLYKGDALEEWLRELLKEKTGNSFATSLLRDLDDDLGK 121
>gnl|CDD|217996 pfam04264, YceI, YceI-like domain. E. coli YceI is a base-induced
periplasmic protein. The recent structure of a member of
this family shows that it binds to polyisoprenoid. The
structure consists of an extended, eight-stranded,
antiparallel beta-barrel that resembles the lipocalin
fold.
Length = 161
Score = 26.9 bits (60), Expect = 5.2
Identities = 6/28 (21%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 106 TWRYDTVKAWNVNWEIKHMMLQLTDGNF 133
T+ D + +V++ ++H+ + G F
Sbjct: 1 TYTLDPAHS-SVSFTVRHLGISEVRGRF 27
>gnl|CDD|220983 pfam11107, FANCF, Fanconi anemia group F protein (FANCF). FANCF
regulates its own expression by methylation at both mRNA
and protein levels. Methylation-induced inactivation of
FANCF has an important role on the occurrence of ovarian
cancers by disrupting the FA-BRCA pathway.
Length = 343
Score = 27.1 bits (60), Expect = 5.3
Identities = 13/31 (41%), Positives = 16/31 (51%)
Query: 83 EELLGVTPSRLMRMELSSGDHVRTWRYDTVK 113
EELL + + LS DHV TW TV+
Sbjct: 2 EELLKNLDRFVEVLALSRSDHVATWDPATVR 32
>gnl|CDD|200568 cd10943, CE4_NodB, Putative catalytic domain of rhizobial NodB
chitooligosaccharide N-deacetylase and its bacterial
homologs. This family corresponds to rhizobial NodB
chitooligosaccharide N-deacetylase (EC 3.5.1.-),
encoded by nodB gene from the nodulation (nod) gene
cluster that is responsible for the biosynthesis of
bacterial nodulation signals, termed Nod factors. NodB
is involved in de-N-acetylating the nonreducing
N-acetylglucosamine residue of chitooligosaccharides to
allow for the attachment of the fatty acyl group by the
acyltransferase NodA. The monosaccharide
N-acetylglucosamine cannot be deacetylated by NodB.
NodB is composed of a 6-stranded barrel catalytic
domain with detectable sequence similarity to the
7-stranded barrel homology domain of polysaccharide
deacetylase (DCA)-like proteins in the larger
carbohydrate esterase 4 (CE4) superfamily.
Length = 193
Score = 26.7 bits (59), Expect = 6.6
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 6/45 (13%)
Query: 6 PTPAISPASLDICAED------YVSSRYIKKLRSKLSQRILEAHA 44
P P+ +P LD+ AE +V Y + + + I E H
Sbjct: 11 PNPSCTPQVLDVLAEHRVPATFFVIGAYAAEHPELIRRMIAEGHE 55
>gnl|CDD|184014 PRK13379, PRK13379, protocatechuate 4,5-dioxygenase subunit
alpha; Provisional.
Length = 119
Score = 25.7 bits (56), Expect = 8.2
Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 31 LRSKLSQRILE-AHANVKDLGLTEAKLSYIRA--WQSLPDYGLTLFVIK 76
+R+ R L+ A A +++ GLTE + IRA W L YG FVI+
Sbjct: 36 IRAPWRDRFLQDAEALMQEAGLTEQEKELIRARDWLGLVQYGANFFVIE 84
>gnl|CDD|227436 COG5105, MIH1, Mitotic inducer, protein phosphatase [Cell division
and chromosome partitioning].
Length = 427
Score = 26.5 bits (58), Expect = 8.3
Identities = 10/43 (23%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 125 MLQLTDGNF---IFECQSADCKVVHEFIGGYIF--LSMRSKDA 162
+ Q+ +G + +C DC+ +E+ GG+I +++ S
Sbjct: 249 LKQVLEGMYNIDFLKCIIIDCRFEYEYRGGHIINAVNISSTKK 291
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
0.320 0.135 0.416
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,084,328
Number of extensions: 813237
Number of successful extensions: 605
Number of sequences better than 10.0: 1
Number of HSP's gapped: 605
Number of HSP's successfully gapped: 22
Length of query: 178
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 87
Effective length of database: 6,901,388
Effective search space: 600420756
Effective search space used: 600420756
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 (21.8 bits)
S2: 56 (25.4 bits)