RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6995
(342 letters)
>gnl|CDD|238492 cd00992, PDZ_signaling, PDZ domain found in a variety of Eumetazoan
signaling molecules, often in tandem arrangements. May
be responsible for specific protein-protein
interactions, as most PDZ domains bind C-terminal
polypeptides, and binding to internal (non-C-terminal)
polypeptides and even to lipids has been demonstrated.
In this subfamily of PDZ domains an N-terminal
beta-strand forms the peptide-binding groove base, a
circular permutation with respect to PDZ domains found
in proteases.
Length = 82
Score = 46.4 bits (111), Expect = 5e-07
Identities = 28/80 (35%), Positives = 45/80 (56%), Gaps = 9/80 (11%)
Query: 251 ELTLKRNGLGQLGFHVQPDG------LVTEVEHMGLAYQEGLKQGCRL--ICKVAVSTLS 302
+TL+++ G LGF ++ V+ VE G A + GL+ G R+ + V+V L+
Sbjct: 3 TVTLRKDPGGGLGFSLRGGKDSGGGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLT 62
Query: 303 HDQMVDLLKTSSL-VTVTVI 321
H++ V+LLK S VT+TV
Sbjct: 63 HEEAVELLKNSGDEVTLTVR 82
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some PDZs
have been shown to bind C-terminal polypeptides; others
appear to bind internal (non-C-terminal) polypeptides.
Different PDZs possess different binding specificities.
Length = 85
Score = 43.1 bits (102), Expect = 1e-05
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 10/82 (12%)
Query: 250 QELTLKRNGLGQLGFHVQPDG------LVTEVEHMGLAYQEGLKQGCRL--ICKVAVSTL 301
+ + L++ G G LGF + +V+ V A + GL+ G + + +V L
Sbjct: 3 RLVELEKGG-GGLGFSLVGGKDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGL 61
Query: 302 SHDQMVDLLK-TSSLVTVTVIP 322
+H + VDLLK VT+TV+
Sbjct: 62 THLEAVDLLKKAGGKVTLTVLR 83
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 41.5 bits (98), Expect = 4e-05
Identities = 28/80 (35%), Positives = 43/80 (53%), Gaps = 9/80 (11%)
Query: 251 ELTLKRNGLGQLGFHVQPDG------LVTEVEHMGLAYQEGLKQGCRL--ICKVAVSTLS 302
E+TL+++G G LGF + V+EV G A GL++G R+ I + LS
Sbjct: 1 EVTLEKSGRGGLGFSLVGGSDGDPGIFVSEVLPGGAAEAGGLQEGDRILSINGQDLENLS 60
Query: 303 HDQMVDLLK-TSSLVTVTVI 321
HD+ V LK + VT+T++
Sbjct: 61 HDEAVLALKGSGGEVTLTIL 80
>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 = 32.7 bits (75), Expect = 0.047
Identities = 13/39 (33%), Positives = 25/39 (64%)
Query: 172 LAISTDSVVLVEEQSRDLVFVAPAKSVLGWATSTNSLRL 210
L I+ +SV+ V+E++++++ V P ++ WA S S L
Sbjct: 22 LGITKESVLRVDEETKEVLKVWPLTTIKRWAASPKSFTL 60
>gnl|CDD|200598 cd10976, CE4_CDA_like_3, Putative catalytic domain of
uncharacterized bacterial hypothetical proteins similar
to insect chitin deacetylase-like proteins. The family
includes many uncharacterized bacterial hypothetical
proteins that show high sequence similarity to insect
chitin deacetylase-like proteins. Chitin deacetylases
(CDAs, EC 3.5.1.41) are secreted metalloproteins
belonging to a family of extracellular chitin-modifying
enzymes that catalyze the N-deacetylation of chitin, a
beta-1,4-linked N-acetylglucosamine polymer, to form
chitosan, a polymer of beta-(1,4)-linked d-glucosamine
residues.
Length = 299
Score = 32.7 bits (75), Expect = 0.24
Identities = 7/31 (22%), Positives = 14/31 (45%)
Query: 255 KRNGLGQLGFHVQPDGLVTEVEHMGLAYQEG 285
++ G +GF + + + AY+EG
Sbjct: 55 QKAGRSNIGFAGSRQEVADRLRQLNAAYREG 85
>gnl|CDD|175999 cd04033, C2_NEDD4_NEDD4L, C2 domain present in the Human neural
precursor cell-expressed, developmentally down-regulated
4 (NEDD4) and NEDD4-like (NEDD4L/NEDD42). Nedd4 and
Nedd4-2 are two of the nine members of the Human Nedd4
family. All vertebrates appear to have both Nedd4 and
Nedd4-2 genes. They are thought to participate in the
regulation of epithelial Na+ channel (ENaC) activity.
They also have identical specificity for ubiquitin
conjugating enzymes (E2). Nedd4 and Nedd4-2 are
composed of a C2 domain, 2-4 WW domains, and a ubiquitin
ligase Hect domain. Their WW domains can bind PPxY (PY)
or LPSY motifs, and in vitro studies suggest that WW3
and WW4 of both proteins bind PY motifs in the key
substrates, with WW3 generally exhibiting higher
affinity. Most Nedd4 family members, especially Nedd4-2,
also have multiple splice variants, which might play
different roles in regulating their substrates. C2
domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions.
Length = 133
Score = 28.5 bits (64), Expect = 2.3
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 11/79 (13%)
Query: 1 MDPDEIEKVLFENIPLEHQ--------NWLGMDDNLGPVAISLKREKVEY-TQESQQMYR 51
++P E+ F P EH+ N L DD LG V + L E E + ++
Sbjct: 50 LNPKWNEEFFFRVNPREHRLLFEVFDENRLTRDDFLGQVEVPLNNLPTETPGNERRYTFK 109
Query: 52 YRLLIRTSELKTGKIGRNL 70
LL S ++ +L
Sbjct: 110 DYLLRPRSS--KSRVKGHL 126
>gnl|CDD|227340 COG5007, COG5007, Predicted transcriptional regulator, BolA
superfamily [Transcription].
Length = 80
Score = 26.6 bits (59), Expect = 5.1
Identities = 13/50 (26%), Positives = 23/50 (46%)
Query: 1 MDPDEIEKVLFENIPLEHQNWLGMDDNLGPVAISLKREKVEYTQESQQMY 50
MD +EI+ +L +PLE G + +A+S + + Q +Y
Sbjct: 1 MDNEEIKSLLENALPLEEVEVEGDGSHFQVIAVSEEFAGKSRVKRQQLVY 50
>gnl|CDD|211349 cd07246, Glo_EDI_BRP_like_8, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping. The structures of this family demonstrate
domain swapping, which is shared by glyoxalase I and
antibiotic resistance proteins.
Length = 123
Score = 27.1 bits (61), Expect = 6.3
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 6/47 (12%)
Query: 165 GSLMHCVLAISTDSVVLVEEQSRDLVFVAPAKSVLGWATSTNSLRLY 211
G +MH L I DSV+++ + F S W + SL LY
Sbjct: 36 GRIMHAELRIG-DSVLMLAD-----EFPEHGASPASWGGTPVSLHLY 76
>gnl|CDD|224552 COG1637, COG1637, Predicted nuclease of the RecB family [DNA
replication, recombination, and repair].
Length = 253
Score = 28.1 bits (63), Expect = 6.9
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 22 LGMDDNLGPVAISLKREKVEYTQESQQMYRYRLLIRT 58
LG D+ V I LKR K + S Q+ RY L+R
Sbjct: 166 LGRDERGNIVIIELKRRKAGLSAVS-QLKRYVELLRE 201
>gnl|CDD|235218 PRK04081, PRK04081, hypothetical protein; Provisional.
Length = 207
Score = 27.8 bits (62), Expect = 7.0
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 13/59 (22%)
Query: 66 IGRNL--SKSGQNTAKRSNHLNQTYERS---FSPPRSSNS--------SGYGTGSSSRS 111
IG L +++ QN +R+ Q Y+RS F+ S++S SG+ GSSS S
Sbjct: 140 IGNKLFNNQNYQNQRQRTYKSPQAYQRSQNSFNKAASASSSSGSSSKKSGFFGGSSSAS 198
>gnl|CDD|217441 pfam03232, COQ7, Ubiquinone biosynthesis protein COQ7. Members of
this family contain two repeats of about 90 amino acids,
that contains two conserved motifs. One of these DXEXXH
may be part of an enzyme active site.
Length = 170
Score = 27.5 bits (62), Expect = 7.6
Identities = 8/34 (23%), Positives = 13/34 (38%), Gaps = 9/34 (26%)
Query: 274 EVEHMGLAYQEG---------LKQGCRLICKVAV 298
E+EH A + G L + C+ A+
Sbjct: 131 ELEHRDTAIEHGAEQAPAYPLLSGAIKAGCRAAI 164
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
0.316 0.131 0.382
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,007,650
Number of extensions: 1593727
Number of successful extensions: 1204
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1199
Number of HSP's successfully gapped: 20
Length of query: 342
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 244
Effective length of database: 6,590,910
Effective search space: 1608182040
Effective search space used: 1608182040
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: 59 (26.6 bits)