RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3499
(108 letters)
>gnl|CDD|241244 cd01208, PTB_X11, X11-like Phosphotyrosine-binding (PTB) domain.
The function of the neuronal protein X11 is unknown to
date. X11 has a PTB domain followed by two PDZ domains.
PTB domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 161
Score = 167 bits (426), Expect = 5e-55
Identities = 68/141 (48%), Positives = 79/141 (56%), Gaps = 39/141 (27%)
Query: 5 PSVLIEGVLFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRIK----------------- 47
P LI+GV+F A YLGSTQL+ E PTKS RM QA+EAVSRIK
Sbjct: 1 PEDLIDGVIFGANYLGSTQLLSERNPTKSVRMQQAQEAVSRIKAPEGESQPSTEVDLFIS 60
Query: 48 ------------EIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEP-------PKIS 88
E MMDHALRTISYIADIG++VVLMARRR + E +
Sbjct: 61 TERIKVLNADTQETMMDHALRTISYIADIGNIVVLMARRRMPRSSSQECIETTPPAQEGK 120
Query: 89 RTPKMICHVFESDE---IASA 106
R KMICHVFES++ IA +
Sbjct: 121 RQYKMICHVFESEDAQLIAQS 141
>gnl|CDD|144292 pfam00640, PID, Phosphotyrosine interaction domain (PTB/PID).
Length = 133
Score = 61.6 bits (150), Expect = 2e-13
Identities = 31/130 (23%), Positives = 47/130 (36%), Gaps = 53/130 (40%)
Query: 14 FRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRI--------------------------- 46
F +YLGS ++ E RM A EA+SR+
Sbjct: 1 FAVKYLGSVEVPEE-------RMDVANEAISRLKMAKNAKRAGLTGHRQPGTSIDLSIST 53
Query: 47 ----------KEIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMICH 96
KE++ DH LR+IS+IA + ++ A + T + CH
Sbjct: 54 DGLKLLDEKTKELLHDHPLRSISFIAVGD--PDDLRTFAYI---AADGA----TGRFACH 104
Query: 97 VFESDEIASA 106
VFE ++ A
Sbjct: 105 VFECEKGAED 114
>gnl|CDD|214675 smart00462, PTB, Phosphotyrosine-binding domain,
phosphotyrosine-interaction (PI) domain. PTB/PI domain
structure similar to those of pleckstrin homology (PH)
and IRS-1-like PTB domains.
Length = 134
Score = 41.1 bits (97), Expect = 9e-06
Identities = 25/130 (19%), Positives = 45/130 (34%), Gaps = 52/130 (40%)
Query: 10 EGVLFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRI----------------------- 46
GV FR +YLGS ++ ++ + +EA+ ++
Sbjct: 2 SGVSFRVKYLGSVEV------PEARGLQVVQEAIRKLRAAQGSEKKEPQKVILSISSRGV 55
Query: 47 -------KEIMMDHALRTISYIADI---GDLVVLMARRRFVSQEADEPPKISRTPKMICH 96
K ++ +H LR IS+ A D+ +AR + + CH
Sbjct: 56 KLIDEDTKAVLHEHPLRRISFCAVGPDDLDVFGYIARD-------------PGSSRFACH 102
Query: 97 VFESDEIASA 106
VF ++ A
Sbjct: 103 VFRCEKAAED 112
>gnl|CDD|241303 cd01273, PTB_CED-6, Cell death protein 6 homolog (CED-6/GULP1)
Phosphotyrosine-binding (PTB) domain. CED6 (also known
as GULP1: engulfment adaptor PTB domain containing 1) is
an adaptor protein involved in the specific recognition
and engulfment of apoptotic cells. CED6 has been shown
to interact with the cytoplasmic tail of another protein
involved in the engulfment of apoptotic cells, CED1.
CED6 has a C-terminal PTB domain, which can bind to NPXY
motifs. PTB domains have a common PH-like fold and are
found in various eukaryotic signaling molecules. This
domain was initially shown to binds peptides with a NPXY
motif with differing requirements for phosphorylation of
the tyrosine, although more recent studies have found
that some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 144
Score = 34.9 bits (81), Expect = 0.002
Identities = 37/132 (28%), Positives = 57/132 (43%), Gaps = 40/132 (30%)
Query: 3 HEPSVLIEG-VLFRARYLGSTQ--------LVCEG--------QPTKS--TRMMQAEEAV 43
H P LI+G V++ ++LG T+ +V E Q KS ++ + E +
Sbjct: 2 HPPEALIKGHVVYLVKFLGCTEVDQPKGTEVVKEAIRKLKFARQIKKSEGAKLPKVELQI 61
Query: 44 S---------RIKEIMMDHALRTISYIAD-IGDLVVLMARRRFVSQEADEPPKISRTPKM 93
S + KEIM L IS+ AD D +R S A K S + K
Sbjct: 62 SIDGVKIQDPKTKEIMHQFPLHRISFCADDKTD-------KRIFSFIA----KDSESNKH 110
Query: 94 ICHVFESDEIAS 105
+C VF+S+++A
Sbjct: 111 LCFVFDSEKLAE 122
>gnl|CDD|241304 cd01274, PTB_Anks, Ankyrin repeat and sterile alpha motif (SAM)
domain-containing (Anks) protein family
Phosphotyrosine-binding (PTB) domain. Both AIDA-1b
(AbetaPP intracellular domain-associated protein 1b) and
Odin (also known as ankyrin repeat and sterile alpha
motif domain-containing 1A; ANKS1A) belong to the Anks
protein family. Both of these family members interacts
with the EphA8 receptor. Ank members consists of
ankyrin repeats, a SAM domain and a C-terminal PTB
domain which is crucial for interaction with the
juxtamembrane (JM) region of EphA8. PTB domains are
classified into three groups, namely,
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains of
which the Anks PTB is a member. PTB domains have a
common PH-like fold and are found in various eukaryotic
signaling molecules. This domain was initially shown to
binds peptides with a NPXY motif with differing
requirements for phosphorylation of the tyrosine,
although more recent studies have found that some types
of PTB domains can bind to peptides lack tyrosine
residues altogether. In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred by
residues amino-terminal to the phosphotyrosine. PTB
domains are classified into three groups:
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 146
Score = 34.5 bits (80), Expect = 0.003
Identities = 33/130 (25%), Positives = 53/130 (40%), Gaps = 40/130 (30%)
Query: 3 HEPSVLIEG-VLFRARYLGSTQLVCEGQPTKSTR-MMQ-------AEEAVSRI------- 46
H P LI G V + A YLGST L+ E + T+ST+ Q + + I
Sbjct: 5 HSPEKLITGSVNYEAHYLGST-LIKELRGTESTKDACQKLKKSTEEMKKIPTIILSISYK 63
Query: 47 ---------KEIMMDHALRTISYIA-DIGDLVVLMARRRFVSQEADEPPKISRTPKMICH 96
K ++ +H +R IS D DL +++++ +T CH
Sbjct: 64 GVKFIDATTKNLICEHEIRNISCACQDPEDLNTFA----YITKDL-------KTDHHYCH 112
Query: 97 VF--ESDEIA 104
VF + ++A
Sbjct: 113 VFCVLTVDLA 122
>gnl|CDD|241236 cd00934, PTB, Phosphotyrosine-binding (PTB) PH-like fold. PTB
domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to bind peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains.
Length = 119
Score = 33.7 bits (77), Expect = 0.005
Identities = 24/119 (20%), Positives = 43/119 (36%), Gaps = 34/119 (28%)
Query: 12 VLFRARYLGSTQLVCEG---QPTKSTRMMQAEEA------------VSRI---------K 47
V F+ +YLGS ++ ++ +++ VS K
Sbjct: 1 VSFQVKYLGSVEVGSPRGVKVIEEALKLLALLLKSSKRKPGPVLLEVSPEGVKLLDLDTK 60
Query: 48 EIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMICHVFESDEIASA 106
E+++ H L ISY D + A F+++ S CHVF+ ++ A
Sbjct: 61 ELLLRHPLSRISYCGRDPDNPKVFA---FIARR-------SGGSGFRCHVFQCEDKEEA 109
>gnl|CDD|241311 cd13157, PTB_tensin-related, Tensin-related Phosphotyrosine-binding
(PTB) domain. Tensin plays critical roles in renal
function, muscle regeneration, and cell migration. It
binds to actin filaments and interacts with the
cytoplasmic tails of beta-integrin via its PTB domain,
allowing tensin to link actin filaments to integrin
receptors. Tensin functions as a platform for assembly
and disassembly of signaling complexes at focal
adhesions by recruiting tyrosine-phosphorylated
signaling molecules, and also by providing interaction
sites for other proteins. In addition to its PTB
domain, it contains a C-terminal SH2 domain. PTB domains
have a common PH-like fold and are found in various
eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains.
Length = 129
Score = 29.6 bits (67), Expect = 0.17
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 13/54 (24%)
Query: 47 KEIMMDHALRTISYIADIGDLVVLMARRR--FVSQEADEPPKISRTPKMICHVF 98
+ ++M HALR +SY A + FV++ T + CHVF
Sbjct: 60 ETVLMAHALRRVSYST------CRPADAQFAFVARNP-----GGPTSRQYCHVF 102
>gnl|CDD|236667 PRK10249, PRK10249, phenylalanine transporter; Provisional.
Length = 458
Score = 29.2 bits (65), Expect = 0.34
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 5/43 (11%)
Query: 64 IGDLVVLMARRRFVSQEADEPPKISRTPKMICHVFESDEIASA 106
IG LVVL+A +V +++ P + MI H +S+ +ASA
Sbjct: 258 IGSLVVLLALYPWVEVKSNSSPFV-----MIFHNLDSNVVASA 295
>gnl|CDD|180295 PRK05862, PRK05862, enoyl-CoA hydratase; Provisional.
Length = 257
Score = 28.9 bits (65), Expect = 0.39
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 7/46 (15%)
Query: 35 RMMQAEEA-----VSRI--KEIMMDHALRTISYIADIGDLVVLMAR 73
RMM A EA VSR+ + ++D AL + IA V+MA+
Sbjct: 163 RMMDAAEAERAGLVSRVVPADKLLDEALAAATTIASFSLPAVMMAK 208
>gnl|CDD|241315 cd13161, PTB_TK_HMTK, Tyrosine-specific kinase/HM-motif TK
(TM/HMTK) Phosphotyrosine-binding (PTB) PH-like fold.
TK kinases catalyzes the transfer of the terminal
phosphate of ATP to a specific tyrosine residue on its
target protein. TK kinases play significant roles in
development and cell division. Tyrosine-protein kinases
can be divided into two subfamilies: receptor tyrosine
kinases, which have an intracellular tyrosine kinase
domain, a transmembrane domain and an extracellular
ligand-binding domain; and non-receptor (cytoplasmic)
tyrosine kinases, which are soluble, cytoplasmic
kinases. In HMTK the conserved His-Arg-Asp sequence
within the catalytic loop is replaced by a His-Met
sequence. TM/HMTK have are 2-3 N-terminal PTB domains.
PTB domains in TKs are thought to function analogously
to the membrane targeting (PH, myristoylation) and pTyr
binding (SH2) domains of Src subgroup kinases. PTB
domains have a common PH-like fold and are found in
various eukaryotic signaling molecules. This domain was
initially shown to binds peptides with a NPXY motif with
differing requirements for phosphorylation of the
tyrosine, although more recent studies have found that
some types of PTB domains can bind to peptides lack
tyrosine residues altogether. In contrast to SH2
domains, which recognize phosphotyrosine and adjacent
carboxy-terminal residues, PTB-domain binding
specificity is conferred by residues amino-terminal to
the phosphotyrosine. PTB domains are classified into
three groups: phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 120
Score = 27.2 bits (61), Expect = 1.1
Identities = 25/117 (21%), Positives = 43/117 (36%), Gaps = 36/117 (30%)
Query: 13 LFRARYLGSTQLVCEGQPTKSTRMMQAEEAVSRIKEIMMD----------HALRTI---- 58
+F A+YLGS + + AV R+K++ + +R +
Sbjct: 3 VFEAKYLGSVPV------KEPKGNEVVMAAVKRLKDLKLKPKKVVLVVTSEGIRVVERKT 56
Query: 59 ------SYIADIGDLVVLMARRR---FVSQEADEPPKISRTPKMICHVFESDEIASA 106
I DI + V ++ F+S + SR ++ CHVF + A A
Sbjct: 57 GEVLTNVPIKDISFVTVDPRDKKLFAFISHD-------SRLGRITCHVFRCKKGAQA 106
>gnl|CDD|131014 TIGR01959, nuoF_fam, NADH-quinone oxidoreductase, F subunit. This
model describes the F chain of complexes that resemble
NADH-quinone oxidoreductases. The electron acceptor is a
quinone, ubiquinone, in mitochondria and most bacteria,
including Escherichia coli, where the recommended gene
symbol is nuoF. This family does not have any members in
chloroplast or cyanobacteria, where the quinone may be
plastoquinone and NADH may be replaced by NADPH, nor in
Methanosarcina, where NADH is replaced by F420H2 [Energy
metabolism, Electron transport].
Length = 411
Score = 26.5 bits (59), Expect = 3.2
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 1 MPHEPSVLIEGVLFRARYLGSTQ 23
M +P LIEG++ A +G+ +
Sbjct: 93 MEFDPHQLIEGMIIAAYAIGAHR 115
>gnl|CDD|235553 PRK05672, dnaE2, error-prone DNA polymerase; Validated.
Length = 1046
Score = 26.4 bits (59), Expect = 3.2
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 6/31 (19%)
Query: 75 RFVSQEADEPPKI------SRTPKMICHVFE 99
RF+S E DEPP I R ++I +V+
Sbjct: 380 RFLSPERDEPPDIDVDFEHDRREEVIQYVYR 410
>gnl|CDD|100004 cd00448, YjgF_YER057c_UK114_family, YjgF, YER057c, and UK114
belong to a large family of proteins present in
bacteria, archaea, and eukaryotes with no definitive
function. The conserved domain is similar in structure
to chorismate mutase but there is no sequence
similarity and no functional connection. Members of
this family have been implicated in isoleucine (Yeo7,
Ibm1, aldR) and purine (YjgF) biosynthesis, as well as
threonine anaerobic degradation (tdcF) and
mitochondrial DNA maintenance (Ibm1). This domain
homotrimerizes forming a distinct intersubunit cavity
that may serve as a small molecule binding site.
Length = 107
Score = 25.2 bits (56), Expect = 4.8
Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 11/60 (18%)
Query: 38 QAEEAVSRIKEIM------MDHALRTISYIADIGDLVVLM-ARRRFVSQEADEPPKISRT 90
Q +A+ ++ ++ +D ++ Y+ D+ D + F E P +RT
Sbjct: 33 QTRQALENLEAVLEAAGGSLDDVVKVTVYLTDMADFAAVNEVYDEFF----GEGPPPART 88
>gnl|CDD|239093 cd02410, archeal_CPSF_KH, The archaeal cleavage and polyadenylation
specificity factor (CPSF) contains an N-terminal K
homology RNA-binding domain (KH). The archeal CPSFs are
predicted to be metal-dependent RNases belonging to the
beta-CASP family, a subgroup enzymes within the
metallo-beta-lactamase fold. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
domains are known to bind single-stranded RNA or DNA and
are found in a wide variety of proteins including
ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 145
Score = 25.3 bits (56), Expect = 6.3
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 12/70 (17%)
Query: 36 MMQAEEAVSRIKEIMMDHA-LRTISYIADIGDLVV-------LMAR----RRFVSQEADE 83
+ EEA+ I EI+ + A + I + D G++++ ++ + R +++E
Sbjct: 48 LKPPEEAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGW 107
Query: 84 PPKISRTPKM 93
PK+ RTP +
Sbjct: 108 APKVVRTPPI 117
>gnl|CDD|139913 PRK13853, PRK13853, type IV secretion system protein VirB4;
Provisional.
Length = 789
Score = 25.2 bits (55), Expect = 8.5
Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 9/86 (10%)
Query: 5 PSVLIEGVLFRARY-------LGSTQLVCEGQP--TKSTRMMQAEEAVSRIKEIMMDHAL 55
P VL + F R L S+Q+ G T+ + + +AE+A++ + +M H L
Sbjct: 262 PLVLTQSFSFLTRAQAHAKLSLKSSQMTSSGDKAVTQISELAEAEDALASNEFVMGSHHL 321
Query: 56 RTISYIADIGDLVVLMARRRFVSQEA 81
Y D+ L AR R +A
Sbjct: 322 SLCVYADDLNSLADRGARARTRLADA 347
>gnl|CDD|224806 COG1894, NuoF, NADH:ubiquinone oxidoreductase, NADH-binding (51 kD)
subunit [Energy production and conversion].
Length = 424
Score = 25.3 bits (56), Expect = 8.5
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 1 MPHEPSVLIEGVLFRARYLGSTQ--LVCEGQPTKSTRMMQA--EEA 42
M +P +LIEG++ A +G+T+ + G+ ++ +Q EEA
Sbjct: 103 MEGDPHLLIEGMIIAAYAVGATKGYIYIRGEYPEAIERLQKAIEEA 148
>gnl|CDD|147082 pfam04740, LXG, LXG domain of WXG superfamily. This domain is
present is the N-terminal region of a group of
polymorphic toxin proteins in bacteria. It is predicted
to use Type VII secretion pathway to mediate export of
bacterial toxins.
Length = 204
Score = 24.9 bits (55), Expect = 9.4
Identities = 7/34 (20%), Positives = 15/34 (44%)
Query: 37 MQAEEAVSRIKEIMMDHALRTISYIADIGDLVVL 70
+ + + + +E + S +A I D+V L
Sbjct: 102 HELKNGLKKAEEKTEELKDAINSILASISDIVHL 135
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
0.321 0.133 0.378
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,467,782
Number of extensions: 462547
Number of successful extensions: 415
Number of sequences better than 10.0: 1
Number of HSP's gapped: 408
Number of HSP's successfully gapped: 32
Length of query: 108
Length of database: 10,937,602
Length adjustment: 73
Effective length of query: 35
Effective length of database: 7,699,760
Effective search space: 269491600
Effective search space used: 269491600
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: 53 (24.2 bits)