RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5022
(359 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 = 247 bits (634), Expect = 1e-82
Identities = 93/169 (55%), Positives = 110/169 (65%), Gaps = 20/169 (11%)
Query: 16 PEDPVVDTGLGPGTLFRLKFLGSVQVDEDDPKCCKRRVKKVMVEEA-----APEGETQPS 70
PED L G +F +LGS Q+ + + V+ +EA APEGE+QPS
Sbjct: 1 PED------LIDGVIFGANYLGSTQLLSERNPT--KSVRMQQAQEAVSRIKAPEGESQPS 52
Query: 71 TEVDLFISTEKIMVLNTDLKEIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEP--- 127
TEVDLFISTE+I VLN D +E MMDHALRTISYIADIG++VVLMARRR + E
Sbjct: 53 TEVDLFISTERIKVLNADTQETMMDHALRTISYIADIGNIVVLMARRRMPRSSSQECIET 112
Query: 128 ----PKISRTPKMICHVFESDEAQFIAQSIGQAFQVAYMEFLKANGIED 172
+ R KMICHVFES++AQ IAQSIGQAF VAY EFL+ANGI
Sbjct: 113 TPPAQEGKRQYKMICHVFESEDAQLIAQSIGQAFSVAYQEFLRANGINP 161
Score = 34.9 bits (81), Expect = 0.026
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 265 VAYMEFLKANGIED 278
VAY EFL+ANGI
Sbjct: 148 VAYQEFLRANGINP 161
>gnl|CDD|144292 pfam00640, PID, Phosphotyrosine interaction domain (PTB/PID).
Length = 133
Score = 116 bits (292), Expect = 6e-32
Identities = 51/142 (35%), Positives = 80/142 (56%), Gaps = 14/142 (9%)
Query: 31 FRLKFLGSVQVDEDDPKCCKRRVKKVMVEE----AAPEGETQPSTEVDLFISTEKIMVLN 86
F +K+LGSV+V E+ + ++ + + A G QP T +DL IST+ + +L+
Sbjct: 1 FAVKYLGSVEVPEERMDVANEAISRLKMAKNAKRAGLTGHRQPGTSIDLSISTDGLKLLD 60
Query: 87 TDLKEIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMICHVFESDE- 145
KE++ DH LR+IS+IA + ++ A + T + CHVFE ++
Sbjct: 61 EKTKELLHDHPLRSISFIAVGD--PDDLRTFAYI---AADGA----TGRFACHVFECEKG 111
Query: 146 AQFIAQSIGQAFQVAYMEFLKA 167
A+ IAQ++GQAF VAY EFL+A
Sbjct: 112 AEDIAQAVGQAFAVAYQEFLRA 133
>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 = 90.5 bits (225), Expect = 3e-22
Identities = 48/150 (32%), Positives = 76/150 (50%), Gaps = 21/150 (14%)
Query: 26 GPGTLFRLKFLGSVQVDEDDP-KCCKRRVKKVMVEEAAPEGETQPSTEVDLFISTEKIMV 84
G G FR+K+LGSV+V E + + ++K+ AA E + +V L IS+ + +
Sbjct: 1 GSGVSFRVKYLGSVEVPEARGLQVVQEAIRKLR---AAQGSEKKEPQKVILSISSRGVKL 57
Query: 85 LNTDLKEIMMDHALRTISYIADI---GDLVVLMARRRFVSQEADEPPKISRTPKMICHVF 141
++ D K ++ +H LR IS+ A D+ +AR + + CHVF
Sbjct: 58 IDEDTKAVLHEHPLRRISFCAVGPDDLDVFGYIARD-------------PGSSRFACHVF 104
Query: 142 ESDE-AQFIAQSIGQAFQVAYMEFLKANGI 170
++ A+ IA +IGQAFQ+AY LKA
Sbjct: 105 RCEKAAEDIALAIGQAFQLAYELKLKARSE 134
>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 = 65.8 bits (161), Expect = 3e-13
Identities = 48/144 (33%), Positives = 73/144 (50%), Gaps = 18/144 (12%)
Query: 31 FRLKFLGSVQVDEDDPK---CCKRRVKKVMVEEAAPEGETQPSTEVDLFISTEKIMVLNT 87
+ +KFLG +VD+ PK K ++K+ + E +V+L IS + + + +
Sbjct: 14 YLVKFLGCTEVDQ--PKGTEVVKEAIRKLKFARQIKKSEGAKLPKVELQISIDGVKIQDP 71
Query: 88 DLKEIMMDHALRTISYIAD-IGDLVVLMARRRFVSQEADEPPKISRTPKMICHVFESD-E 145
KEIM L IS+ AD D +R S A K S + K +C VF+S+
Sbjct: 72 KTKEIMHQFPLHRISFCADDKTD-------KRIFSFIA----KDSESNKHLCFVFDSEKL 120
Query: 146 AQFIAQSIGQAFQVAYMEFLKANG 169
A+ I +IGQAF +AY FL++NG
Sbjct: 121 AEEITLTIGQAFDLAYKRFLESNG 144
>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 = 64.5 bits (157), Expect = 7e-13
Identities = 35/129 (27%), Positives = 57/129 (44%), Gaps = 15/129 (11%)
Query: 31 FRLKFLGSVQVDEDDPKCCKRRVKKVMVEEAAPEGETQPSTEVDLFISTEKIMVLNTDLK 90
F++K+LGSV+V K++ V L +S E + +L+ D K
Sbjct: 3 FQVKYLGSVEVGSPRGVKVIEEALKLLALLLKSSKRK--PGPVLLEVSPEGVKLLDLDTK 60
Query: 91 EIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMICHVFESD---EAQ 147
E+++ H L ISY D + A F+++ S CHVF+ + EA+
Sbjct: 61 ELLLRHPLSRISYCGRDPDNPKVFA---FIARR-------SGGSGFRCHVFQCEDKEEAE 110
Query: 148 FIAQSIGQA 156
I ++GQA
Sbjct: 111 EILNALGQA 119
>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 = 55.3 bits (134), Expect = 5e-10
Identities = 23/47 (48%), Positives = 30/47 (63%)
Query: 313 ICSLLRGGIAERGGVRVGHRIIEINNQSVVAVPHEKIVNLLATSVGE 359
+ + GG AERGG+RVG RI+E+N SV + HE+ V LL S E
Sbjct: 30 VSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELLKNSGDE 76
Score = 48.7 bits (117), Expect = 9e-08
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 205 KEVVVPKAKGEILGVVIVESGWGSMLPTVVIANLAPAGAAARCGQLNIGDQIIAVNGVSL 264
+ V + K G LG + + ++ + P G A R G L +GD+I+ VNGVS+
Sbjct: 2 RTVTLRKDPGGGLGFSLRGGKDSGG--GIFVSRVEPGGPAER-GGLRVGDRILEVNGVSV 58
Query: 265 V 265
Sbjct: 59 E 59
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 53.8 bits (130), Expect = 1e-09
Identities = 19/47 (40%), Positives = 28/47 (59%)
Query: 313 ICSLLRGGIAERGGVRVGHRIIEINNQSVVAVPHEKIVNLLATSVGE 359
+ +L GG AE GG++ G RI+ IN Q + + H++ V L S GE
Sbjct: 28 VSEVLPGGAAEAGGLQEGDRILSINGQDLENLSHDEAVLALKGSGGE 74
Score = 51.1 bits (123), Expect = 1e-08
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 206 EVVVPKAKGEILGVVIVESGWGSMLPTVVIANLAPAGAAARCGQLNIGDQIIAVNGVSLV 265
EV + K+ LG +V G P + ++ + P GAA G L GD+I+++NG L
Sbjct: 1 EVTLEKSGRGGLGFSLVGGSDGD--PGIFVSEVLPGGAAEA-GGLQEGDRILSINGQDLE 57
>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 = 54.6 bits (132), Expect = 2e-09
Identities = 35/137 (25%), Positives = 61/137 (44%), Gaps = 25/137 (18%)
Query: 30 LFRLKFLGSVQVDEDDPK-CCKRRVKKVMVEEAAPEGETQPSTEVDLFISTEKIMVLNTD 88
+F K+LGSV V E VK++ + P +V L +++E I V+
Sbjct: 3 VFEAKYLGSVPVKEPKGNEVVMAAVKRLKDLKLKP-------KKVVLVVTSEGIRVVERK 55
Query: 89 LKEIMMDHALRTISYIADIGDLVVLMARRR---FVSQEADEPPKISRTPKMICHVFES-D 144
E++ + ++ IS++ V ++ F+S + SR ++ CHVF
Sbjct: 56 TGEVLTNVPIKDISFVT------VDPRDKKLFAFISHD-------SRLGRITCHVFRCKK 102
Query: 145 EAQFIAQSIGQAFQVAY 161
AQ I +I +AF+ A
Sbjct: 103 GAQAICDTIAEAFKAAA 119
>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 = 53.5 bits (129), Expect = 6e-09
Identities = 36/133 (27%), Positives = 60/133 (45%), Gaps = 19/133 (14%)
Query: 34 KFLGSVQVDEDDPKCCKRRVKKVMVEEAAPEGETQPSTEVDLFISTEKIMVLNTDLKEIM 93
+++GS V D + V K + ++ ++ V L IS I + + D + ++
Sbjct: 7 QYIGSFPVSGLDLQERADSVGKQL--DSLKPSTSR-GRPVILSISLSGIKICSEDGETVL 63
Query: 94 MDHALRTISYIADIGDLVVLMARRR--FVSQEADEPPKISRTPKMICHVFES---DEAQF 148
M HALR +SY A + FV++ P T + CHVF + EAQ
Sbjct: 64 MAHALRRVSYST------CRPADAQFAFVARN----PG-GPTSRQYCHVFVTPSPGEAQE 112
Query: 149 IAQSIGQAFQVAY 161
+ + +AFQ+AY
Sbjct: 113 LNLLLCRAFQLAY 125
>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 = 46.6 bits (111), Expect = 5e-07
Identities = 17/47 (36%), Positives = 29/47 (61%)
Query: 313 ICSLLRGGIAERGGVRVGHRIIEINNQSVVAVPHEKIVNLLATSVGE 359
+ S++ G A + G+RVG I+E+N SV + H + V+LL + G+
Sbjct: 30 VSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHLEAVDLLKKAGGK 76
Score = 42.4 bits (100), Expect = 2e-05
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 205 KEVVVPKAKGEILGVVIVESGWGSMLPTVVIANLAPAGAAARCGQLNIGDQIIAVNGVSL 264
+ V + K G LG +V VV++++ P AA+ G L +GD I+ VNG S+
Sbjct: 3 RLVELEK-GGGGLGFSLVGGKDEGG--GVVVSSVVPGSPAAKAG-LRVGDVILEVNGTSV 58
>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 = 48.4 bits (116), Expect = 5e-07
Identities = 36/145 (24%), Positives = 63/145 (43%), Gaps = 26/145 (17%)
Query: 31 FRLKFLGSVQVDE----DDPKCCKRRVKKVMVEEAAPEGETQPSTEVDLFISTEKIMVLN 86
+ +LGS + E + K +++KK E + + L IS + + ++
Sbjct: 17 YEAHYLGSTLIKELRGTESTKDACQKLKK-------STEEMKKIPTIILSISYKGVKFID 69
Query: 87 TDLKEIMMDHALRTISYIA-DIGDLVVLMARRRFVSQEADEPPKISRTPKMICHVF---E 142
K ++ +H +R IS D DL +++++ +T CHVF
Sbjct: 70 ATTKNLICEHEIRNISCACQDPEDLNTFA----YITKDL-------KTDHHYCHVFCVLT 118
Query: 143 SDEAQFIAQSIGQAFQVAYMEFLKA 167
D A I ++GQAF+VAY L+A
Sbjct: 119 VDLAYEIILTLGQAFEVAYQLALQA 143
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization through
PDZ-PDZ domain interactions adds to the domain's
versatility, and PDZ domain-mediated interactions may be
modulated dynamically through target phosphorylation.
Some PDZ domains play a role in scaffolding
supramolecular complexes. PDZ domains are found in
diverse signaling proteins in bacteria, archebacteria,
and eurkayotes. This CD contains two distinct structural
subgroups with either a N- or C-terminal beta-strand
forming the peptide-binding groove base. The circular
permutation placing the strand on the N-terminus appears
to be found in Eumetazoa only, while the C-terminal
variant is found in all three kingdoms of life, and
seems to co-occur with protease domains. PDZ domains
have been named after PSD95(post synaptic density
protein), DlgA (Drosophila disc large tumor suppressor),
and ZO1, a mammalian tight junction protein.
Length = 70
Score = 45.0 bits (107), Expect = 2e-06
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 313 ICSLLRGGIAERGGVRVGHRIIEINNQSVVAVPHEKIVNLLATSVGE 359
+ S+ G AER G++ G I+ +N V + E + LL VGE
Sbjct: 17 VLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEVGE 63
Score = 31.1 bits (71), Expect = 0.10
Identities = 14/32 (43%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 233 VVIANLAPAGAAARCGQLNIGDQIIAVNGVSL 264
VV+ ++ P A R G L GD I+AVNG +
Sbjct: 15 VVVLSVEPGSPAERAG-LQAGDVILAVNGTDV 45
>gnl|CDD|241248 cd01212, PTB_JIP, JNK-interacting protein-like (JIP)
Phosphotyrosine-binding (PTB) domain. JIP is a
mitogen-activated protein kinase scaffold protein. JIP
consists of a C-terminal SH3 domain, followed by a PTB
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. This
cd is part of the Dab-like subgroup.
Length = 149
Score = 44.6 bits (106), Expect = 1e-05
Identities = 19/37 (51%), Positives = 25/37 (67%), Gaps = 2/37 (5%)
Query: 138 CHVFESDE-AQFIAQSIGQAFQVAYMEFLK-ANGIED 172
CHVF S E + +A+S+G+AFQ Y EFL+ A ED
Sbjct: 109 CHVFVSQESTRPVAESVGRAFQRFYQEFLEYACPTED 145
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 45.0 bits (107), Expect = 3e-05
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 298 GDELQMFAKKELQKEICSLLRGGIAERGGVRVGHRIIEINNQSVVAVPHEKIVNLLATSV 357
G ELQM + ++ S + G A + G++ G II+I+ +SV V ++ V L+
Sbjct: 103 GIELQMEDIGGV--KVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKP 160
Query: 358 GE 359
G
Sbjct: 161 GT 162
Score = 28.5 bits (64), Expect = 6.9
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 233 VVIANLAPAGAAARCGQLNIGDQIIAVNGVS 263
V + + AA+ G + GD II ++G S
Sbjct: 114 VKVVSPIDGSPAAKAG-IKPGDVIIKIDGKS 143
>gnl|CDD|241313 cd13159, PTB_LDLRAP-mammal-like, Low Density Lipoprotein Receptor
Adaptor Protein 1 (LDLRAP1) in mammals and similar
proteins Phosphotyrosine-binding (PTB) PH-like fold.
The null mutations in the LDL receptor adaptor protein 1
(LDLRAP1) gene, which serves as an adaptor for LDLR
endocytosis in the liver, causes autosomal recessive
hypercholesterolemia (ARH). LDLRAP1 contains a single
PTB 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. This
cd contains mammals, insects, and sponges.
Length = 123
Score = 41.9 bits (99), Expect = 6e-05
Identities = 36/136 (26%), Positives = 59/136 (43%), Gaps = 19/136 (13%)
Query: 28 GTLFRLKFLGSVQVDE-DDPKCCKRRVKKVMVEEAAPEGETQPSTEVDLFISTEKIMVLN 86
G F LK+LGS V++ VK ++ A + Q +V L +S + I V +
Sbjct: 2 GVTFYLKYLGSTLVEKPKGEGATAEAVKTIIATAKASGKKLQ---KVTLTVSPKGIKVTD 58
Query: 87 TDLKEIMMDHALRTISY-IADIGDLVVLMARRRFVSQEADEPPKISRTPKMICHVF---E 142
+ E +++ ++ ISY AD V F++Q D K+ CH F +
Sbjct: 59 SATNETILEVSIYRISYCTADANHDKVFA----FIAQNQD-------NEKLECHAFLCAK 107
Query: 143 SDEAQFIAQSIGQAFQ 158
AQ + ++ QAF
Sbjct: 108 RKMAQAVTLTVAQAFN 123
>gnl|CDD|241245 cd01209, PTB_Shc, Shc-like phosphotyrosine-binding (PTB) domain.
Shc is a substrate for receptor tyrosine kinases, which
can interact with phosphoproteins at NPXY motifs. Shc
contains an PTB domain followed by an 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. This
cd is part of the Shc-like subgroup.
Length = 170
Score = 41.8 bits (99), Expect = 1e-04
Identities = 42/175 (24%), Positives = 72/175 (41%), Gaps = 46/175 (26%)
Query: 24 GLGPGTLFRLKFLGSVQVD----------------EDDPKCC----------KRRVKKVM 57
GLGPG + ++++G ++V E + C K+R K +
Sbjct: 10 GLGPGVSYPVRYMGCIEVLQSMRSLDFNTRTQVTREAINRVCEAVPGAKGAKKKRKSKAL 69
Query: 58 VEEAAPEGETQPSTEVDLFISTEKIMVLNTDLKEIMMDHALRTISY----IADIGDLVVL 113
+ L IST + + D +I+ +H +++IS+ D D V
Sbjct: 70 SSILGKSNLQFAGMNISLTISTSGLNLSTPDTGQIIANHHMQSISFASGGDPDTTDYVAY 129
Query: 114 MARRRFVSQEADEPPKISRTPKMICHVFE-SDE-AQFIAQSIGQAFQVAYMEFLK 166
+A+ V+Q A CHV E D AQ + +IGQAF++ + ++LK
Sbjct: 130 VAKDP-VNQRA-------------CHVLECGDGLAQDVIATIGQAFELRFKQYLK 170
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function in
posttranslational protein processing, maturation, and
disassembly or degradation, in Bacteria, Archaea, and
plant chloroplasts. May be responsible for substrate
recognition and/or binding, 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
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 85
Score = 39.5 bits (93), Expect = 2e-04
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 312 EICSLLRGGIAERGGVRVGHRIIEINNQSVVAVPHEKIVNLLATSVG 358
I S+L G A + G++ G I+ I+ + V + E +V LL G
Sbjct: 16 VITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAG 62
Score = 29.5 bits (67), Expect = 0.58
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 217 LGVVIVESGWGSMLPTVVIANLAPAGAAARCGQLNIGDQIIAVNGVSL 264
+G+ + G +VI ++ P AA+ G + GD I+A++G +
Sbjct: 4 IGLELKYDDGG-----LVITSVLPGSPAAKAG-IKAGDIIVAIDGEPV 45
>gnl|CDD|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be responsible
for substrate recognition and/or binding, 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
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 79
Score = 35.3 bits (82), Expect = 0.004
Identities = 18/46 (39%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 216 ILGVVIVESGWGSMLPTVVIANLAPAGAAARCGQLNIGDQIIAVNG 261
ILG V G VI + P AA+ G L GD+I+A+NG
Sbjct: 2 ILGFVP-----GGPPIEPVIGEVVPGSPAAKAG-LKAGDRILAING 41
Score = 28.4 bits (64), Expect = 1.5
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 319 GGIAERGGVRVGHRIIEINNQSV 341
G A + G++ G RI+ IN Q +
Sbjct: 22 GSPAAKAGLKAGDRILAINGQKI 44
>gnl|CDD|232883 TIGR00225, prc, C-terminal peptidase (prc). A C-terminal peptidase
with different substrates in different species including
processing of D1 protein of the photosystem II reaction
center in higher plants and cleavage of a peptide of 11
residues from the precursor form of penicillin-binding
protein in E.coli E.coli and H influenza have the most
distal branch of the tree and their proteins have an
N-terminal 200 amino acids that show no homology to
other proteins in the database [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Protein fate, Protein modification and repair].
Length = 334
Score = 35.8 bits (83), Expect = 0.029
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 312 EICSLLRGGIAERGGVRVGHRIIEINNQSVVAVPHEKIVNLL 353
I S G AE+ G++ G +II+IN +SV + + V L+
Sbjct: 65 VIVSPFEGSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALI 106
>gnl|CDD|109373 pfam00312, Ribosomal_S15, Ribosomal protein S15.
Length = 83
Score = 30.8 bits (70), Expect = 0.21
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 51 RRVKKVMVEEAAPEGETQPSTEVDLFISTEKIMVLNTDLKEIMMDHA 97
++ E E +T S EV + + TE+I+ L L+E D+
Sbjct: 1 MATGLIISEFLKAEKDT-GSVEVQIALLTERIVRLRKHLEEHKKDYH 46
>gnl|CDD|241312 cd13158, PTB_APPL, Adaptor protein containing PH domain, PTB
domain, and Leucine zipper motif (APPL; also called
DCC-interacting protein (DIP)-13alpha)
Phosphotyrosine-binding (PTB) domain. APPL interacts
with oncoprotein serine/threonine kinase AKT2, tumor
suppressor protein DCC (deleted in colorectal cancer),
Rab5, GIPC (GAIP-interacting protein, C terminus), human
follicle-stimulating hormone receptor (FSHR), and the
adiponectin receptors AdipoR1 and AdipoR2. There are two
isoforms of human APPL: APPL1 and APPL2, which share
about 50% sequence identity. APPL has a BAR and a PH
domain near its N terminus, and the two domains are
thought to function as a unit (BAR-PH domain).
C-terminal to this is a PTB domain. Lipid binding assays
show that the BAR, PH, and PTB domains can bind
phospholipids. 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 = 135
Score = 31.2 bits (71), Expect = 0.37
Identities = 28/132 (21%), Positives = 56/132 (42%), Gaps = 10/132 (7%)
Query: 30 LFRLKFLGSVQVDEDD-PKCCKRRVKKVMVEEAAPEGETQPSTEVDLFISTEKIMVLNTD 88
LF ++FLGS++V D + +++++ A TE L ++++ + +++
Sbjct: 12 LFIVRFLGSMEVKSDRTSEVIYEAMRQILAARAI--HNIFRMTESHLLVTSDCLRLIDPQ 69
Query: 89 LKEIMMDHALRTISYIADIGDLVVLMARRRFVSQEADEPPKISRTPKMICHVFESD-EAQ 147
+ L +S A + L FV + P C+VFES+ E +
Sbjct: 70 TQVTRARFPLANVSQFAAHQENKRLFG---FVVRSRGGD---GGRPSYSCYVFESNTEGE 123
Query: 148 FIAQSIGQAFQV 159
I +I A ++
Sbjct: 124 KICDAISLAKEI 135
>gnl|CDD|238487 cd00987, PDZ_serine_protease, PDZ domain of tryspin-like serine
proteases, such as DegP/HtrA, which are oligomeric
proteins involved in heat-shock response, chaperone
function, and apoptosis. May be responsible for
substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 90
Score = 29.9 bits (68), Expect = 0.40
Identities = 14/30 (46%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 233 VVIANLAPAGAAARCGQLNIGDQIIAVNGV 262
V++A++ P AA+ G L GD I+AVNG
Sbjct: 26 VLVASVDPGSPAAKAG-LKPGDVILAVNGK 54
Score = 27.6 bits (62), Expect = 3.1
Identities = 8/29 (27%), Positives = 16/29 (55%)
Query: 313 ICSLLRGGIAERGGVRVGHRIIEINNQSV 341
+ S+ G A + G++ G I+ +N + V
Sbjct: 28 VASVDPGSPAAKAGLKPGDVILAVNGKPV 56
>gnl|CDD|238490 cd00990, PDZ_glycyl_aminopeptidase, PDZ domain associated with
archaeal and bacterial M61 glycyl-aminopeptidases. May
be responsible for substrate recognition and/or binding,
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 protease-associated PDZ domains a C-terminal
beta-strand is presumed to form the peptide-binding
groove base, a circular permutation with respect to PDZ
domains found in Eumetazoan signaling proteins.
Length = 80
Score = 29.3 bits (66), Expect = 0.67
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 233 VVIANLAPAGAAARCGQLNIGDQIIAVNGVSLVAYMEFLK 272
+ + A + G L GD+++AVNG + A + LK
Sbjct: 14 GKVTFVRDDSPADKAG-LVAGDELVAVNGWRVDALQDRLK 52
>gnl|CDD|148706 pfam07256, DUF1435, Protein of unknown function (DUF1435). This
family consists of several hypothetical Enterobacterial
proteins of around 80 residues in length. The function
of this family is unknown.
Length = 78
Score = 29.3 bits (66), Expect = 0.72
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 223 ESGWGSMLPTVVIANLAPAGAAARCGQLNIGDQIIAVNGVSLVAYMEF 270
SGWG +LP +I LA AG +A Q +++ V G+ A M +
Sbjct: 7 GSGWGVLLPGALIPGLAWAGLSA--DQW----RVLIVVGLLATAVMLY 48
>gnl|CDD|182723 PRK10779, PRK10779, zinc metallopeptidase RseP; Provisional.
Length = 449
Score = 31.2 bits (71), Expect = 0.79
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 234 VIANLAPAGAAARCGQLNIGDQIIAVNGVSLVAYMEF 270
V+A + P AA++ G L GD+I+ V+G L + F
Sbjct: 224 VLAEVQPNSAASKAG-LQAGDRIVKVDGQPLTQWQTF 259
>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 = 29.2 bits (66), Expect = 0.95
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 13/67 (19%)
Query: 75 LFISTEKIMVLNTDLKEIMMDHALRTI--------SYIADIGDLVVLMARRRFVSQEADE 126
L I+ E ++ ++ + KE++ L TI S+ D GD + S + E
Sbjct: 22 LGITKESVLRVDEETKEVLKVWPLTTIKRWAASPKSFTLDFGDY-----SDNYYSVQTTE 76
Query: 127 PPKISRT 133
+IS+
Sbjct: 77 GEQISQL 83
>gnl|CDD|232801 TIGR00054, TIGR00054, RIP metalloprotease RseP. Members of this
nearly universal bacterial protein family are regulated
intramembrane proteolysis (RIP) proteases. Older and
synonymous gene symbols include yaeL in E. coli, mmpA in
Caulobacter crescentus, etc. This family includes a
region that hits the PDZ domain, found in a number of
proteins targeted to the membrane by binding to a
peptide ligand. The N-terminal region of this family
contains a perfectly conserved motif HEXGH as found in a
number of metalloproteinases, where the Glu is the
active site and the His residues coordinate the metal
cation [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 419
Score = 30.9 bits (70), Expect = 0.99
Identities = 24/129 (18%), Positives = 49/129 (37%), Gaps = 18/129 (13%)
Query: 192 GDELQMFAKKELQ--KEV--VVPKAKGEILGVVIVESGWGSMLPTV-----------VIA 236
GDE+ ++ K+V + GE + ++ E + V++
Sbjct: 148 GDEILSVNGNKIPGFKDVRQQIADIAGEPMVEILAERENWTFEVMKELIPRGPKIEPVLS 207
Query: 237 NLAPAGAAARCGQLNIGDQIIAVNGVSLVAYMEFLKA--NGIEDHSFVKEMDYQEVLNSQ 294
++ P A + G L GD I ++NG L ++ +F+ A +K E L+
Sbjct: 208 DVTPNSPAEKAG-LKEGDYIQSINGEKLRSWTDFVSAVKENPGKSMDIKVERNGETLSIS 266
Query: 295 EIFGDELQM 303
+ ++
Sbjct: 267 LTPEAKGKI 275
>gnl|CDD|223262 COG0184, RpsO, Ribosomal protein S15P/S13E [Translation,
ribosomal structure and biogenesis].
Length = 89
Score = 28.3 bits (64), Expect = 1.9
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 50 KRRVKKVMVEEAAPEGETQPSTEVDLFISTEKIMVLNTDLKEIMMDHALR 99
+++ E PE +T S EV L + TE+I L LKE DH R
Sbjct: 5 SEIKQELRDEYGIPEVDTG-SGEVQLALLTERINNLTEHLKEHKKDHHSR 53
>gnl|CDD|226483 COG3975, COG3975, Predicted protease with the C-terminal PDZ domain
[General function prediction only].
Length = 558
Score = 30.1 bits (68), Expect = 2.0
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 232 TVVIANLAPAGAAARCGQLNIGDQIIAVNGVSL 264
I + P G A + G L+ GD+I+A+NG+S
Sbjct: 463 HEKITFVFPGGPAYKAG-LSPGDKIVAINGISD 494
>gnl|CDD|236873 PRK11186, PRK11186, carboxy-terminal protease; Provisional.
Length = 667
Score = 29.9 bits (68), Expect = 2.3
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 234 VIANLAPAGAAARCGQLNIGDQIIAV 259
VI +L G AA+ +L++GD+I+ V
Sbjct: 258 VINSLVAGGPAAKSKKLSVGDKIVGV 283
>gnl|CDD|182774 PRK10846, PRK10846, bifunctional folylpolyglutamate synthase/
dihydrofolate synthase; Provisional.
Length = 416
Score = 29.3 bits (66), Expect = 3.4
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 230 LPTVVIANLAPAGAAARCGQLNIGDQII 257
LP V + N A A AA R L + +Q I
Sbjct: 250 LPNVPLPNAATALAALRASGLEVSEQAI 277
>gnl|CDD|223343 COG0265, DegQ, Trypsin-like serine proteases, typically
periplasmic, contain C-terminal PDZ domain
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 29.1 bits (65), Expect = 3.5
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 233 VVIANLAPAGAAARCGQLNIGDQIIAVNGV 262
V+ + P AA+ G + GD I AVNG
Sbjct: 272 AVVLGVLPGSPAAKAG-IKAGDIITAVNGK 300
>gnl|CDD|241251 cd01215, PTB_Dab, Disabled (Dab) Phosphotyrosine-binding domain.
Dab is a cystosolic adaptor protein, which binds to the
cytoplasmic tails of lipoprotein receptors, such as
ApoER2 and VLDLR, via its PTB domain. The dab PTB domain
has a preference for unphosphorylated tyrosine within an
NPxY motif. Additionally, the Dab PTB domain, which is
structurally similar to PH domains, binds to
phosphatidlyinositol phosphate 4,5 bisphosphate in a
manner characteristic of phosphoinositide binding PH
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 = 150
Score = 28.4 bits (64), Expect = 3.7
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 26 GPGTLFRLKFLGSVQVDED--DPKCCKRRVKKVMVEEAAPEGETQPSTEVDLFISTEKIM 83
G G F+ K +G +V D K C+ + K+ A + + + L IS E I
Sbjct: 13 GDGVRFKAKLIGIDEVPAARGD-KMCQDAMMKLKGIVKAAGSQGEHKQRIWLNISLEGIK 71
Query: 84 VLNTDLKEIMMDHALRTISYIA 105
+L+ ++ H + IS+IA
Sbjct: 72 ILDEKTGALLHHHPVHKISFIA 93
>gnl|CDD|233695 TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ
family. This family consists of a set proteins various
designated DegP, heat shock protein HtrA, and protease
DO. The ortholog in Pseudomonas aeruginosa is designated
MucD and is found in an operon that controls mucoid
phenotype. This family also includes the DegQ (HhoA)
paralog in E. coli which can rescue a DegP mutant, but
not the smaller DegS paralog, which cannot. Members of
this family are located in the periplasm and have
separable functions as both protease and chaperone.
Members have a trypsin domain and two copies of a PDZ
domain. This protein protects bacteria from thermal and
other stresses and may be important for the survival of
bacterial pathogens.// The chaperone function is
dominant at low temperatures, whereas the proteolytic
activity is turned on at elevated temperatures [Protein
fate, Protein folding and stabilization, Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 428
Score = 29.1 bits (66), Expect = 4.0
Identities = 36/139 (25%), Positives = 46/139 (33%), Gaps = 33/139 (23%)
Query: 233 VVIANLAPAGAAARCGQLNIGDQIIAVNGVS------LVAYMEFLKAN-----GIEDHSF 281
++A + P A + G L GD I +VNG L + LK GI
Sbjct: 259 ALVAQVLPGSPAEKAG-LKAGDVITSVNGKPISSFADLRRAIGTLKPGKKVTLGILRKG- 316
Query: 282 VKEMDYQEVL-NSQEIFGDELQMFAK---KELQKEICSLLR---------------GGIA 322
KE L S E F L EI LR G A
Sbjct: 317 -KEKTITVTLGASPEEQASSSNPFLGLTVANLSPEIRKELRLKGDVKGVVVTKVVSGSPA 375
Query: 323 ERGGVRVGHRIIEINNQSV 341
R G++ G I+ +N Q V
Sbjct: 376 ARAGLQPGDVILSVNQQPV 394
>gnl|CDD|215900 pfam00398, RrnaAD, Ribosomal RNA adenine dimethylase.
Length = 254
Score = 28.8 bits (65), Expect = 4.2
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 16 PEDPVVDTGLGPGTLFR--LKFLGSVQVDEDDPKCCKR 51
D V++ G G G L K V E DP+ KR
Sbjct: 29 ESDTVLEIGPGKGALTTELAKRAKQVVAIEIDPRLAKR 66
>gnl|CDD|241298 cd01268, PTB_Numb, Numb Phosphotyrosine-binding (PTB) domain. Numb
is a membrane associated adaptor protein which plays
critical roles in cell fate determination. Numb proteins
are involved in control of asymmetric cell division and
cell fate choice, endocytosis, cell adhesion, cell
migration, ubiquitination of specific substrates and a
number of signaling pathways (Notch, Hedgehog, p53).
Mutations in Numb plays a critical role in disease
(cancer). Numb has an N-terminal PTB domain and a
C-terminal NumbF 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. This
cd is part of the Dab-like subgroup.
Length = 135
Score = 27.7 bits (62), Expect = 6.1
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 31 FRLKFLGSVQVDED-DPKCCKRRVKKVMVEEAAPEGETQPSTEVDLFISTEKIMVLNTDL 89
F +K+LG V+V E + C+ +KK+ P L++S + + V++
Sbjct: 17 FPVKYLGCVEVGESRGMQVCEEALKKLKASRKKP-------VRAVLWVSGDGLRVVDEKT 69
Query: 90 KEIMMDHALRTISYIA 105
K +++D + +S+ A
Sbjct: 70 KGLIVDQTIEKVSFCA 85
>gnl|CDD|238859 cd01821, Rhamnogalacturan_acetylesterase_like,
Rhamnogalacturan_acetylesterase_like subgroup of
SGNH-hydrolases. Rhamnogalacturan acetylesterase removes
acetyl esters from rhamnogalacturonan substrates, and
renders them susceptible to degradation by
rhamnogalacturonases. Rhamnogalacturonans are highly
branched regions in pectic polysaccharides, consisting
of repeating -(1,2)-L-Rha-(1,4)-D-GalUA disaccharide
units, with many rhamnose residues substituted by
neutral oligosaccharides such as arabinans, galactans
and arabinogalactans. Extracellular enzymes
participating in the degradation of plant cell wall
polymers, such as Rhamnogalacturonan acetylesterase,
would typically be found in saprophytic and plant
pathogenic fungi and bacteria.
Length = 198
Score = 27.9 bits (63), Expect = 6.3
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 5/29 (17%)
Query: 223 ESGWGSMLP-----TVVIANLAPAGAAAR 246
++GWG LP + + N A G ++R
Sbjct: 20 QAGWGQALPQYLDTGITVVNHAKGGRSSR 48
>gnl|CDD|236277 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
Length = 819
Score = 28.5 bits (64), Expect = 6.7
Identities = 17/85 (20%), Positives = 31/85 (36%), Gaps = 7/85 (8%)
Query: 259 VNGVSLVAYMEFLKANGIEDHSFVKEMDYQEVLNSQEIFGDELQMFAKKE-LQKEICSLL 317
+N S + Y +K N I + S EV + I L+ F ++E + K +
Sbjct: 398 MNKASGL-YFHPIKDNVIANLSKNFFCITHEVGAEEIILYFLLKKFLEEEAILKSLEEFK 456
Query: 318 RGGIAERGGVRVGHRIIEINNQSVV 342
+ I+E + V+
Sbjct: 457 -----QSIVKEAALSILEEIREKVL 476
>gnl|CDD|223821 COG0750, COG0750, Predicted membrane-associated Zn-dependent
proteases 1 [Cell envelope biogenesis, outer membrane].
Length = 375
Score = 28.2 bits (63), Expect = 8.0
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 216 ILGVVIVESGWGSMLPTVVIANLAPAGAAARCGQLNIGDQIIAVNG 261
+L VV+ + + V+ +AP AAA G L GD+I+AV+G
Sbjct: 114 VLFVVLFFVIGLVPVASPVVGEVAPKSAAALAG-LRPGDRIVAVDG 158
>gnl|CDD|216951 pfam02261, Asp_decarbox, Aspartate decarboxylase. Decarboxylation
of aspartate is the major route of beta-alanine
production in bacteria, and is catalyzed by the enzyme
aspartate decarboxylase EC:4.1.1.11 which requires a
pyruvoyl group for its activity. It is synthesised
initially as a proenzyme which is then proteolytically
cleaved to an alpha (C-terminal) and beta (N-terminal)
subunit and a pyruvoyl group. This family contains both
chains of aspartate decarboxylase.
Length = 115
Score = 26.6 bits (60), Expect = 8.7
Identities = 9/16 (56%), Positives = 10/16 (62%), Gaps = 2/16 (12%)
Query: 242 GAAARCGQLNIGDQII 257
GAAAR Q GD +I
Sbjct: 72 GAAARLVQ--PGDLVI 85
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
0.319 0.136 0.384
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: 18,635,658
Number of extensions: 1882415
Number of successful extensions: 1625
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1599
Number of HSP's successfully gapped: 62
Length of query: 359
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 261
Effective length of database: 6,590,910
Effective search space: 1720227510
Effective search space used: 1720227510
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 (21.7 bits)
S2: 60 (26.9 bits)