RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1030
(114 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 = 52.2 bits (126), Expect = 3e-10
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 1 MKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLREVVQKPGPIKLVVA 53
GG G + GD IL+VN ++ E ++++EAV +L+ + L V
Sbjct: 34 EPGGPAER-GGLRVGDRILEVNGVSVEGLTHEEAVELLKNS---GDEVTLTVR 82
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 50.7 bits (122), Expect = 9e-10
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 1 MKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLREVVQKPGPIKLVVA 53
+ GGA G ++ GD IL +N + EN+S+DEAV L+ G + L +
Sbjct: 32 LPGGAAEAGG-LQEGDRILSINGQDLENLSHDEAVLALKG---SGGEVTLTIL 80
>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 = 47.4 bits (113), Expect = 2e-08
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 1 MKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLREVVQKPGPIKLVV 52
+ G A G + GD+IL+VN + E +++ EAV +L++ G + L V
Sbjct: 34 VPGSPAAKAG-LRVGDVILEVNGTSVEGLTHLEAVDLLKKA---GGKVTLTV 81
>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 = 39.2 bits (92), Expect = 2e-05
Identities = 13/49 (26%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 4 GAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLREVVQKPGPIKLVV 52
G+ A ++ GD+IL VN + +N++ ++ +L++ V + + L V
Sbjct: 23 GSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEVGE--KVTLTV 69
>gnl|CDD|223864 COG0793, Prc, Periplasmic protease [Cell envelope biogenesis, outer
membrane].
Length = 406
Score = 35.8 bits (83), Expect = 0.002
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 8/82 (9%)
Query: 1 MKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLREVVQKPG-PIKLVVAKCWDPN 59
+ G A G I+PGD+I++++ + +S DEAV+++R KPG + L + +
Sbjct: 120 IDGSPAAKAG-IKPGDVIIKIDGKSVGGVSLDEAVKLIRG---KPGTKVTLTILRAGGGK 175
Query: 60 PKGYFTIPRTEPVRPIDPGAWV 81
P T+ R E ++ A
Sbjct: 176 PF-TVTLTREE--IELEDVAAK 194
>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 = 31.0 bits (71), Expect = 0.032
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 4 GAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLR 39
G+ A I+ GD+I+ ++ + +S ++ V++LR
Sbjct: 23 GSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLR 58
>gnl|CDD|70841 pfam07390, P30, Mycoplasma P30 protein. This family consists of
several P30 proteins which seem to be specific to
Mycoplasma agalactiae. P30 is a 30-kDa immunodominant
antigen and is known to be a transmembrane protein.
Length = 266
Score = 29.8 bits (66), Expect = 0.22
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 48 IKLVVAKCWDPNPKGYFTIPRTEPVRPID 76
I V AKC + + K T P+ EP +P+D
Sbjct: 19 IPFVAAKCSEDDKKEKVTKPKNEPTKPVD 47
>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 = 30.0 bits (68), Expect = 0.23
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 7/75 (9%)
Query: 4 GAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLREVVQKPG-PIKLVVAKCWDPNPKG 62
G+ A I+PGD I+++N + MS D+AV ++R K G + L + +
Sbjct: 72 GSPAEKAGIKPGDKIIKINGKSVAGMSLDDAVALIR---GKKGTKVSLEILR---AGKSK 125
Query: 63 YFTIPRTEPVRPIDP 77
T +
Sbjct: 126 PLTFTLKRDRIELQT 140
>gnl|CDD|183172 PRK11517, PRK11517, transcriptional regulatory protein YedW;
Provisional.
Length = 223
Score = 29.1 bits (65), Expect = 0.43
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 3/45 (6%)
Query: 10 GRIEPGDMIL-QVNDINFENMSN--DEAVRVLREVVQKPGPIKLV 51
G I P +I ++ INF++ +N D A+R LR V P P KL+
Sbjct: 164 GEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVDDPFPEKLI 208
>gnl|CDD|234386 TIGR03900, prc_long_Delta, putative carboxyl-terminal-processing
protease, deltaproteobacterial. This model describes a
multidomain protein of about 1070 residues, restricted
to the order Myxococcales in the Deltaproteobacteria.
Members contain a PDZ domain (pfam00595), an S41 family
peptidase domain (pfam03572), and an SH3 domain
(pfam06347). A core region of this family, including PDZ
and S41 regions, is described by TIGR00225, C-terminal
processing peptidase, which recognizes the Prc protease.
The species distribution of this family approximates
that of largely Deltaproteobacterial C-terminal putative
protein-sorting domain, TIGR03901, analogous to LPXTG
and PEP-CTERM, but the co-occurrence may reflect shared
restriction to the Myxococcales rather than a
substrate/target relationship.
Length = 973
Score = 29.4 bits (66), Expect = 0.44
Identities = 9/28 (32%), Positives = 20/28 (71%)
Query: 12 IEPGDMILQVNDINFENMSNDEAVRVLR 39
++ D+I++++D + NM+ ++AV LR
Sbjct: 169 LQRNDVIVKIDDESTVNMTLNDAVGRLR 196
>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 = 26.8 bits (60), Expect = 1.0
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 1 MKGGAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLREVVQKPG-PIKLVV 52
+ G A G ++ GD IL +N ++ + ++ V + PG P+ L V
Sbjct: 20 VPGSPAAKAG-LKAGDRILAINGQKIKSWED-----LVDAVQENPGKPLTLTV 66
>gnl|CDD|234035 TIGR02860, spore_IV_B, stage IV sporulation protein B. SpoIVB, the
stage IV sporulation protein B of endospore-forming
bacteria such as Bacillus subtilis, is a serine
proteinase, expressed in the spore (rather than mother
cell) compartment, that participates in a proteolytic
activation cascade for Sigma-K. It appears to be
universal among endospore-forming bacteria and occurs
nowhere else [Cellular processes, Sporulation and
germination].
Length = 402
Score = 27.3 bits (61), Expect = 1.7
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 8/45 (17%)
Query: 10 GRIEPGDMILQVNDINFENMSNDEAVRVLREVVQKPG--PIKLVV 52
I+ GD IL++N +NM + L ++ K G + L +
Sbjct: 129 AGIQIGDRILKINGEKIKNMDD------LANLINKAGGEKLTLTI 167
>gnl|CDD|130454 TIGR01387, cztR_silR_copR, heavy metal response regulator. Members
of this family contain a response regulator receiver
domain (pfam00072) and an associated transcriptional
regulatory region (pfam00486). This group is separated
phylogenetically from related proteins with similar
architecture and contains a number of proteins
associated with heavy metal resistance efflux systems
for copper, silver, cadmium, and/or zinc. Most members
encoded by genes adjacent to genes for encoding a member
of the heavy metal sensor histidine kinase family
(TIGRFAMs:TIGR01386), its partner in the two-component
response regulator system.
Length = 218
Score = 27.1 bits (60), Expect = 1.9
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 10 GRIEPGDMIL-QVNDINFENMSN--DEAVRVLREVVQKPGPIKLV 51
G + P +I V +NF++ +N D A+R LR V P KL+
Sbjct: 164 GEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVDDPFEEKLI 208
>gnl|CDD|133178 cd05046, PTK_CCK4, Pseudokinase domain of the Protein Tyrosine
Kinase, Colon Carcinoma Kinase 4. Protein Tyrosine
Kinase (PTK) family; Colon Carcinoma Kinase 4 (CCK4);
pseudokinase domain. The PTKc (catalytic domain) family,
to which this subfamily belongs, includes the catalytic
domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. CCK4,
also called protein tyrosine kinase 7 (PTK7), is an
orphan receptor tyr kinase (RTK) containing an
extracellular region with seven immunoglobulin domains,
a transmembrane segment, and an intracellular inactive
pseudokinase domain. Studies in mice reveal that CCK4 is
essential for neural development. Mouse embryos
containing a truncated CCK4 die perinatally and display
craniorachischisis, a severe form of neural tube defect.
The mechanism of action of the CCK4 pseudokinase is
still unknown. Other pseudokinases such as HER3 rely on
the activity of partner RTKs.
Length = 275
Score = 27.0 bits (60), Expect = 2.0
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 7/43 (16%)
Query: 26 FENMSNDEAVRVLREVVQK-------PGPIKLVVAKCWDPNPK 61
F +S++E + L+ + P + ++ +CW NPK
Sbjct: 219 FYGLSDEEVLNRLQAGKLELPVPEGCPSRLYKLMTRCWAVNPK 261
>gnl|CDD|222196 pfam13523, Acetyltransf_8, Acetyltransferase (GNAT) domain. This
domain catalyzes N-acetyltransferase reactions.
Length = 152
Score = 26.9 bits (60), Expect = 2.2
Identities = 13/70 (18%), Positives = 21/70 (30%), Gaps = 7/70 (10%)
Query: 33 EAVRVLREVVQKPGPIKLVVAKCWDPNPKGYFTIPRTEPVRPIDPGAW------VAHTAA 86
E + E + ++ +D P GYF I + P D
Sbjct: 33 EELEDYLEKLLADPHSHPLIG-EFDGEPFGYFEIYWAKEDYPADDYDRGIHLLVGEPRFR 91
Query: 87 IRGDGFPFLR 96
+G +LR
Sbjct: 92 GKGFTRAWLR 101
>gnl|CDD|241390 cd13236, PH2_FGD1-4, FYVE, RhoGEF and PH domain
containing/faciogenital dysplasia proteins pleckstrin
homology (PH) domain, C-terminus. In general, FGDs
have a RhoGEF (DH) domain, followed by an N-terminal PH
domain, a FYVE domain and a C-terminal PH domain. All
FGDs are guanine nucleotide exchange factors that
activates the Rho GTPase Cdc42, an important regulator
of membrane trafficking. The RhoGEF domain is
responsible for GEF catalytic activity, while the
N-terminal PH domain is involved in intracellular
targeting of the DH domain. Not much is known about
FGD2. FGD1 is the best characterized member of the
group with mutations here leading to the X-linked
disorder known as faciogenital dysplasia (FGDY). Both
FGD1 and FGD3 are targeted by the ubiquitin ligase
SCF(FWD1/beta-TrCP) upon phosphorylation of two serine
residues in its DSGIDS motif and subsequently degraded
by the proteasome. However, FGD1 and FGD3 induced
significantly different morphological changes in HeLa
Tet-Off cells and while FGD1 induced long finger-like
protrusions, FGD3 induced broad sheet-like protrusions
when the level of GTP-bound Cdc42 was significantly
increased by the inducible expression of FGD3. They
also reciprocally regulated cell motility in inducibly
expressed in HeLa Tet-Off cells, FGD1 stimulated cell
migration while FGD3 inhibited it. FGD1 and FGD3
therefore play different roles to regulate cellular
functions, even though their intracellular levels are
tightly controlled by the same destruction pathway
through SCF(FWD1/beta-TrCP). FGD4 is one of the genes
associated with Charcot-Marie-Tooth neuropathy type 4
(CMT4), a group of progressive motor and sensory axonal
and demyelinating neuropathies that are distinguished
from other forms of CMT by autosomal recessive
inheritance. Those affected have distal muscle weakness
and atrophy associated with sensory loss and,
frequently, pes cavus foot deformity. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They
share little sequence conservation, but all have a
common fold, which is electrostatically polarized. Less
than 10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 105
Score = 25.7 bits (57), Expect = 3.5
Identities = 9/18 (50%), Positives = 10/18 (55%), Gaps = 3/18 (16%)
Query: 54 KCWDPNPKGYFTIPRTEP 71
K W K + IPRTEP
Sbjct: 21 KTW---QKVWCVIPRTEP 35
>gnl|CDD|224643 COG1729, COG1729, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 262
Score = 26.3 bits (58), Expect = 3.6
Identities = 9/32 (28%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 16 DMILQVNDINFENMSNDEAVRVLREVVQK-PG 46
D +L++ + DEA L++V+++ PG
Sbjct: 216 DALLKLGVSLGRLGNTDEACATLQQVIKRYPG 247
>gnl|CDD|235633 PRK05872, PRK05872, short chain dehydrogenase; Provisional.
Length = 296
Score = 25.7 bits (57), Expect = 5.5
Identities = 15/60 (25%), Positives = 20/60 (33%), Gaps = 19/60 (31%)
Query: 36 RVLREVVQKPGPIKLVVAKCWDPNPKGYFTIPRTEPVRPIDPGAW----------VAHTA 85
E V++ G I +VVA I V +DP A+ V HT
Sbjct: 74 AAAEEAVERFGGIDVVVANA---------GIASGGSVAQVDPDAFRRVIDVNLLGVFHTV 124
>gnl|CDD|171849 PRK13033, PRK13033, formyl peptide receptor-like 1 inhibitory
protein; Reviewed.
Length = 133
Score = 25.4 bits (55), Expect = 5.6
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 13 EPGDMILQVNDINFENMSNDEAVRVLREVVQK--PGPIKLVVAKCWDPNPKGYFTIPRTE 70
E D +++ +D N E V L +V+K G +K V + D P+ Y+T T
Sbjct: 52 ERIDKLMKESDKNLTPYKA-ETVNDLYLIVKKLSQGDVKKAVVRIKDGGPRDYYTFDLTR 110
Query: 71 PV 72
P+
Sbjct: 111 PL 112
>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 = 24.9 bits (55), Expect = 5.7
Identities = 7/19 (36%), Positives = 14/19 (73%)
Query: 12 IEPGDMILQVNDINFENMS 30
++PGD+IL VN ++++
Sbjct: 42 LKPGDVILAVNGKPVKSVA 60
>gnl|CDD|223735 COG0663, PaaY, Carbonic anhydrases/acetyltransferases, isoleucine
patch superfamily [General function prediction only].
Length = 176
Score = 25.6 bits (57), Expect = 5.8
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 75 IDPGAWVAHTAAIRGD 90
IDP A+VA +A + GD
Sbjct: 14 IDPTAFVAPSATVIGD 29
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 25.9 bits (58), Expect = 6.0
Identities = 10/33 (30%), Positives = 19/33 (57%), Gaps = 7/33 (21%)
Query: 27 ENMSNDEAVRVLREVVQK-------PGPIKLVV 52
+ + + +AVR+ R++ +K PG IK+ V
Sbjct: 477 DKVDDLQAVRLARDIAKKIEEELQYPGQIKVTV 509
>gnl|CDD|236232 PRK08309, PRK08309, short chain dehydrogenase; Provisional.
Length = 177
Score = 25.5 bits (56), Expect = 6.2
Identities = 8/24 (33%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 31 NDEAVRV-LREVVQKPGPIKLVVA 53
+D+A+++ ++ ++K GP L VA
Sbjct: 58 DDDALKLAIKSTIEKNGPFDLAVA 81
>gnl|CDD|215143 PLN02255, PLN02255, H(+) -translocating inorganic pyrophosphatase.
Length = 765
Score = 26.0 bits (57), Expect = 6.6
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 56 WDPNPKGYFTIPRTEPVRPIDPGAWVAHTAAIRGD--GFPFLRVN-PTLN 102
WD N K Y +E R + P H AA+ GD G P + P+LN
Sbjct: 689 WD-NAKKYIEAGASEHARSLGPKGSDPHKAAVIGDTIGDPLKDTSGPSLN 737
>gnl|CDD|215560 PLN03076, PLN03076, ARF guanine nucleotide exchange factor
(ARF-GEF); Provisional.
Length = 1780
Score = 25.9 bits (57), Expect = 6.6
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 21 VNDINFENMSNDEAVRVLREVVQKPG 46
V+ +F+ M DEA+R + + PG
Sbjct: 685 VDSFDFQGMEFDEAIRAFLQGFRLPG 710
>gnl|CDD|149951 pfam09077, Phage-MuB_C, Mu B transposition protein, C terminal.
The C terminal domain of the B transposition protein
from Bacteriophage Mu comprises four alpha-helices
arranged in a loosely packed bundle, where helix alpha1
runs parallel to alpha3, and anti-parallel to helices
alpha2 and alpha4. The domain allows for non-specific
binding of Mu to double-stranded DNA, allowing for
integration into the bacterial genome, and mediates
dimerisation of the protein.
Length = 78
Score = 24.6 bits (54), Expect = 6.7
Identities = 7/25 (28%), Positives = 18/25 (72%)
Query: 28 NMSNDEAVRVLREVVQKPGPIKLVV 52
+ ++E ++VL+ + +KPG ++L+
Sbjct: 25 GLQDEEELKVLQAISEKPGALRLLT 49
>gnl|CDD|237519 PRK13812, PRK13812, orotate phosphoribosyltransferase; Provisional.
Length = 176
Score = 25.1 bits (55), Expect = 7.5
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 3 GGAVALDGRIEPGDMILQVNDINFENMSNDEAVRVLREV 41
G ++GR++ G+ ++ + DI S +AV LRE
Sbjct: 95 GTGNRIEGRLDEGEEVVVLEDIATTGQSAVDAVEALREA 133
>gnl|CDD|201816 pfam01472, PUA, PUA domain. The PUA domain named after
Pseudouridine synthase and Archaeosine
transglycosylase, was detected in archaeal and
eukaryotic pseudouridine synthases, archaeal
archaeosine synthases, a family of predicted ATPases
that may be involved in RNA modification, a family of
predicted archaeal and bacterial rRNA methylases.
Additionally, the PUA domain was detected in a family
of eukaryotic proteins that also contain a domain
homologous to the translation initiation factor
eIF1/SUI1; these proteins may comprise a novel type of
translation factors. Unexpectedly, the PUA domain was
detected also in bacterial and yeast glutamate kinases;
this is compatible with the demonstrated role of these
enzymes in the regulation of the expression of other
genes. It is predicted that the PUA domain is an RNA
binding domain.
Length = 74
Score = 24.4 bits (54), Expect = 8.7
Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 6/51 (11%)
Query: 1 MKGGAVALDGRIEPGDMILQVNDINFE------NMSNDEAVRVLREVVQKP 45
+ G V +DG GD ++ V + N S++E ++ K
Sbjct: 20 LAPGVVEVDGDFRRGDEVVVVTEKGELVAVGLANYSSEEMAKIKGGKAVKV 70
>gnl|CDD|241246 cd01210, PTB_EPS8, Epidermal growth factor receptor kinase
substrate (EPS8)-like Phosphotyrosine-binding (PTB)
domain. EPS8 is a regulator of Rac signaling. It
consists of a PTB and an SH3 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 = 131
Score = 24.8 bits (55), Expect = 9.5
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 10 GRIEPGDMILQVND 23
G+I +M+LQVND
Sbjct: 38 GKIWSQEMLLQVND 51
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 0.141 0.447
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,100,897
Number of extensions: 530315
Number of successful extensions: 591
Number of sequences better than 10.0: 1
Number of HSP's gapped: 591
Number of HSP's successfully gapped: 49
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
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: 53 (24.1 bits)