RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1222
(60 letters)
>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1. The eukaryotic Sm and
Sm-like (LSm) proteins associate with RNA to form the
core domain of the ribonucleoprotein particles involved
in a variety of RNA processing events including
pre-mRNA splicing, telomere replication, and mRNA
degradation. Members of this family share a highly
conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet. LSMD1 proteins have a single Sm-like domain
structure. Sm-like proteins exist in archaea as well as
prokaryotes, forming heptameric and hexameric ring
structures similar to those found in eukaryotes.
Length = 73
Score = 84.9 bits (211), Expect = 4e-24
Identities = 34/58 (58%), Positives = 42/58 (72%), Gaps = 6/58 (10%)
Query: 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
+TDGRVLVGTF+CTD+D N+IL + EY P + GA+E R LGLVMVPG+HI
Sbjct: 16 LTDGRVLVGTFVCTDKDGNIILSNAEEYRKP------SDLGAEEPRSLGLVMVPGKHI 67
>gnl|CDD|212464 cd01717, Sm_B, Sm protein B. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold, containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet.
Length = 80
Score = 56.4 bits (137), Expect = 7e-13
Identities = 21/58 (36%), Positives = 36/58 (62%)
Query: 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
+ DGR VGTFL D+ N++L C E+ + + K+ +E R+LGLV++ G+++
Sbjct: 17 LQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEEREEKRVLGLVLLRGENV 74
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins. The eukaryotic Sm and
Sm-like (LSm) proteins associate with RNA to form the
core domain of the ribonucleoprotein particles involved
in a variety of RNA processing events including
pre-mRNA splicing, telomere replication, and mRNA
degradation. Members of this family share a highly
conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet. Sm-like proteins exist in archaea as well
as prokaryotes that form heptameric and hexameric ring
structures similar to those found in eukaryotes.
Length = 63
Score = 38.0 bits (89), Expect = 1e-05
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 11/58 (18%)
Query: 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
+ DGRVL GT + D+ N++L E R+LGLV++ G +I
Sbjct: 13 LKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKV-----------RVLGLVLIRGSNI 59
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 35.9 bits (84), Expect = 7e-05
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 10/58 (17%)
Query: 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
+ +GR GT D+ N++L E + ++ R LGLV + G +I
Sbjct: 15 LKNGREYRGTLKGFDQFMNLVLEDVEETV----------KDGEKKRKLGLVFIRGNNI 62
>gnl|CDD|212474 cd01727, LSm8, Like-Sm protein 8. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. LSm657 is
believed to be an assembly intermediate for both the
LSm1-7 and LSm2-8 rings. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 91
Score = 32.1 bits (74), Expect = 0.003
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 2 TDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
TDGRV+VGT D+ N+IL +C E V+ S E LGL ++ G ++
Sbjct: 17 TDGRVIVGTLKGFDQTTNLILSNCHER----VYSSDEGVEEVP---LGLYLLRGDNV 66
>gnl|CDD|201787 pfam01423, LSM, LSM domain. The LSM domain contains Sm proteins
as well as other related LSM (Like Sm) proteins. The
U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein
particles (snRNPs) involved in pre-mRNA splicing
contain seven Sm proteins (B/B', D1, D2, D3, E, F and
G) in common, which assemble around the Sm site present
in four of the major spliceosomal small nuclear RNAs.
The U6 snRNP binds to the LSM (Like Sm) proteins. Sm
proteins are also found in archaebacteria, which do not
have any splicing apparatus suggesting a more general
role for Sm proteins. All Sm proteins contain a common
sequence motif in two segments, Sm1 and Sm2, separated
by a short variable linker. This family also includes
the bacterial Hfq (host factor Q) proteins. Hfq are
also RNA-binding proteins, that form hexameric rings.
Length = 66
Score = 29.8 bits (68), Expect = 0.018
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 11/58 (18%)
Query: 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
+ +GR L GT D+ N++L E + + LGLV++ G +I
Sbjct: 15 LKNGRELRGTLKGFDQFMNLVLDDVEETIKDG-----------KVNKLGLVLIRGNNI 61
>gnl|CDD|173684 cd05593, STKc_PKB_gamma, Catalytic domain of the Protein
Serine/Threonine Kinase, Protein Kinase B gamma.
Serine/Threonine Kinases (STKs), Protein Kinase B (PKB)
or Akt subfamily, gamma (or Akt3) isoform, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The PKB subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. There are three
PKB isoforms from different genes, PKB-alpha (or Akt1),
PKB-beta (or Akt2), and PKB-gamma (or Akt3). PKB
contains an N-terminal pleckstrin homology (PH) domain
and a C-terminal catalytic domain. PKB-gamma is
predominantly expressed in neuronal tissues. Mice
deficient in PKB-gamma show a reduction in brain weight
due to the decreases in cell size and cell number.
PKB-gamma has also been shown to be upregulated in
estrogen-deficient breast cancer cells,
androgen-independent prostate cancer cells, and primary
ovarian tumors. It acts as a key mediator in the genesis
of ovarian cancer.
Length = 328
Score = 29.3 bits (65), Expect = 0.068
Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 3 DGRVLVGTF-LCTD--RDANVILGSCG--EYLSPEVFESKEENGAQEARLLGLVM 52
DG + + F LC + DA + CG EYL+PEV E + A + LG+VM
Sbjct: 131 DGHIKITDFGLCKEGITDAATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVM 185
>gnl|CDD|173685 cd05594, STKc_PKB_alpha, Catalytic domain of the Protein
Serine/Threonine Kinase, Protein Kinase B alpha.
Serine/Threonine Kinases (STKs), Protein Kinase B (PKB)
or Akt subfamily, alpha (or Akt1) isoform, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The PKB subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. There are three
PKB isoforms from different genes, PKB-alpha (or Akt1),
PKB-beta (or Akt2), and PKB-gamma (or Akt3). PKB
contains an N-terminal pleckstrin homology (PH) domain
and a C-terminal catalytic domain. PKB-alpha is
predominantly expressed in endothelial cells. It is
critical for the regulation of angiogenesis and the
maintenance of vascular integrity. It also plays a role
in adipocyte differentiation. Mice deficient in
PKB-alpha exhibit perinatal morbidity, growth
retardation, reduction in body weight accompanied by
reduced sizes of multiple organs, and enhanced apoptosis
in some cell types. PKB-alpha activity has been reported
to be frequently elevated in breast and prostate
cancers. In some cancer cells, PKB-alpha may act as a
suppressor of metastasis.
Length = 325
Score = 28.8 bits (64), Expect = 0.098
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 3 DGRVLVGTF-LCTD--RDANVILGSCG--EYLSPEVFESKEENGAQEARLLGLVM 52
DG + + F LC + +D + CG EYL+PEV E + A + LG+VM
Sbjct: 132 DGHIKITDFGLCKEGIKDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVM 186
>gnl|CDD|223953 COG1022, FAA1, Long-chain acyl-CoA synthetases (AMP-forming) [Lipid
metabolism].
Length = 613
Score = 28.8 bits (65), Expect = 0.11
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 4 GRVLVGTFLC-TDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQ 56
G + +L T R +I S G+ ++PE ESK ++ L+ + V G
Sbjct: 457 GELDEDGYLVITGRKKELIKLSNGKNIAPEPIESK----LAKSPLIEQICVVGD 506
>gnl|CDD|212476 cd01729, LSm7, Like-Sm protein 7. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. LSm657 is
believed to be an assembly intermediate for both the
LSm1-7 and LSm2-8 rings. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 89
Score = 27.6 bits (62), Expect = 0.18
Identities = 18/53 (33%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 4 GRVLVGTFLCTDRDANVILGSCGEYL-SPEVFESKEENGAQEARLLGLVMVPG 55
GR + G D+ N++L EYL PE E R LGLV+ G
Sbjct: 22 GREVTGILKGYDQLLNLVLDDTVEYLRDPE----DPYKLTDETRSLGLVVCRG 70
>gnl|CDD|173662 cd05571, STKc_PKB, Catalytic domain of the Protein Serine/Threonine
Kinase, Protein Kinase B. Serine/Threonine Kinases
(STKs), Protein Kinase B (PKB) or Akt subfamily,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The PKB subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase (PI3K). There are
three PKB isoforms from different genes, PKB-alpha (or
Akt1), PKB-beta (or Akt2), and PKB-gamma (or Akt3). PKB
contains an N-terminal pleckstrin homology (PH) domain
and a C-terminal catalytic domain. It is activated
downstream of PI3K and plays important roles in diverse
cellular functions including cell survival, growth,
proliferation, angiogenesis, motility, and migration.
PKB also has a central role in a variety of human
cancers, having been implicated in tumor initiation,
progression, and metastasis.
Length = 323
Score = 27.9 bits (62), Expect = 0.21
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 3 DGRVLVGTF-LCTD--RDANVILGSCG--EYLSPEVFESKEENGAQEARLLGLVM 52
DG + + F LC + D + CG EYL+PEV E + A + LG+VM
Sbjct: 131 DGHIKITDFGLCKEGISDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVM 185
>gnl|CDD|173686 cd05595, STKc_PKB_beta, Catalytic domain of the Protein
Serine/Threonine Kinase, Protein Kinase B beta.
Serine/Threonine Kinases (STKs), Protein Kinase B (PKB)
or Akt subfamily, beta (or Akt2) isoform, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The PKB subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. There are three
PKB isoforms from different genes, PKB-alpha (or Akt1),
PKB-beta (or Akt2), and PKB-gamma (or Akt3). PKB
contains an N-terminal pleckstrin homology (PH) domain
and a C-terminal catalytic domain. PKB-beta is the
predominant PKB isoform expressed in insulin-responsive
tissues. It plays a critical role in the regulation of
glucose homeostasis. It is also implicated in muscle
cell differentiation. Mice deficient in PKB-beta display
normal growth weights but exhibit severe insulin
resistance and diabetes, accompanied by lipoatrophy and
B-cell failure.
Length = 323
Score = 28.0 bits (62), Expect = 0.23
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 3 DGRVLVGTF-LCTD--RDANVILGSCG--EYLSPEVFESKEENGAQEARLLGLVM 52
DG + + F LC + D + CG EYL+PEV E + A + LG+VM
Sbjct: 131 DGHIKITDFGLCKEGISDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVM 185
>gnl|CDD|140289 PTZ00263, PTZ00263, protein kinase A catalytic subunit;
Provisional.
Length = 329
Score = 27.9 bits (62), Expect = 0.25
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 25 CG--EYLSPEVFESKEENGAQEARLLGLVM 52
CG EYL+PEV +SK A + +G+++
Sbjct: 176 CGTPEYLAPEVIQSKGHGKAVDWWTMGVLL 205
>gnl|CDD|173771 cd08529, STKc_FA2-like, Catalytic domain of the Protein
Serine/Threonine Kinase, Chlamydomonas reinhardtii FA2
and similar domains. Serine/Threonine Kinases (STKs),
Chlamydomonas reinhardtii FA2-like subfamily, catalytic
(c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The Chlamydomonas
reinhardtii FA2-like subfamily belongs to the
(NIMA)-related kinase (Nek) family. The Nek family
includes seven different Chlamydomonas Neks (CNKs 1-6
and Fa2). This subfamily includes FA2 and CNK4. The Nek
family is part of a larger superfamily that includes the
catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. Chlamydomonas reinhardtii FA2 was discovered
in a genetic screen for deflagellation-defective
mutants. It is essential for
basal-body/centriole-associated microtubule severing,
and plays a role in cell cycle progression. No cellular
function has yet been ascribed to CNK4.
Length = 256
Score = 27.1 bits (60), Expect = 0.42
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 18 ANVILGSCGEYLSPEVFESKEENGAQEARLLGLVM 52
AN I+G+ YLSPE+ E K N + LG+V+
Sbjct: 158 ANTIVGT-PYYLSPELCEDKPYNEKSDVWALGVVL 191
>gnl|CDD|173703 cd05612, STKc_PRKX_like, Catalytic domain of PRKX-like Protein
Serine/Threonine Kinases. Serine/Threonine Kinases
(STKs), cAMP-dependent protein kinase (PKA) subfamily,
PRKX-like kinases, catalytic (c) subunit. STKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The PKA
subfamily is part of a larger superfamily that includes
the catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. Members of this group include human PRKX (X
chromosome-encoded protein kinase), Drosophila DC2, and
similar proteins. PRKX is present in many tissues
including fetal and adult brain, kidney, and lung. The
PRKX gene is located in the Xp22.3 subregion and has a
homolog called PRKY on the Y chromosome. An abnormal
interchange between PRKX aand PRKY leads to the sex
reversal disorder of XX males and XY females. PRKX is
implicated in granulocyte/macrophage lineage
differentiation, renal cell epithelial migration, and
tubular morphogenesis in the developing kidney.
Length = 291
Score = 27.0 bits (60), Expect = 0.49
Identities = 14/30 (46%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 25 CG--EYLSPEVFESKEENGAQEARLLGLVM 52
CG EYL+PEV +SK N A + LG+++
Sbjct: 159 CGTPEYLAPEVIQSKGHNKAVDWWALGILI 188
>gnl|CDD|173660 cd05123, STKc_AGC, Catalytic domain of AGC family Protein
Serine/Threonine Kinases. Serine/Threonine Kinases
(STKs), AGC (Protein Kinases A, G and C) family,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The AGC family is part
of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and Phosphoinositide 3-Kinase (PI3K). Members of
this family include cAMP-dependent Protein Kinase (PKA),
cGMP-dependent Protein Kinase (PKG), Protein Kinase C
(PKC), Protein Kinase B (PKB), G protein-coupled
Receptor Kinase (GRK), Serum- and Glucocorticoid-induced
Kinase (SGK), and 70 kDa ribosomal Protein S6 Kinase
(p70S6K or S6K), among others. AGC kinases share an
activation mechanism based on the phosphorylation of up
to three sites: the activation loop (A-loop), the
hydrophobic motif (HM) and the turn motif.
Phosphorylation at the A-loop is required of most AGC
kinases, which results in a disorder-to-order transition
of the A-loop. The ordered conformation results in the
access of substrates and ATP to the active site. A
subset of AGC kinases with C-terminal extensions
containing the HM also requires phosphorylation at this
site. Phosphorylation at the HM allows the C-terminal
extension to form an ordered structure that packs into
the hydrophobic pocket of the catalytic domain, which
then reconfigures the kinase into an active bi-lobed
state. In addition, growth factor-activated AGC kinases
such as PKB, p70S6K, RSK, MSK, PKC, and SGK, require
phosphorylation at the turn motif (also called tail or
zipper site), located N-terminal to the HM at the
C-terminal extension. AGC kinases regulate many cellular
processes including division, growth, survival,
metabolism, motility, and differentiation. Many are
implicated in the development of various human diseases.
Length = 250
Score = 26.3 bits (59), Expect = 0.86
Identities = 9/16 (56%), Positives = 10/16 (62%), Gaps = 2/16 (12%)
Query: 25 CG--EYLSPEVFESKE 38
CG EYL+PEV K
Sbjct: 154 CGTPEYLAPEVLLGKG 169
>gnl|CDD|173671 cd05580, STKc_PKA, Catalytic domain of the Protein Serine/Threonine
Kinase, cAMP-dependent protein kinase. Serine/Threonine
Kinases (STKs), cAMP-dependent protein kinase (PKA)
subfamily, catalytic (c) subunit. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The PKA
subfamily is part of a larger superfamily that includes
the catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase (PI3K). This subfamily is composed of the
cAMP-dependent proteins kinases, PKA and PRKX. The
inactive PKA holoenzyme is a heterotetramer composed of
two phosphorylated and active catalytic (C) subunits
with a dimer of regulatory (R) subunits. Activation is
achieved through the binding of the important second
messenger cAMP to the R subunits, which leads to the
dissociation of PKA into the R dimer and two active C
subunits. PKA is present ubiquitously in cells and
interacts with many different downstream targets. It
plays a role in the regulation of diverse processes such
as growth, development, memory, metabolism, gene
expression, immunity, and lipolysis.
Length = 290
Score = 25.6 bits (57), Expect = 1.6
Identities = 9/15 (60%), Positives = 11/15 (73%), Gaps = 2/15 (13%)
Query: 25 CG--EYLSPEVFESK 37
CG EYL+PE+ SK
Sbjct: 159 CGTPEYLAPEIILSK 173
>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. LSm657 is
believed to be an assembly intermediate for both the
LSm1-7 and LSm2-8 rings. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 68
Score = 24.4 bits (54), Expect = 2.3
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 3 DGRVLVGTFLCTDRDANVILGSCGEY 28
+G G C D N++L EY
Sbjct: 20 NGVEYRGVLACLDGYMNLVLEDTEEY 45
>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1. The eukaryotic LSm proteins
(LSm1-7) assemble into a hetero-heptameric ring around
the 3'-terminus of the gamma-methyl triphosphate
(gamma-m-P3) capped U6 snRNA. Accumulation of
uridylated RNAs in an lsm1 mutant suggests an
involvement of the LSm1-7 complex in recognition of the
3' uridylation tag and recruitment of the decapping
machinery. LSm1-7, together with Pat1, are also called
the decapping activator. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 74
Score = 24.0 bits (53), Expect = 3.2
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 3 DGRVLVGTFLCTDRDANVIL 22
DGR L+G D+ AN++L
Sbjct: 21 DGRKLIGILRSFDQFANLVL 40
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 23.8 bits (52), Expect = 3.7
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 7/58 (12%)
Query: 1 MTDGRVLVGTFLCTDRDANVILGSCGEYLSPEVFESKEENGAQEARLLGLVMVPGQHI 58
+ +GR GT + D+ N++L E +S E RL G V++ G +I
Sbjct: 24 LKNGREYRGTLVGFDQYMNLVLDDVEEIIS-----HDGEKNV--RRLGGEVLIRGDNI 74
>gnl|CDD|241474 cd13320, PH_OCRL-like, oculocerebrorenal syndrome of Lowe family
Pleckstrin homology-like domain. The OCRL family has
two members: OCRL1 (also called INPP5F, LOCR, NPHL2, or
phosphatidylinositol polyphosphate 5-phosphatase) and
OCRL2 ( also called IPNNB5, inositol
polyphosphate-5-phosphatase, phosphoinositide
5-phosphatase, 5PTase, or type II
inositol-1,4,5-trisphosphate 5-phosphatase). The OCRL
proteins hydrolyze phosphatidylinositol
4,5-bisphosphate (PtIns(4,5)P2) and the signaling
molecule phosphatidylinositol 1,4,5-trisphosphate
(PtIns(1,4,5)P3), and thereby modulates cellular
signaling events. They interact with APPL1, FAM109A and
FAM109B and several Rab GTPases which might both target
them to the specific membranes and as well as
stimulating the phosphatase activity. All OCRL family
members contain a PH domain and a Rho-GAP domain. 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 = 107
Score = 24.0 bits (52), Expect = 4.5
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 40 NGAQEARLLGLVMVPGQH 57
G++E RLLGLV GQH
Sbjct: 10 GGSREPRLLGLVERGGQH 27
>gnl|CDD|100090 cd03088, ManB, ManB is a bacterial phosphomannomutase (PMM) that
catalyzes the conversion of mannose 6-phosphate to
mannose-1-phosphate in the second of three steps in the
GDP-mannose pathway, in which GDP-D-mannose is
synthesized from fructose-6-phosphate. In Mycobacterium
tuberculosis, the causative agent of tuberculosis, PMM
is involved in the biosynthesis of mannosylated
lipoglycans that participate in the association of
mycobacteria with host macrophage phagocytic receptors.
ManB belongs to the the alpha-D-phosphohexomutase
superfamily which includes several related enzymes that
catalyze a reversible intramolecular phosphoryl
transfer on their sugar substrates. Other members of
this superfamily include the phosphoglucomutases (PGM1
and PGM2), phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each
of these enzymes has four domains with a centrally
located active site formed by four loops, one from each
domain. All four domains are included in this alignment
model.
Length = 459
Score = 23.7 bits (52), Expect = 7.0
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 51 VMVPGQHIPA 60
+MV G HIPA
Sbjct: 90 IMVTGSHIPA 99
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
0.318 0.138 0.408
Gapped
Lambda K H
0.267 0.0838 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,067,467
Number of extensions: 208230
Number of successful extensions: 193
Number of sequences better than 10.0: 1
Number of HSP's gapped: 190
Number of HSP's successfully gapped: 23
Length of query: 60
Length of database: 10,937,602
Length adjustment: 31
Effective length of query: 29
Effective length of database: 9,562,628
Effective search space: 277316212
Effective search space used: 277316212
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: 53 (24.0 bits)