RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4659
(132 letters)
>gnl|CDD|176898 cd08889, SRPBCC_PITPNM1-2_like, Lipid-binding SRPBCC domain of
mammalian PITPNM1-2 and related proteins (Class IIA
PITPs). This subgroup includes an N-terminal SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of
mammalian Class II phosphatidylinositol transfer protein
(PITPs), PITPNM1/PITPalphaI/Nir2 (PYK2 N-terminal
domain-interacting receptor2) and
PITPNM2/PITPalphaII/Nir3), Drosophila RdgB, and related
proteins. These are membrane associated multidomain
proteins belonging to the PITP family of lipid transfer
proteins, and to the SRPBCC domain superfamily of
proteins that bind hydrophobic ligands. SRPBCC domains
have a deep hydrophobic ligand-binding pocket. In vitro,
PITPs bind phosphatidylinositol (PtdIns), as well as
phosphatidylcholine (PtdCho) but with a lower affinity.
They transfer these lipids from one membrane compartment
to another. The cellular roles of PITPs include inositol
lipid signaling, PtdIns metabolism, and membrane
trafficking. Ablation of the mouse gene encoding PITPNM1
results in early embryonic death. PITPNM1 is localized
chiefly to the Golgi apparatus, and under certain
conditions translocates to the lipid droplets. Targeting
to the latter is dependent on a specific threonine
residue within the SRPBCC domain. PITPNM1 plays a part
in Golgi-mediated transport. It regulates diacylglycerol
(DAG) production at the trans-Golgi network (TGN) via
the CDP-choline pathway. Drosophila RdgB, the founding
member of the PITP family, is implicated in the visual
and olfactory transduction. RdgB is required for
maintenance of ultra structure in photoreceptors and for
sensory transduction. The mouse PITPNM1 gene rescues the
phenotype of Drosophila rdgB mutant flies. In addition
to the SRPBCC domain, PITPNM1 and -2 contain a
Rho-inhibitory domain (Rid), six hydrophobic stretches,
a DDHD calcium binding region, and a C-terminal tyrosine
kinase Pyk2-binding / HAD-like phosphohydrolase domain.
PITPNM1 has a role in regulating cell morphogenesis
through its Rho inhibitory domain (Rid). This
SRPBCC_PITPNM1-2_like domain model includes the first 52
residues of the 224 residues Rid (Rho-inhibitory
domain).
Length = 260
Score = 110 bits (276), Expect = 9e-31
Identities = 39/78 (50%), Positives = 51/78 (65%), Gaps = 8/78 (10%)
Query: 20 LYGGDYVREEDPSIYVSKTTGRGPLSENWISEYWNAVKEDPTVSHDNKSMMCAYKLCKIQ 79
+ G DY EEDP +YVS+ TGRGPLS++WI EY + +MCAYKLCK++
Sbjct: 148 VPGSDYKAEEDPKLYVSEKTGRGPLSDDWIEEYKDPPG--------KGPIMCAYKLCKVE 199
Query: 80 LNYWGIQSKVERFIADTG 97
YWG+Q+K+ERFI D
Sbjct: 200 FRYWGMQTKIERFIHDVA 217
>gnl|CDD|111058 pfam02121, IP_trans, Phosphatidylinositol transfer protein. Along
with the structurally unrelated Sec14p family (found in
pfam00650), this family can bind/exchange one molecule
of phosphatidylinositol (PI) or phosphatidylcholine (PC)
and thus aids their transfer between different membrane
compartments. There are three sub-families - all share
an N-terminal PITP-like domain, whose sequence is highly
conserved. It is described as consisting of three
regions. The N-terminal region is thought to bind the
lipid and contains two helices and an eight-stranded,
mostly antiparallel beta-sheet. An intervening loop
region, which is thought to play a role in
protein-protein interactions, separates this from the
C-terminal region, which exhibits the greatest sequence
variation and may be involved in membrane binding. PITP
alpha has a 16-fold greater affinity for PI than PC.
Together with PITP beta, it is expressed ubiquitously in
all tissues.
Length = 254
Score = 93.4 bits (232), Expect = 2e-24
Identities = 40/94 (42%), Positives = 51/94 (54%), Gaps = 15/94 (15%)
Query: 20 LYGGDYVREEDPSIYVSKTTGRGPLSENWISEYWNAVKEDPTVSHDNKSMMCAYKLCKIQ 79
+ GDY EEDP ++ S TGRGPL +W +E + P +MCAYKLC ++
Sbjct: 148 VSSGDYKAEEDPKLFHSVKTGRGPLGPDWKAELVKT-GDCP--------LMCAYKLCTVE 198
Query: 80 LNYWGIQSKVERFIADTGKPSGRALPRHFRRALR 113
YWG+Q+KVE FI D AL R RA R
Sbjct: 199 FRYWGMQTKVENFIHDQ------ALRRTMTRAHR 226
>gnl|CDD|176857 cd07815, SRPBCC_PITP, Lipid-binding SRPBCC domain of Class I and
Class II Phosphatidylinositol Transfer Proteins. This
family includes the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of the
phosphatidylinositol transfer protein (PITP) family of
lipid transfer proteins. This family of proteins
includes Class 1 PITPs (PITPNA/PITPalpha and
PITPNB/PITPbeta, Drosophila vibrator and related
proteins), Class IIA PITPs (PITPNM1/PITPalphaI/Nir2,
PITPNM2/PITPalphaII/Nir3, Drosophila RdgB, and related
proteins), and Class IIB PITPs (PITPNC1/RdgBbeta and
related proteins). The PITP family belongs to the SRPBCC
domain superfamily of proteins that bind hydrophobic
ligands. SRPBCC domains have a deep hydrophobic
ligand-binding pocket. In vitro, PITPs bind
phosphatidylinositol (PtdIns), as well as
phosphatidylcholine (PtdCho) but with a lower affinity.
They transfer these lipids from one membrane compartment
to another. The cellular roles of PITPs include inositol
lipid signaling, PtdIns metabolism, and membrane
trafficking. Class III PITPs, exemplified by the Sec14p
family, are found in yeast and plants but are unrelated
in sequence and structure to Class I and II PITPs and
belong to a different superfamily.
Length = 251
Score = 84.3 bits (209), Expect = 7e-21
Identities = 31/77 (40%), Positives = 39/77 (50%), Gaps = 14/77 (18%)
Query: 22 GGDYVREEDPSIYVSKTTGRGPLSENWISEYWNAVKEDPTVSHDNKSMMCAYKLCKIQLN 81
DY EEDP ++ SK TGRGPL + W K +MCAYKL +
Sbjct: 148 SKDYKPEEDPKLFKSKKTGRGPLRKGWRKS--------------TKPIMCAYKLVTVDFP 193
Query: 82 YWGIQSKVERFIADTGK 98
YWG+Q+KVE FI +
Sbjct: 194 YWGLQNKVENFIQKVER 210
>gnl|CDD|176897 cd08888, SRPBCC_PITPNA-B_like, Lipid-binding SRPBCC domain of
mammalian PITPNA, -B, and related proteins (Class I
PITPs). This subgroup includes the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of
mammalian Class 1 phosphatidylinositol transfer proteins
(PITPs), PITPNA/PITPalpha and PITPNB/PITPbeta,
Drosophila vibrator, and related proteins. These are
single domain proteins belonging to the PITP family of
lipid transfer proteins, and to the SRPBCC domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. In vitro, PITPs bind phosphatidylinositol
(PtdIns), as well as phosphatidylcholine (PtdCho) but
with a lower affinity. They transfer these lipids from
one membrane compartment to another. The cellular roles
of PITPs include inositol lipid signaling, PtdIns
metabolism, and membrane trafficking. In addition,
PITPNB transfers sphingomyelin in vitro, with a low
affinity. PITPNA is found chiefly in the nucleus and
cytoplasm; it is enriched in the brain and predominantly
localized in the axons. A reduced expression of PITPNA
contributes to the neurodegenerative phenotype of the
mouse vibrator mutation. The role of PITPNA in vivo may
be to provide PtdIns for localized PI3K-dependent
signaling, thereby controlling the polarized extension
of axonal processes. PITPNA homozygous null mice die
soon after birth from complicated organ failure,
including intestinal and hepatic steatosis,
hypoglycemia, and spinocerebellar disease. PITPNB is
associated with the Golgi and ER, and is highly
expressed in the liver. Deletion of the PITPNB gene
results in embryonic lethality. The PtdIns and PtdCho
exchange activity of PITPNB is required for
COPI-mediated retrograde transport from the Golgi to the
ER. Drosophila vibrator localizes to the ER, and has an
essential role in cytokinesis during mitosis and
meiosis.
Length = 258
Score = 75.6 bits (186), Expect = 1e-17
Identities = 30/72 (41%), Positives = 42/72 (58%), Gaps = 9/72 (12%)
Query: 22 GGDYVREEDPSIYVSKTTGRGPLSENWISEYWNAVKEDPTVSHDNKSMMCAYKLCKIQLN 81
DY +EDP+ + S+ TGRGPL NW E ++D +MCAYKL ++
Sbjct: 150 PKDYKADEDPAKFQSEKTGRGPLGPNWKKE--LVNQKDC-------PIMCAYKLVTVEFK 200
Query: 82 YWGIQSKVERFI 93
+WG+Q+KVE FI
Sbjct: 201 WWGLQNKVENFI 212
>gnl|CDD|176899 cd08890, SRPBCC_PITPNC1_like, Lipid-binding SRPBCC domain of
mammalian PITPNC1,and related proteins (Class IIB
PITPs). This subgroup includes the N-terminal SRPBCC
(START/RHO_alpha_C /PITP /Bet_v1/CoxG/CalC) domain of
mammalian Class IIB phosphatidylinositol transfer
protein (PITP), PITPNC1/RdgBbeta, and related proteins.
These are metazoan proteins belonging to the PITP family
of lipid transfer proteins, and to the SRPBCC domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. In vitro, PITPs bind phosphatidylinositol
(PtdIns), as well as phosphatidylcholine (PtdCho) but
with a lower affinity. They transfer these lipids from
one membrane compartment to another. The cellular roles
of PITPs include inositol lipid signaling, PtdIns
metabolism, and membrane trafficking. Mammalian PITPNC1
contains an amino-terminal SRPBCC PITP-like domain and a
short carboxyl-terminal domain. It is a cytoplasmic
protein, and is ubiquitously expressed. It can transfer
phosphatidylinositol (PtdIns) in vitro with a similar
ability to other PITPs.
Length = 250
Score = 61.4 bits (149), Expect = 2e-12
Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 14/69 (20%)
Query: 25 YVREEDPSIYVSKTTGRGPLSENWISEYWNAVKEDPTVSHDNKSMMCAYKLCKIQLNYWG 84
Y EEDP + S+ TGRGPL E W +K +MC+YKL ++ WG
Sbjct: 150 YKEEEDPKYFKSEKTGRGPLKEGW--------------RETHKPIMCSYKLVTVKFEVWG 195
Query: 85 IQSKVERFI 93
+Q++VE+F+
Sbjct: 196 LQTRVEQFV 204
>gnl|CDD|223690 COG0617, PcnB, tRNA nucleotidyltransferase/poly(A) polymerase
[Translation, ribosomal structure and biogenesis].
Length = 412
Score = 27.8 bits (62), Expect = 2.0
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 15/42 (35%)
Query: 85 IQSKVERFIADTGKPSGRALPRHFR-------RALRFAVTLD 119
++++V R I G S R FR RA RFA L
Sbjct: 139 LENRVLRHI---GDASER-----FREDPLRILRAARFAARLG 172
>gnl|CDD|147044 pfam04691, ApoC-I, Apolipoprotein C-I (ApoC-1). Apolipoprotein
C-I (ApoC-1) is a water-soluble protein component of
plasma lipoprotein. It solubalises lipids and regulates
lipid metabolism. ApoC-1 transfers among HDL (high
density lipoprotein), VLDL (very low-density
lipoprotein) and chylomicrons. ApoC-1 activates
lecithin:choline acetyltransferase (LCAT), inhibits
cholesteryl ester transfer protein, can inhibit hepatic
lipase and phospholipase 2 and can stimulate cell
growth. ApoC-1 delays the clearance of beta-VLDL by
inhibiting its uptake via the LDL receptor-related
pathway. ApoC-1 has been implicated in
hypertriglyceridemia, and Alzheimer's disease.
Length = 61
Score = 25.2 bits (55), Expect = 4.8
Identities = 15/51 (29%), Positives = 20/51 (39%), Gaps = 11/51 (21%)
Query: 8 TEVGNTLYKTKCLYGGDYVREEDPSIYVSKTTGRGPLSENWISEYWNAVKE 58
E GNTL D + I S+ + + NW SE + VKE
Sbjct: 16 KEFGNTL--------EDKAKTAIDRIKQSELMAK---TRNWFSETFEKVKE 55
>gnl|CDD|238642 cd01317, DHOase_IIa, Dihydroorotase (DHOase), subgroup IIa; DHOases
catalyze the reversible interconversion of carbamoyl
aspartate to dihydroorotate, a key reaction in
pyrimidine biosynthesis. This subgroup also contains
proteins that lack the active site, like unc-33, a
C.elegans protein involved in axon growth.
Length = 374
Score = 26.0 bits (58), Expect = 7.2
Identities = 14/42 (33%), Positives = 17/42 (40%), Gaps = 4/42 (9%)
Query: 93 IADTGKPSGRALPRHFRRALRFAVTLDKP--CRCLESMLARH 132
+D GKP RRAL +A LD P + LA
Sbjct: 109 FSDDGKPI--QDAELLRRALEYAAMLDLPIIVHPEDPSLAGG 148
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 0.133 0.419
Gapped
Lambda K H
0.267 0.0694 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,420,533
Number of extensions: 531618
Number of successful extensions: 431
Number of sequences better than 10.0: 1
Number of HSP's gapped: 426
Number of HSP's successfully gapped: 11
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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 (24.3 bits)