RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11574
(136 letters)
>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 = 100 bits (250), Expect = 7e-27
Identities = 41/54 (75%), Positives = 43/54 (79%), Gaps = 5/54 (9%)
Query: 10 YQVGQLYSVAEASKNETGGGEGIEVLVNEPFDNVPLLGGKFTKGQYTKKIYHLQ 63
YQVGQLYSVAEASKNETGGGEGIEVLVNEP++ KGQYT KIYHLQ
Sbjct: 16 YQVGQLYSVAEASKNETGGGEGIEVLVNEPYEK-----DDGEKGQYTHKIYHLQ 64
>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 = 80.4 bits (199), Expect = 2e-19
Identities = 33/55 (60%), Positives = 39/55 (70%), Gaps = 5/55 (9%)
Query: 9 MYQVGQLYSVAEASKNETGGGEGIEVLVNEPFDNVPLLGGKFTKGQYTKKIYHLQ 63
YQ+GQLY VA+ASK ETG GEG+EVL NEP+++ KGQYT KIYHL
Sbjct: 15 EYQIGQLYMVAKASKEETGSGEGVEVLKNEPYED-----ENGGKGQYTHKIYHLG 64
>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 = 79.1 bits (195), Expect = 6e-19
Identities = 31/55 (56%), Positives = 40/55 (72%), Gaps = 6/55 (10%)
Query: 10 YQVGQLYSVAEASKNETGG-GEGIEVLVNEPFDNVPLLGGKFTKGQYTKKIYHLQ 63
YQV QLY +A+ S+NE+ G G G+E+L NEP+++ P GG KGQYT KIYHL
Sbjct: 17 YQVAQLYMIAKKSRNESHGEGSGVEILSNEPYEDGP--GG---KGQYTHKIYHLG 66
>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 = 59.0 bits (143), Expect = 2e-11
Identities = 24/54 (44%), Positives = 35/54 (64%), Gaps = 6/54 (11%)
Query: 10 YQVGQLYSVAEASKNET-GGGEGIEVLVNEPFDNVPLLGGKFTKGQYTKKIYHL 62
Y++ QLY + + S+ E+ G G G+E+L N P+ + P GG GQYT KIYH+
Sbjct: 17 YRIAQLYMIQKKSREESKGEGSGVEILENRPYTDGP--GG---SGQYTHKIYHI 65
>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 = 47.9 bits (114), Expect = 2e-07
Identities = 21/53 (39%), Positives = 34/53 (64%), Gaps = 5/53 (9%)
Query: 10 YQVGQLYSVAEASKNETGGGEGIEVLVNEPFDNVPLLGGKFTKGQYTKKIYHL 62
Y++GQLY ++ S ++ GEG+EV+ NEP ++ P G GQ+T+K +L
Sbjct: 16 YRIGQLYMISRHSHEQSERGEGVEVVQNEPCED-PEHG----NGQFTEKRVYL 63
>gnl|CDD|222478 pfam13966, zf-RVT, zinc-binding in reverse transcriptase. This
domain would appear to be a zinc-binding region of a
putative reverse transcriptase.
Length = 86
Score = 31.0 bits (71), Expect = 0.044
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 56 TKKIYHLQRSSRQIS-RSELICVRKCEKNPPKTSFFGFLALW 96
K Y L R + ++I K PPK SFF +LA W
Sbjct: 4 VKSAYRLLRPTSPPVFWKKIIWFSKA---PPKVSFFAWLAAW 42
>gnl|CDD|148617 pfam07111, HCR, Alpha helical coiled-coil rod protein (HCR). This
family consists of several mammalian alpha helical
coiled-coil rod HCR proteins. The function of HCR is
unknown but it has been implicated in psoriasis in
humans and is thought to affect keratinocyte
proliferation.
Length = 739
Score = 30.4 bits (68), Expect = 0.28
Identities = 17/42 (40%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 52 KGQYTKKIYHLQRSSRQISRSELICV-----RKCEKNPPKTS 88
KG T + +LQ S ISR E ICV NPP T
Sbjct: 698 KGSLTVLLDNLQGLSEAISRDEDICVEDNQHPHTSPNPPPTP 739
>gnl|CDD|165177 PHA02834, PHA02834, chemokine receptor-like protein; Provisional.
Length = 323
Score = 27.2 bits (60), Expect = 2.9
Identities = 21/84 (25%), Positives = 33/84 (39%), Gaps = 8/84 (9%)
Query: 39 PFDNVPLLGGKFTKGQYTKKIYHLQRSSRQISRSELICVRKCEKNPPKTSFFGFLALWFS 98
PF+ V + + G YH ++ I +ELI C NP +F
Sbjct: 244 PFNIVLFINSLQSVGLIDIGCYHFKKIVYSIDIAELISFVHCCVNPIIYAFV-------- 295
Query: 99 GQNLHHHFRVPGKKTFNLIYRSTS 122
G+N F+ +T N+ R +S
Sbjct: 296 GKNFKKVFKNMFCRTNNIFIRQSS 319
>gnl|CDD|99918 cd05535, POLBc_epsilon, DNA polymerase type-B epsilon subfamily
catalytic domain. Three DNA-dependent DNA polymerases
type B (alpha, delta, and epsilon) have been identified
as essential for nuclear DNA replication in eukaryotes.
DNA polymerase (Pol) epsilon has been proposed to play a
role in elongation of the leading strand during DNA
replication. Pol epsilon might also have a role in DNA
repair. The structure of pol epsilon is characteristic
of this family with the exception that it contains a
large c-terminal domain with an unclear function.
Phylogenetic analyses indicate that Pol epsilon is the
ortholog to the archaeal Pol B3 rather than to Pol
alpha, delta, or zeta. This might be because pol epsilon
is ancestral to both archaea and eukaryotes DNA
polymerases type B.
Length = 621
Score = 26.9 bits (60), Expect = 3.6
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 55 YTKKIYHLQRSSRQISRSELICVR 78
Y++K+Y +++ RS IC R
Sbjct: 196 YSRKVYKKTHVTKEEERSTTICQR 219
>gnl|CDD|129988 TIGR00910, 2A0307_GadC, glutamate:gamma-aminobutyrate antiporter.
Lowered cutoffs from 1000/500 to 800/300, promoted from
subfamily to equivalog, and put into a Genome Property
DHH 9/1/2009 [Transport and binding proteins, Amino
acids, peptides and amines].
Length = 507
Score = 26.4 bits (58), Expect = 5.5
Identities = 9/29 (31%), Positives = 12/29 (41%)
Query: 89 FFGFLALWFSGQNLHHHFRVPGKKTFNLI 117
F G+ L +L F +PG LI
Sbjct: 379 FIGYFVLILKHPDLKRTFNIPGGIGGKLI 407
>gnl|CDD|185611 PTZ00428, PTZ00428, 60S ribosomal protein L4; Provisional.
Length = 381
Score = 25.8 bits (57), Expect = 7.9
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 40 FDNVPLLGGKFTKGQYTKKIYHLQRS 65
F + + G +T+ KK Y L R
Sbjct: 256 FKKLDKIFGTYTEASALKKGYTLPRP 281
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 0.135 0.410
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,839,908
Number of extensions: 582286
Number of successful extensions: 463
Number of sequences better than 10.0: 1
Number of HSP's gapped: 457
Number of HSP's successfully gapped: 18
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
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: 54 (24.6 bits)