RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11575
(80 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 = 146 bits (371), Expect = 6e-46
Identities = 52/69 (75%), Positives = 59/69 (85%)
Query: 1 MTCYKLVTAEFKWFGFQGRVENFIHKAERRLFTNFHRQVFCWIDRWHDLTMEDIRRIEEE 60
M YKLVT EFKW+G Q +VENFI K ERRLFTNFHRQVFCW+D+WH LTM+DIRR+E+E
Sbjct: 189 MCAYKLVTVEFKWWGLQNKVENFIQKQERRLFTNFHRQVFCWLDKWHGLTMDDIRRMEDE 248
Query: 61 TKKELDRQR 69
TKKELD R
Sbjct: 249 TKKELDEMR 257
>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 = 122 bits (307), Expect = 2e-36
Identities = 44/69 (63%), Positives = 52/69 (75%)
Query: 1 MTCYKLVTAEFKWFGFQGRVENFIHKAERRLFTNFHRQVFCWIDRWHDLTMEDIRRIEEE 60
M YKLVT +F ++G Q +VENFI K ER +F N+HRQ FCWID W DLTMEDIR EEE
Sbjct: 182 MCAYKLVTVDFPYWGLQNKVENFIQKVERDVFLNYHRQAFCWIDEWFDLTMEDIREFEEE 241
Query: 61 TKKELDRQR 69
TK+ LD +R
Sbjct: 242 TKELLDAKR 250
>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 = 105 bits (263), Expect = 8e-30
Identities = 38/66 (57%), Positives = 45/66 (68%), Gaps = 1/66 (1%)
Query: 1 MTCYKLVTAEFKWFGFQGRVENFIHKAE-RRLFTNFHRQVFCWIDRWHDLTMEDIRRIEE 59
M YKL T EF+++G Q +VENFIH RR T HRQ +CW D W LTMEDIRR+EE
Sbjct: 189 MCAYKLCTVEFRYWGMQTKVENFIHDQALRRTMTRAHRQAWCWQDEWTGLTMEDIRRLEE 248
Query: 60 ETKKEL 65
ET+ L
Sbjct: 249 ETQLHL 254
>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 = 78.6 bits (194), Expect = 1e-19
Identities = 33/68 (48%), Positives = 46/68 (67%), Gaps = 1/68 (1%)
Query: 1 MTCYKLVTAEFKWFGFQGRVENFIHK-AERRLFTNFHRQVFCWIDRWHDLTMEDIRRIEE 59
M YKL EF+++G Q ++E FIH A R++ HRQ +CW D W+ LTMEDIR++EE
Sbjct: 190 MCAYKLCKVEFRYWGMQTKIERFIHDVALRKVMLRAHRQAWCWQDEWYGLTMEDIRKLEE 249
Query: 60 ETKKELDR 67
ET+ L +
Sbjct: 250 ETQLALAQ 257
>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 = 75.2 bits (185), Expect = 2e-18
Identities = 29/68 (42%), Positives = 44/68 (64%)
Query: 1 MTCYKLVTAEFKWFGFQGRVENFIHKAERRLFTNFHRQVFCWIDRWHDLTMEDIRRIEEE 60
M YKLVT +F+ +G Q RVE F+HK R + HRQ F W+D W+D+TM+D+R E
Sbjct: 181 MCSYKLVTVKFEVWGLQTRVEQFVHKVVRDILLLGHRQAFAWVDEWYDMTMDDVREYERT 240
Query: 61 TKKELDRQ 68
+++ + +
Sbjct: 241 IQEKTNEK 248
>gnl|CDD|237273 PRK13018, PRK13018, cell division protein FtsZ; Provisional.
Length = 378
Score = 27.3 bits (61), Expect = 0.77
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 11/42 (26%)
Query: 47 HDLTMEDIRRIEEETKKELD-----------RQRLEGEVRGM 77
DLT+++ +ELD +EG+VR M
Sbjct: 284 PDLTLKEANEAASRITEELDPEANIIWGARIDPDMEGKVRVM 325
>gnl|CDD|169406 PRK08366, vorA, 2-ketoisovalerate ferredoxin oxidoreductase subunit
alpha; Reviewed.
Length = 390
Score = 26.5 bits (58), Expect = 1.6
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 48 DLTMEDIRRIEEETKKELDRQRLEGEV 74
D T+ D++ I E+ KK +++ +L+ EV
Sbjct: 357 DFTVNDVKAIAEDMKKVIEKGKLDKEV 383
>gnl|CDD|163660 cd07417, MPP_PP5_C, PP5, C-terminal metallophosphatase domain.
Serine/threonine protein phosphatase-5 (PP5) is a member
of the PPP gene family of protein phosphatases that is
highly conserved among eukaryotes and widely expressed
in mammalian tissues. PP5 has a C-terminal phosphatase
domain and an extended N-terminal TPR (tetratricopeptide
repeat) domain containing three TPR motifs. The PPP
(phosphoprotein phosphatase) family, to which PP5
belongs, is one of two known protein phosphatase
families specific for serine and threonine. The PPP
family also includes: PP1, PP2A, PP2B (calcineurin),
PP4, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4
hydrolase. The PPP catalytic domain is defined by three
conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The
PPP enzyme family is ancient with members found in all
eukaryotes, and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 316
Score = 26.1 bits (58), Expect = 1.7
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 21/64 (32%)
Query: 12 KWFGFQGRVENFIHKAERRLFTNFHRQVFCWIDRWH-----------------DLTMEDI 54
K +GF+G V K ++F + +VF W+ H +T++DI
Sbjct: 136 KMYGFEGEV---KAKYNEQMF-DLFSEVFNWLPLAHLINGKVLVVHGGLFSDDGVTLDDI 191
Query: 55 RRIE 58
R+I+
Sbjct: 192 RKID 195
>gnl|CDD|131777 TIGR02730, carot_isom, carotene isomerase. Members of this family,
including sll0033 (crtH) of Synechocystis sp. PCC 6803,
catalyze a cis-trans isomerization of carotenes to the
all-trans lycopene, a reaction that can also occur
non-enzymatically in light through photoisomerization
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 493
Score = 25.5 bits (56), Expect = 3.3
Identities = 8/38 (21%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 42 WIDRWHDLTMEDIRRIEEETKKELDRQRLEGEVRGMKA 79
++ W L+ +D +E + + RLE G+ +
Sbjct: 377 SMEDWQGLSPKDYEAKKEADAERI-IDRLEKIFPGLDS 413
>gnl|CDD|217433 pfam03223, V-ATPase_C, V-ATPase subunit C.
Length = 371
Score = 24.9 bits (55), Expect = 5.1
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 13/58 (22%)
Query: 20 VENFIHKA-ERRLFTNFHRQVFCWIDRWHDLTMEDIRRIEEE-TKKELDRQRLEGEVR 75
VE+F K E++ +I R + E + E TK D ++ EG +
Sbjct: 234 VEDFKTKCREKK-----------FIVRDFKYSEELSEEEKRERTKLATDEKKQEGALL 280
>gnl|CDD|217096 pfam02547, Queuosine_synth, Queuosine biosynthesis protein.
Queuosine (Q) biosynthesis protein, or
S-adenosylmethionine:tRNA -ribosyltransferase-isomerase,
is required for the synthesis of the queuosine precursor
(oQ). It catalyzes the transfer and isomerisation of the
ribose moiety from AdoMet to the 7-aminomethyl group of
7-deazaguanine (preQ1-tRNA) to form epoxyqueuosine
(oQ-tRNA). Q is a hypermodified nucleoside usually found
at the first position of the anticodon of asparagine,
aspartate, histidine, and tyrosine tRNAs.
Length = 341
Score = 24.7 bits (55), Expect = 5.5
Identities = 9/26 (34%), Positives = 11/26 (42%), Gaps = 5/26 (19%)
Query: 16 FQGRVENFIH-----KAERRLFTNFH 36
G + FI+ K L TNFH
Sbjct: 273 GSGETDIFIYPGYRFKVVDALLTNFH 298
>gnl|CDD|233382 TIGR01372, soxA, sarcosine oxidase, alpha subunit family,
heterotetrameric form. This model describes the alpha
subunit of a family of known and putative
heterotetrameric sarcosine oxidases. Five operons of
such oxidases are found in Mesorhizobium loti and three
in Agrobacterium tumefaciens, a high enough copy number
to suggest that not all members are share the same
function. The model is designated as subfamily rather
than equivalog for this reason.Sarcosine oxidase
catalyzes the oxidative demethylation of sarcosine to
glycine. The reaction converts tetrahydrofolate to
5,10-methylene-tetrahydrofolate. The enzyme is known in
monomeric and heterotetrameric (alpha,beta,gamma,delta)
forms [Energy metabolism, Amino acids and amines].
Length = 985
Score = 24.7 bits (54), Expect = 5.8
Identities = 5/26 (19%), Positives = 13/26 (50%)
Query: 31 LFTNFHRQVFCWIDRWHDLTMEDIRR 56
L+ + ++D +D+T +D+
Sbjct: 495 LWPVPAGKGKAFVDYQNDVTAKDVEL 520
>gnl|CDD|133399 cd04772, HTH_TioE_rpt1, First Helix-Turn-Helix DNA binding domain
of the regulatory protein TioE. Putative
helix-turn-helix (HTH) regulatory protein, TioE, and
related proteins. TioE is part of the thiocoraline gene
cluster, which is involved in the biosynthesis of the
antitumor thiocoraline from the marine actinomycete,
Micromonospora. These proteins share the N-terminal DNA
binding domain with other transcription regulators of
the MerR superfamily that promote transcription by
reconfiguring the spacer between the -35 and -10
promoter elements. Proteins in this family are unique
within the MerR superfamily in that they are composed
of just two adjacent MerR-like N-terminal domains; this
CD contains the N-terminal or first repeat (rpt1) of
these tandem MerR-like domain proteins.
Length = 99
Score = 23.9 bits (52), Expect = 7.6
Identities = 7/25 (28%), Positives = 10/25 (40%), Gaps = 5/25 (20%)
Query: 21 ENFIHKAER-----RLFTNFHRQVF 40
I AER R++T+ H
Sbjct: 23 LGLIPPAERTANGYRIYTDKHIAAL 47
>gnl|CDD|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 24.4 bits (54), Expect = 9.1
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 9 AEFKWFGFQGRVENFIHKAERRLFTNFHRQ 38
AE FG + R + + E++ RQ
Sbjct: 211 AELTLFGAEDRYRQQLEQTEQQWLAAQRRQ 240
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
0.328 0.140 0.459
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,214,887
Number of extensions: 342597
Number of successful extensions: 762
Number of sequences better than 10.0: 1
Number of HSP's gapped: 760
Number of HSP's successfully gapped: 36
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.0 bits)