RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy607
(129 letters)
>gnl|CDD|237981 cd00014, CH, Calponin homology domain; actin-binding domain which
may be present as a single copy or in tandem repeats
(which increases binding affinity). The CH domain is
found in cytoskeletal and signal transduction proteins,
including actin-binding proteins like spectrin,
alpha-actinin, dystrophin, utrophin, and fimbrin,
proteins essential for regulation of cell shape
(cortexillins), and signaling proteins (Vav).
Length = 107
Score = 32.3 bits (74), Expect = 0.022
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 67 MKEDLAEWLNNLYVE-LHMNVANFMDRLDTGVTLCR 101
KE+L W+N + E + + NF L G+ LC+
Sbjct: 2 QKEELLRWINKVLGEYGPVTINNFSTDLKDGIALCK 37
>gnl|CDD|131957 TIGR02911, sulfite_red_B, sulfite reductase, subunit B. Members of
this protein family include the B subunit, one of three
subunits, of the anaerobic sulfite reductase of
Salmonella, and close homologs from various Clostridum
species, where the three-gene neighborhood is preserved.
Two such gene clusters are found in Clostridium
perfringens, but it may be that these sets of genes
correspond to the distinct assimilatory and
dissimilatory forms as seen in Clostridium pasteurianum
[Central intermediary metabolism, Sulfur metabolism].
Length = 261
Score = 30.5 bits (69), Expect = 0.18
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 57 FKSSEEYLYAMKEDLAEWLNNLYVELHMNVANFMDRLDTG 96
FK+ ++ L+ KED+AEW N+ + L ++ A + + G
Sbjct: 137 FKTPDDILF--KEDIAEWKGNINLTLTLDEAEEDYKGNIG 174
>gnl|CDD|226303 COG3780, COG3780, DNA endonuclease related to intein-encoded
endonucleases [DNA replication, recombination, and
repair].
Length = 266
Score = 30.2 bits (68), Expect = 0.25
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 54 LRPFKSSEEYLYA-MKEDLAEWLNNLYVELHMNVANFMDRLDTGVTLCRGKSTFFKSSIK 112
+R F SE Y+ KE + ++NL +EL M +++L T+ G S + IK
Sbjct: 158 VRGFFDSEGYVEIDRKEKVYVAVSNLILELLMFSRGLLEKLGIKSTILEGGSKGSRVLIK 217
Query: 113 EQRRSY 118
+R Y
Sbjct: 218 GERYVY 223
>gnl|CDD|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is
composed of two C4-type zinc fingers. DNA-binding
domain of Tailless (TLX) is composed of two C4-type zinc
fingers. Each zinc finger contains a group of four Cys
residues which co-ordinates a single zinc atom. TLX
interacts with specific DNA sites upstream of the target
gene and modulates the rate of transcriptional
initiation. TLX is an orphan receptor that is expressed
by neural stem/progenitor cells in the adult brain of
the subventricular zone (SVZ) and the dentate gyrus
(DG). It plays a key role in neural development by
promoting cell cycle progression and preventing
apoptosis in the developing brain. Like other members of
the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, TLX has a
central well conserved DNA-binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 92
Score = 27.8 bits (62), Expect = 0.82
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 96 GVTLCRGKSTFFKSSIKEQRRSYC 119
G+ C G S FFK SI+ R+ C
Sbjct: 22 GIYACDGCSGFFKRSIRRNRQYVC 45
>gnl|CDD|219562 pfam07766, LETM1, LETM1-like protein. Members of this family are
inner mitochondrial membrane proteins which play a role
in potassium and hydrogen ion exchange. Deletion of
LETM1 is thought to be involved in the development of
Wolf-Hirschhorn syndrome in humans.
Length = 268
Score = 28.4 bits (64), Expect = 0.92
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 52 RGLRPFKSSEEYLYAMKEDLAEWLN 76
RG+R SEE +++ L EWL+
Sbjct: 232 RGMRALGLSEE---RLRDQLQEWLD 253
>gnl|CDD|143515 cd06957, NR_DBD_PNR_like_2, DNA-binding domain of the photoreceptor
cell-specific nuclear receptor (PNR) like is composed of
two C4-type zinc fingers. The DNA-binding domain of the
photoreceptor cell-specific nuclear receptor (PNR)
nuclear receptor-like family is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which coordinates a single zinc atom. PNR
interacts with specific DNA sites upstream of the target
gene and modulates the rate of transcriptional
initiation. This family includes nuclear receptor
Tailless (TLX), photoreceptor cell-specific nuclear
receptor (PNR) and related receptors. TLX is an orphan
receptor that plays a key role in neural development by
regulating cell cycle progression and exit of neural
stem cells in the developing brain. PNR is expressed
only in the outer layer of retinal photoreceptor cells.
It may be involved in the signaling pathway regulating
photoreceptor differentiation and/or maintenance. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, PNR-like
receptors have a central well-conserved DNA-binding
domain (DBD), a variable N-terminal domain, a flexible
hinge and a C-terminal ligand binding domain (LBD).
Length = 82
Score = 27.4 bits (61), Expect = 0.99
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 17/42 (40%)
Query: 96 GVTLCRGKSTFFKSSIKEQ-----------------RRSYCP 120
GV C G S FFK S+++ RR++CP
Sbjct: 14 GVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCP 55
>gnl|CDD|214479 smart00033, CH, Calponin homology domain. Actin binding domains
present in duplicate at the N-termini of spectrin-like
proteins (including dystrophin, alpha-actinin). These
domains cross-link actin filaments into bundles and
networks. A calponin homology domain is predicted in
yeasst Cdc24p.
Length = 101
Score = 27.3 bits (61), Expect = 1.1
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 69 EDLAEWLNNLYVE-LHMNVANFMDRLDTGVTLCR 101
+ L W+N+L E V NF L GV LC
Sbjct: 1 KTLLRWVNSLLAEYDKPPVTNFSSDLKDGVALCA 34
>gnl|CDD|143545 cd07171, NR_DBD_ER, DNA-binding domain of estrogen receptors (ER)
is composed of two C4-type zinc fingers. DNA-binding
domain of estrogen receptors (ER) is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which coordinates a single zinc
atom. ER interacts with specific DNA sites upstream of
the target gene and modulates the rate of
transcriptional initiation. Estrogen receptor is a
transcription regulator that mediates the biological
effects of hormone estrogen. The binding of estrogen to
the receptor triggers the dimerization and the binding
of the receptor dimer to estrogen response element,
which is a palindromic inverted repeat:
5'GGTCAnnnTGACC-3', of target genes. Through ER,
estrogen regulates development, reproduction and
homeostasis. Like other members of the nuclear receptor
(NR) superfamily of ligand-activated transcription
factors, ER has a central well-conserved DNA binding
domain (DBD), a variable N-terminal domain, a
non-conserved hinge and a C-terminal ligand binding
domain (LBD).
Length = 82
Score = 27.2 bits (60), Expect = 1.3
Identities = 11/25 (44%), Positives = 12/25 (48%)
Query: 96 GVTLCRGKSTFFKSSIKEQRRSYCP 120
GV C G FFK SI+ CP
Sbjct: 19 GVWSCEGCKAFFKRSIQGHNDYICP 43
>gnl|CDD|213358 cd12824, ZntB-like, Salmonella typhimurium Zn2+ transporter
ZntB-like subfamily. A bacterial subfamily belonging to
the Escherichia coli CorA-Salmonella typhimurium
ZntB_like family (EcCorA_ZntB-like) family of the MIT
superfamily of essential membrane proteins involved in
transporting divalent cations (uptake or efflux) across
membranes. This subfamily includes the Zn2+ transporter
Salmonella typhimurium ZntB which mediates the efflux of
Zn2+ (and Cd2+). Structures of the intracellular domain
of Vibrio parahaemolyticus and Salmonella typhimurium
ZntB form funnel-shaped homopentamers, the tip of the
funnel is formed from two C-terminal transmembrane (TM)
helices from each monomer, and the large opening of the
funnel from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA, and
Mrs2p. Natural variants such as GVN and GIN, which occur
in proteins belonging to this subfamily, may be
associated with the transport of different divalent
cations, such as zinc and cadmium. The functional
diversity of MIT transporters may also be due to minor
structural differences regulating gating, substrate
selection, and transport.
Length = 290
Score = 27.9 bits (62), Expect = 1.7
Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 5/79 (6%)
Query: 42 ATPTATLVETRGL-----RPFKSSEEYLYAMKEDLAEWLNNLYVELHMNVANFMDRLDTG 96
A P L+ + R + ++ L + D AE L E +N + R
Sbjct: 144 APPPYALIALQRRLFRIRRQIRPQQQALRPLITDPAELLVTSDRETLRRASNNVTRYLET 203
Query: 97 VTLCRGKSTFFKSSIKEQR 115
+ CR + + IK QR
Sbjct: 204 LDFCRTRVALLQDEIKAQR 222
>gnl|CDD|143518 cd06960, NR_DBD_HNF4A, DNA-binding domain of heptocyte nuclear
factor 4 (HNF4) is composed of two C4-type zinc fingers.
DNA-binding domain of hepatocyte nuclear factor 4
(HNF4) is composed of two C4-type zinc fingers. Each
zinc finger contains a group of four Cys residues which
co-ordinates a single zinc atom. HNF4 interacts with a
DNA site, composed of two direct repeats of AGTTCA with
1 bp spacer, which is upstream of target genes and
modulates the rate of transcriptional initiation. HNF4
is a member of the nuclear receptor superfamily. HNF4
plays a key role in establishing and maintenance of
hepatocyte differentiation in the liver. It is also
expressed in gut, kidney, and pancreatic beta cells.
HNF4 was originally classified as an orphan receptor,
but later it is found that HNF4 binds with very high
affinity to a variety of fatty acids. However, unlike
other nuclear receptors, the ligands do not act as a
molecular switch for HNF4. They seem to constantly bind
to the receptor, which is constitutively active as a
transcription activator. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, HNF4 has a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 76
Score = 26.4 bits (59), Expect = 1.9
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 96 GVTLCRGKSTFFKSSIKEQRRSYCP 120
GV C G FF+ S+++ R C
Sbjct: 14 GVLSCNGCKGFFRRSVRKNRTYTCR 38
>gnl|CDD|143539 cd07165, NR_DBD_DmE78_like, DNA-binding domain of Drosophila
ecdysone-induced protein 78 (E78) like is composed of
two C4-type zinc fingers. DNA-binding domain of
proteins similar to Drosophila ecdysone-induced protein
78 (E78) is composed of two C4-type zinc fingers. Each
zinc finger contains a group of four Cys residues which
coordinates a single zinc atom. E78 interacts with
specific DNA sites upstream of the target gene and
modulates the rate of transcriptional initiation.
Drosophila ecdysone-induced protein 78 (E78) is a
transcription factor belonging to the nuclear receptor
superfamily. E78 is a product of the ecdysone-inducible
gene found in an early late puff locus at position 78C
during the onset of Drosophila metamorphosis. An E78
orthologue from the Platyhelminth Schistosoma mansoni
(SmE78) has also been identified. It is the first E78
orthologue known outside of the molting animals--the
Ecdysozoa. The SmE78 may be involved in transduction of
an ecdysone signal in S. mansoni, consistent with its
function in Drosophila. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, E78-like receptors have a central
well conserved DNA-binding domain (DBD), a variable
N-terminal domain, a non-conserved hinge and a
C-terminal ligand binding domain (LBD).
Length = 81
Score = 26.4 bits (58), Expect = 2.0
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 96 GVTLCRGKSTFFKSSIKEQRRSYC 119
GVT C G FF+ SI++Q C
Sbjct: 14 GVTSCEGCKGFFRRSIQKQIEYRC 37
>gnl|CDD|143527 cd06969, NR_DBD_NGFI-B, DNA-binding domain of the orphan nuclear
receptor, nerve growth factor-induced-B. DNA-binding
domain (DBD) of the orphan nuclear receptor, nerve
growth factor-induced-B (NGFI-B) is composed of two
C4-type zinc fingers. Each zinc finger contains a group
of four Cys residues which co-ordinates a single zinc
atom. NGFI-B interacts with specific DNA sites upstream
of the target gene and modulates the rate of
transcriptional initiation. NGFI-B is a member of the
nuclear-steroid receptor superfamily. NGFI-B is
classified as an orphan receptor because no ligand has
yet been identified. NGFI-B is an early immediate gene
product of embryo development that is rapidly produced
in response to a variety of cellular signals including
nerve growth factor. It is involved in T-cell-mediated
apoptosis, as well as neuronal differentiation and
function. NGFI-B regulates transcription by binding to a
specific DNA target upstream of its target genes and
regulating the rate of transcriptional initiation.
NGFI-B binds to the NGFI-B response element (NBRE)
5'-(A/T)AAAGGTCA as a monomer. Like other members of the
nuclear receptor (NR) superfamily of ligand-activated
transcription factors, NGFI-B has a central
well-conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 75
Score = 26.3 bits (58), Expect = 2.3
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 96 GVTLCRGKSTFFKSSIKEQRRSYC 119
GV C G FFK ++++ + C
Sbjct: 16 GVRTCEGCKGFFKRTVQKNAKYVC 39
>gnl|CDD|143529 cd07154, NR_DBD_PNR_like, The DNA-binding domain of the
photoreceptor cell-specific nuclear receptor (PNR)
nuclear receptor-like family. The DNA-binding domain of
the photoreceptor cell-specific nuclear receptor (PNR)
nuclear receptor-like family is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which coordinates a single zinc atom. PNR
interacts with specific DNA sites upstream of the target
gene and modulates the rate of transcriptional
initiation. This family includes nuclear receptor
Tailless (TLX), photoreceptor cell-specific nuclear
receptor (PNR) and related receptors. TLX is an orphan
receptor that plays a key role in neural development by
regulating cell cycle progression and exit of neural
stem cells in the developing brain. PNR is expressed
only in the outer layer of retinal photoreceptor cells.
It may be involved in the signaling pathway regulating
photoreceptor differentiation and/or maintenance. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, PNR-like
receptors have a central well-conserved DNA-binding
domain (DBD), a variable N-terminal domain, a flexible
hinge and a C-terminal ligand binding domain (LBD).
Length = 73
Score = 26.0 bits (57), Expect = 2.5
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 96 GVTLCRGKSTFFKSSIKEQRRSYC 119
GV C G S FFK SI+ C
Sbjct: 14 GVYACDGCSGFFKRSIRRNLLYTC 37
>gnl|CDD|176730 cd08315, Death_TRAILR_DR4_DR5, Death domain of Tumor necrosis
factor-Related Apoptosis-Inducing Ligand Receptors.
Death Domain (DD) found in Tumor necrosis
factor-Related Apoptosis-Inducing Ligand (TRAIL)
Receptors. In mammals, this family includes TRAILR1
(also called DR4 or TNFRSF10A) and TRAILR2 (also called
DR5, TNFRSF10B, or KILLER). They function as receptors
for the cytokine TRAIL and are involved in apoptosis
signaling pathways. TRAIL preferentially induces
apoptosis in cancer cells while exhibiting little
toxicity in normal cells. DDs are protein-protein
interaction domains found in a variety of domain
architectures. Their common feature is that they form
homodimers by self-association or heterodimers by
associating with other members of the DD superfamily
including CARD (Caspase activation and recruitment
domain), DED (Death Effector Domain), and PYRIN. They
serve as adaptors in signaling pathways and can recruit
other proteins into signaling complexes.
Length = 96
Score = 26.1 bits (58), Expect = 2.9
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 10/65 (15%)
Query: 12 TLKYSWRDFLIQSYEIPYPNWHQLMNMAQMATPTATLVETRGLRPFKSSEEYLYAMKEDL 71
TL+ S+ F E+P+ +W++LM ++ + + + + E LY M L
Sbjct: 5 TLRRSFDHF---IKEVPFDSWNRLMRQLGLSENEIDVAKAN----ERVTREQLYQM---L 54
Query: 72 AEWLN 76
W+N
Sbjct: 55 LTWVN 59
>gnl|CDD|153367 cd07683, F-BAR_srGAP1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase
Activating Protein 1. F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. Slit-Robo GTPase Activating Proteins
(srGAPs) are Rho GAPs that interact with Robo1, the
transmembrane receptor of Slit proteins. Slit proteins
are secreted proteins that control axon guidance and the
migration of neurons and leukocytes. Vertebrates contain
three isoforms of srGAPs. srGAP1, also called Rho
GTPase-Activating Protein 13 (ARHGAP13), is a Cdc42- and
RhoA-specific GAP and is expressed later in the
development of CNS (central nervous system) tissues. It
is an important downstream signaling molecule of Robo1.
srGAP1 contains an N-terminal F-BAR domain, a Rho GAP
domain, and a C-terminal SH3 domain. F-BAR domains form
banana-shaped dimers with a positively-charged concave
surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 253
Score = 26.6 bits (58), Expect = 3.6
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 47 TLVETRGLRPFKSSEEYLYAMKEDLAEWLNNLY 79
+ R FK S+E + + EDL + LN LY
Sbjct: 105 MQISEDSTRMFKKSKEIAFQLHEDLMKVLNELY 137
>gnl|CDD|143538 cd07164, NR_DBD_PNR_like_1, DNA-binding domain of the photoreceptor
cell-specific nuclear receptor (PNR) like proteins is
composed of two C4-type zinc fingers. DNA-binding
domain of the photoreceptor cell-specific nuclear
receptor (PNR) like proteins is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom. PNR
interacts with specific DNA sites upstream of the target
gene and modulates the rate of transcriptional
initiation. PNR is a member of nuclear receptor
superfamily of the ligand-activated transcription
factors. PNR is expressed only in the outer layer of
retinal photoreceptor cells. It may be involved in the
signaling pathway regulating photoreceptor
differentiation and/or maintenance. It most likely binds
to DNA as a homodimer. Like other members of the nuclear
receptor (NR) superfamily of ligand-activated
transcription factors, PNR has a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 78
Score = 25.5 bits (56), Expect = 3.9
Identities = 11/26 (42%), Positives = 12/26 (46%)
Query: 96 GVTLCRGKSTFFKSSIKEQRRSYCPE 121
GV C G FFK SI+ C E
Sbjct: 14 GVPSCDGCRGFFKRSIRRNLAYVCKE 39
>gnl|CDD|173255 PRK14794, PRK14794, lipoprotein signal peptidase; Provisional.
Length = 136
Score = 26.2 bits (57), Expect = 4.0
Identities = 10/46 (21%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 9 FGNTLKYSWRDFLIQSYEIPYPNWH-QLMNMAQMATPTATLVETRG 53
GN + +R +++ S++ + +WH N+A +A L+
Sbjct: 74 MGNLIDRVFRGYVVDSFDFYWRDWHWPAFNLADIAIVLGALLFVSS 119
>gnl|CDD|211331 cd02557, PseudoU_synth_ScRIB2, Pseudouridine synthases similar to
Saccharomyces cerevisiae RIB2. Pseudouridine synthase,
Saccharomyces cerevisiae RIB2_like. This group is
comprised of eukaryotic and bacterial proteins similar
to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p
and human hRPUDSD2. S. cerevisiae RIB2 displays two
distinct catalytic activities. The N-terminal domain of
RIB2 is RNA:psi-synthase which makes psi32 on
cytoplasmic tRNAs. Psi32 is highly phylogenetically
conserved. The C-terminal domain of RIB2 has a DRAP
deaminase activity which catalyses the formation of
5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione
5'-phosphate from
2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone
5'-phosphate during riboflavin biosynthesis. S.
cerevisiae Pus6p makes the psi31 of cytoplasmic and
mitochondrial tRNAs.
Length = 213
Score = 26.4 bits (59), Expect = 4.6
Identities = 8/20 (40%), Positives = 11/20 (55%), Gaps = 3/20 (15%)
Query: 13 LKYSWRDFLIQSYEIPYPNW 32
L+Y D+ SYE P+W
Sbjct: 195 LRYEGPDW---SYETELPDW 211
>gnl|CDD|143512 cd06916, NR_DBD_like, DNA-binding domain of nuclear receptors is
composed of two C4-type zinc fingers. DNA-binding
domain of nuclear receptors is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom. It
interacts with a specific DNA site upstream of the
target gene and modulates the rate of transcriptional
initiation. Nuclear receptors form a superfamily of
ligand-activated transcription regulators, which
regulate various physiological functions, from
development, reproduction, to homeostasis and metabolism
in animals (metazoans). The family contains not only
receptors for known ligands but also orphan receptors
for which ligands do not exist or have not been
identified. NRs share a common structural organization
with a central well conserved DNA binding domain (DBD),
a variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD). Most nuclear
receptors bind as homodimers or heterodimers to their
target sites, which consist of two hexameric half-sites.
Specificity is determined by the half-site sequence, the
relative orientation of the half-sites and the number of
spacer nucleotides between the half-sites. However, a
growing number of nuclear receptors have been reported
to bind to DNA as monomers.
Length = 72
Score = 25.2 bits (56), Expect = 5.2
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 96 GVTLCRGKSTFFKSSIKEQRRSYCP 120
GV C G FF+ S++ CP
Sbjct: 14 GVLTCEGCKGFFRRSVRRNLEYTCP 38
>gnl|CDD|201004 pfam00105, zf-C4, Zinc finger, C4 type (two domains). In nearly
all cases, this is the DNA binding domain of a nuclear
hormone receptor. The alignment contains two Zinc finger
domains that are too dissimilar to be aligned with each
other.
Length = 70
Score = 24.5 bits (54), Expect = 7.9
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 96 GVTLCRGKSTFFKSSIKEQRRSYCP 120
GV C G FF+ SI++ CP
Sbjct: 16 GVLTCEGCKGFFRRSIQKNIVYTCP 40
>gnl|CDD|185340 PRK15443, pduE, propanediol dehydratase small subunit; Provisional.
Length = 138
Score = 25.3 bits (56), Expect = 8.0
Identities = 8/18 (44%), Positives = 15/18 (83%)
Query: 54 LRPFKSSEEYLYAMKEDL 71
LRP++S++E L A+ ++L
Sbjct: 91 LRPYRSTKEELLAIADEL 108
>gnl|CDD|213299 cd05933, ACSBG_like, Bubblegum-like very long-chain fatty acid CoA
synthetase (VL-FACS). This family of very long-chain
fatty acid CoA synthetase is named bubblegum because
Drosophila melanogaster mutant bubblegum (BGM) has
elevated levels of very-long-chain fatty acids (VLCFA)
caused by a defective gene of this family. The human
homolog (hsBG) has been characterized as a very long
chain fatty acid CoA synthetase that functions
specifically in the brain; hsBG may play a central role
in brain VLCFA metabolism and myelinogenesis. VL-FACS is
involved in the first reaction step of very long chain
fatty acid degradation. It catalyzes the formation of
fatty acyl-CoA in a two-step reaction: the formation of
a fatty acyl-AMP molecule as an intermediate, and the
formation of a fatty acyl-CoA. Free fatty acids must be
"activated" to their CoA thioesters before participating
in most catabolic and anabolic reactions.
Length = 594
Score = 25.8 bits (57), Expect = 9.1
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 15 YSWRDFLIQSYEIPYPNWHQLMNMAQMATPTATLVETRG 53
YSW++F+ IP ++ +Q TL+ T G
Sbjct: 123 YSWKEFMELGRSIPDEQLDAIIE-SQKPNQCCTLIYTSG 160
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 0.133 0.410
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,536,396
Number of extensions: 539183
Number of successful extensions: 493
Number of sequences better than 10.0: 1
Number of HSP's gapped: 491
Number of HSP's successfully gapped: 29
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
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 (21.9 bits)
S2: 53 (24.3 bits)