RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6019
(93 letters)
>gnl|CDD|233277 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum
calcium-translocating P-type ATPase. This model
describes the P-type ATPase responsible for
translocating calcium ions across the endoplasmic
reticulum membrane of eukaryotes , and is of particular
importance in the sarcoplasmic reticulum of skeletal
and cardiac muscle in vertebrates. These pumps transfer
Ca2+ from the cytoplasm to the lumen of the endoplasmic
reticulum. In humans and mice, at least, there are
multiple isoforms of the SERCA pump with overlapping
but not redundant functions. Defects in SERCA isoforms
are associated with diseases in humans. The calcium
P-type ATPases have been characterized as Type IIA
based on a phylogenetic analysis which distinguishes
this group from the Type IIB PMCA calcium pump modelled
by TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the latter of which is
modelled by TIGR01522 [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 917
Score = 63.6 bits (155), Expect = 2e-13
Identities = 29/46 (63%), Positives = 35/46 (76%), Gaps = 2/46 (4%)
Query: 45 KERNAESAIEALKEYEPEMGKVIRGDKSGVQKVRAKEIVPGDIVEV 90
+ERNAE AIEALKEYE E KV+R + V K AK++VPGDIVE+
Sbjct: 56 QERNAEKAIEALKEYESEHAKVLRDGRWSVIK--AKDLVPGDIVEL 99
>gnl|CDD|233438 TIGR01494, ATPase_P-type, ATPase, P-type (transporting), HAD
superfamily, subfamily IC. The P-type ATPases are a
large family of trans-membrane transporters acting on
charged substances. The distinguishing feature of the
family is the formation of a phosphorylated
intermediate (aspartyl-phosphate) during the course of
the reaction. Another common name for these enzymes is
the E1-E2 ATPases based on the two isolable
conformations: E1 (unphosphorylated) and E2
(phosphorylated). Generally, P-type ATPases consist of
only a single subunit encompassing the ATPase and ion
translocation pathway, however, in the case of the
potassium (TIGR01497) and sodium/potassium (TIGR01106)
varieties, these functions are split between two
subunits. Additional small regulatory or stabilizing
subunits may also exist in some forms. P-type ATPases
are nearly ubiquitous in life and are found in numerous
copies in higher organisms (at least 45 in Arabidopsis
thaliana, for instance ). Phylogenetic analyses have
revealed that the P-type ATPase subfamily is divided up
into groups based on substrate specificities and this
is represented in the various subfamily and equivalog
models that have been made: IA (K+) TIGR01497, IB
(heavy metals) TIGR01525, IIA1 (SERCA-type Ca++)
TIGR01116, IIA2 (PMR1-type Ca++) TIGR01522, IIB
(PMCA-type Ca++) TIGR01517, IIC (Na+/K+, H+/K+
antiporters) TIGR01106, IID (fungal-type Na+ and K+)
TIGR01523, IIIA (H+) TIGR01647, IIIB (Mg++) TIGR01524,
IV (phospholipid, flippase) TIGR01652 and V (unknown
specificity) TIGR01657. The crystal structure of one
calcium-pumping ATPase and an analysis of the fold of
the catalytic domain of the P-type ATPases have been
published. These reveal that the catalytic core of
these enzymes is a haloacid dehalogenase(HAD)-type
aspartate-nucleophile hydrolase. The location of the
ATP-binding loop in between the first and second HAD
conserved catalytic motifs defines these enzymes as
members of subfamily I of the HAD superfamily (see also
TIGR01493, TIGR01509, TIGR01549, TIGR01544 and
TIGR01545). Based on these classifications, the P-type
ATPase _superfamily_ corresponds to the IC subfamily of
the HAD superfamily.
Length = 543
Score = 45.8 bits (109), Expect = 3e-07
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 32 LASMAYFALTEYQKERNAESAIEALKEYE--PEMGKVIRGDKSGVQKVRAKEIVPGDIVE 89
L + F L +++ AE + +L + V+R G +++ AK++VPGD+V
Sbjct: 3 LFLVLVFVLLVVKQKLKAEDILRSLSDRLVNTRPATVLRN---GWKEIPAKDLVPGDVVL 59
Query: 90 VSE 92
V
Sbjct: 60 VKS 62
>gnl|CDD|223550 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 917
Score = 42.3 bits (100), Expect = 6e-06
Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 46 ERNAESAIEALKEYEPEMGKVIRGDKSGVQKVRAKEIVPGDIVEVSE 92
E AE A+EALK+ KV+R K ++ A E+VPGDIV +
Sbjct: 124 EYRAEKALEALKKMSSPKAKVLRDGK--FVEIPASELVPGDIVLLEA 168
>gnl|CDD|215733 pfam00122, E1-E2_ATPase, E1-E2 ATPase.
Length = 222
Score = 41.8 bits (99), Expect = 6e-06
Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 39 ALTEYQKERNAESAIEALKEYEPEMG-KVIRGDKSGVQKVRAKEIVPGDIVEV 90
AL E +E A A++ALK+ P VIR K +++ A E+V GDIV +
Sbjct: 10 ALLEAYQEYRARKALKALKKLLPPTAATVIRDGK--EEEIPADELVVGDIVLL 60
>gnl|CDD|233506 TIGR01647, ATPase-IIIA_H, plasma-membrane proton-efflux P-type
ATPase. This model describes the plasma membrane proton
efflux P-type ATPase found in plants, fungi, protozoa,
slime molds and archaea. The best studied representative
is from yeast.
Length = 754
Score = 39.6 bits (93), Expect = 6e-05
Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 46 ERNAESAIEALKEYEPEMGKVIRGDKSGVQKVRAKEIVPGDIV 88
E A +A+EALK+ +V+R K Q++ A E+VPGD+V
Sbjct: 76 ENKAGNAVEALKQSLAPKARVLRDGK--WQEIPASELVPGDVV 116
>gnl|CDD|233447 TIGR01525, ATPase-IB_hvy, heavy metal translocating P-type
ATPase. This model encompasses two equivalog models
for the copper and cadmium-type heavy metal
transporting P-type ATPases (TIGR01511 and TIGR01512)
as well as those species which score ambiguously
between both models. For more comments and references,
see the files on TIGR01511 and 01512.
Length = 556
Score = 37.2 bits (87), Expect = 4e-04
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 40 LTEYQKERNAESAIEALKEYEPEMGKVIRGDKSGVQKVRAKEIVPGDIVEVS 91
L E K R A A+ AL P +V++GD S ++V +E+ GDIV V
Sbjct: 34 LEERAKGR-ASDALSALLALAPSTARVLQGDGS-EEEVPVEELQVGDIVIVR 83
>gnl|CDD|225127 COG2217, ZntA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 713
Score = 35.7 bits (83), Expect = 0.001
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 39 ALTEYQKERNAESAIEALKEYEPEMGKVIRGDKSGVQKVRAKEIVPGDIVEV 90
L K R A AI AL + P+ V+RGD ++V +E+ GDIV V
Sbjct: 189 YLEARAKGR-ARRAIRALLDLAPKTATVVRGDG-EEEEVPVEEVQVGDIVLV 238
>gnl|CDD|211664 TIGR01512, ATPase-IB2_Cd, heavy
metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase.
This model describes the P-type ATPase primarily
responsible for translocating cadmium ions (and other
closely-related divalent heavy metals such as cobalt,
mercury, lead and zinc) across biological membranes.
These transporters are found in prokaryotes and plants.
Experimentally characterized members of the seed
alignment include: SP|P37617 from E. coli, SP|Q10866
from Mycobacterium tuberculosis and SP|Q59998 from
Synechocystis PCC6803. The cadmium P-type ATPases have
been characterized as Type IB based on a phylogenetic
analysis which combines the copper-translocating
ATPases with the cadmium-translocating species. This
model and that describing the copper-ATPases
(TIGR01511) are well separated, and thus we further
type the copper-ATPases as IB1 and the cadmium-ATPases
as IB2. Several sequences which have not been
characterized experimentally fall just below trusted
cutoff for both of these models (SP|Q9CCL1 from
Mycobacterium leprae, GP|13816263 from Sulfolobus
solfataricus, OMNI|NTL01CJ01098 from Campylobacter
jejuni, OMNI|NTL01HS01687 from Halobacterium sp.,
GP|6899169 from Ureaplasma urealyticum and OMNI|HP1503
from Helicobacter pylori) [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 536
Score = 33.8 bits (78), Expect = 0.006
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 42 EYQKERNAESAIEALKEYEPEMGKVIRGDKSGVQKVRAKEIVPGDIVEV 90
E A A++AL E P+ +V+RG +++V +E+ GD+V V
Sbjct: 35 EEYASGRARRALKALMELAPDTARVLRGG--SLEEVAVEELKVGDVVVV 81
>gnl|CDD|233445 TIGR01511, ATPase-IB1_Cu, copper-(or silver)-translocating P-type
ATPase. This model describes the P-type ATPase
primarily responsible for translocating copper ions
accross biological membranes. These transporters are
found in prokaryotes and eukaryotes. This model
encompasses those species which pump copper ions out of
cells or organelles (efflux pumps such as CopA of
Escherichia coli ) as well as those which pump the ion
into cells or organelles either for the purpose of
supporting life in extremely low-copper environments
(for example CopA of Enterococcus hirae ) or for the
specific delivery of copper to a biological complex for
which it is a necessary component (for example FixI of
Bradyrhizobium japonicum, or CtaA and PacS of
Synechocystis). The substrate specificity of these
transporters may, to a varying degree, include silver
ions (for example, CopA from Archaeoglobus fulgidus).
Copper transporters from this family are well known as
the genes which are mutated in two human disorders of
copper metabolism, Wilson's and Menkes' diseases. The
sequences contributing to the seed of this model are all
experimentally characterized. The copper P-type ATPases
have been characterized as Type IB based on a
phylogenetic analysis which combines the
copper-translocating ATPases with the
cadmium-translocating species. This model and that
describing the cadmium-ATPases (TIGR01512) are well
separated, and thus we further type the copper-ATPases
as IB1 (and the cadmium-ATPases as IB2). Several
sequences which have not been characterized
experimentally fall just below the cutoffs for both of
these models. A sequence from Enterococcus faecalis
scores very high against this model, but yet is
annotated as an "H+/K+ exchanging ATPase". BLAST of this
sequence does not hit anything else annotated in this
way. This error may come from the characterization paper
published in 1987. Accession GP|7415611 from
Saccharomyces cerevisiae appears to be mis-annotated as
a cadmium resistance protein. Accession
OMNI|NTL01HS00542 from Halobacterium which scores above
trusted for this model is annotated as
"molybdenum-binding protein" although no evidence can be
found for this classification [Cellular processes,
Detoxification, Transport and binding proteins, Cations
and iron carrying compounds].
Length = 572
Score = 33.0 bits (76), Expect = 0.013
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 47 RNAESAIEALKEYEPEMGKVIRGDKSGVQKVRAKEIVPGDIVEV 90
A A+ L + +P ++ D + V + + PGDIV V
Sbjct: 76 GRASDALSKLAKLQPSTATLLTDDGEIEE-VPVELLQPGDIVRV 118
>gnl|CDD|130176 TIGR01106, ATPase-IIC_X-K, sodium or proton efflux -- potassium
uptake antiporter, P-type ATPase, alpha subunit. This
model describes the P-type ATPases responsible for the
exchange of either protons or sodium ions for potassium
ions across the plasma membranes of eukaryotes. Unlike
most other P-type ATPases, members of this subfamily
require a beta subunit for activity. This model
encompasses eukaryotes and consists of two functional
types, a Na/K antiporter found widely distributed in
eukaryotes and a H/K antiporter found only in
vertebrates. The Na+ or H+/K+ antiporter P-type ATPases
have been characterized as Type IIC based on a published
phylogenetic analysis. Sequences from Blastocladiella
emersonii (GP|6636502, GP|6636502 and PIR|T43025), C.
elegans (GP|2315419, GP|6671808 and PIR|T31763) and
Drosophila melanogaster (GP|7291424) score below trusted
cutoff, apparently due to long branch length (excessive
divergence from the last common ancestor) as evidenced
by a phylogenetic tree. Experimental evidence is needed
to determine whether these sequences represent ATPases
with conserved function. Aside from fragments, other
sequences between trusted and noise appear to be
bacterial ATPases of unclear lineage, but most likely
calcium pumps [Energy metabolism, ATP-proton motive
force interconversion].
Length = 997
Score = 31.7 bits (72), Expect = 0.030
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 43 YQKERNAESAIEALKEYEPEMGKVIR-GDKSGVQKVRAKEIVPGDIVEV 90
Y +E + +E+ K P+ VIR G+K + A+++V GD+VEV
Sbjct: 122 YYQEAKSSKIMESFKNMVPQQALVIRDGEK---MSINAEQVVVGDLVEV 167
>gnl|CDD|130586 TIGR01523, ATPase-IID_K-Na, potassium and/or sodium efflux P-type
ATPase, fungal-type. Initially described as a calcium
efflux ATPase , more recent work has shown that the S.
pombe CTA3 gene is in fact a potassium ion efflux pump.
This model describes the clade of fungal P-type ATPases
responsible for potassium and sodium efflux. The degree
to which these pumps show preference for sodium or
potassium varies. This group of ATPases has been
classified by phylogentic analysis as type IID. The
Leishmania sequence (GP|3192903), which falls between
trusted and noise in this model, may very well turn out
to be an active potassium pump.
Length = 1053
Score = 31.1 bits (70), Expect = 0.047
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 45 KERNAESAIEALKEYEPEMGKVIRGDKSGVQKVRAKEIVPGDIVEV 90
+E AE +++LK M VIR KS + + ++VPGDI +
Sbjct: 101 QEYKAEKTMDSLKNLASPMAHVIRNGKS--DAIDSHDLVPGDICLL 144
>gnl|CDD|130585 TIGR01522, ATPase-IIA2_Ca, golgi membrane calcium-translocating
P-type ATPase. This model describes the P-type ATPase
responsible for translocating calcium ions across the
golgi membrane of fungi and animals , and is of
particular importance in the sarcoplasmic reticulum of
skeletal and cardiac muscle in vertebrates. The calcium
P-type ATPases have been characterized as Type IIA based
on a phylogenetic analysis which distinguishes this
group from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the former of which is
modelled by TIGR01116.
Length = 884
Score = 31.0 bits (70), Expect = 0.057
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 45 KERNAESAIEALKEYEPEMGKVIRGDKSGVQKVRAKEIVPGDIVEVS 91
+E +E ++EAL + P +IR K + V A +VPGD+V +S
Sbjct: 100 QEYRSEKSLEALNKLVPPECHLIREGKL--EHVLASTLVPGDLVCLS 144
>gnl|CDD|163028 TIGR02812, fadR_gamma, fatty acid metabolism transcriptional
regulator FadR. Members of this family are FadR, a
transcriptional regulator of fatty acid metabolism,
including both biosynthesis and beta-oxidation. It is
found exclusively in a subset of Gammaproteobacteria,
with strictly one copy per genome. It has an N-terminal
DNA-binding domain and a less well conserved C-terminal
long chain acyl-CoA-binding domain. FadR from this
family heterologously expressed in Escherichia coli show
differences in regulatory response and fatty acid
binding profiles. The family is nevertheless designated
equivalog, as all member proteins have at least
nominally the same function [Fatty acid and phospholipid
metabolism, Biosynthesis, Fatty acid and phospholipid
metabolism, Degradation, Regulatory functions, DNA
interactions].
Length = 235
Score = 30.0 bits (68), Expect = 0.11
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 9/60 (15%)
Query: 30 RNLASMAYFALTEYQKERNAESAIEALKEYEPEMGKVIRGDKSGVQKVRAKEIVPGDIVE 89
R LA Y L K N + + +++Y G +SG + ++ +P D+ E
Sbjct: 185 RELALQFYKELQALCKAGNHDEVPDCIRQY---------GIESGEIWHQMQDELPQDLSE 235
>gnl|CDD|236827 PRK11033, zntA, zinc/cadmium/mercury/lead-transporting ATPase;
Provisional.
Length = 741
Score = 29.2 bits (66), Expect = 0.28
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 49 AESAIEALKEYEPEMGKVIRGDKSGVQKVRAKEIVPGDIVEVS 91
A + AL PE +R + ++V ++ PGD++EV+
Sbjct: 230 ARRGVSALMALVPETATRLRDGER--EEVAIADLRPGDVIEVA 270
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an
RNA binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands
and two helices arranged in an alpha/beta sandwich,
with a third helix present during RNA binding in some
cases The C-terminal beta strand (4th strand) and final
helix are hard to align and have been omitted in the
SEED alignment The LA proteins have an N terminal rrm
which is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 27.6 bits (62), Expect = 0.39
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 38 FALTEYQKERNAESAIEALKEYEPEMGKVIR 68
FA E++ E +AE A+EAL E G+ +R
Sbjct: 41 FAFVEFEDEEDAEKALEALNGKEL-GGRELR 70
>gnl|CDD|237914 PRK15122, PRK15122, magnesium-transporting ATPase; Provisional.
Length = 903
Score = 28.5 bits (64), Expect = 0.42
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 5/53 (9%)
Query: 43 YQKERNAESAIEALKEYEPEMGKVIRGDKSGVQKVR----AKEIVPGDIVEVS 91
+Q+ R+ ++A EALK V+R +G + VR +E+VPGDIV +S
Sbjct: 130 WQEFRSNKAA-EALKAMVRTTATVLRRGHAGAEPVRREIPMRELVPGDIVHLS 181
>gnl|CDD|130587 TIGR01524, ATPase-IIIB_Mg, magnesium-translocating P-type ATPase.
This model describes the magnesium translocating P-type
ATPase found in a limited number of bacterial species
and best described in Salmonella typhimurium, which
contains two isoforms. These transporters are active in
low external Mg2+ concentrations and pump the ion into
the cytoplasm. The magnesium ATPases have been
classified as type IIIB by a phylogenetic analysis
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 867
Score = 27.9 bits (62), Expect = 0.76
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 40 LTEYQKERNAESAIEALKEYEPEMGKVIR---GDKSGVQ-KVRAKEIVPGDIVEVS 91
L + +E AE A ALK V+R + +G +V +VPGD++E++
Sbjct: 103 LLGFIQESRAERAAYALKNMVKNTATVLRVINENGNGSMDEVPIDALVPGDLIELA 158
>gnl|CDD|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in
serine/arginine-rich splicing factor 3 (SRSF3) and
similar proteins. This subfamily corresponds to the
RRM of two serine/arginine (SR) proteins,
serine/arginine-rich splicing factor 3 (SRSF3) and
serine/arginine-rich splicing factor 7 (SRSF7). SRSF3,
also termed pre-mRNA-splicing factor SRp20, modulates
alternative splicing by interacting with RNA
cis-elements in a concentration- and cell
differentiation-dependent manner. It is also involved
in termination of transcription, alternative RNA
polyadenylation, RNA export, and protein translation.
SRSF3 is critical for cell proliferation, and tumor
induction and maintenance. It can shuttle between the
nucleus and cytoplasm. SRSF7, also termed splicing
factor 9G8, plays a crucial role in both constitutive
splicing and alternative splicing of many pre-mRNAs.
Its localization and functions are tightly regulated by
phosphorylation. SRSF7 is predominantly present in the
nuclear and can shuttle between nucleus and cytoplasm.
It cooperates with the export protein, Tap/NXF1, helps
mRNA export to the cytoplasm, and enhances the
expression of unspliced mRNA. Moreover, SRSF7 inhibits
tau E10 inclusion through directly interacting with the
proximal downstream intron of E10, a clustering region
for frontotemporal dementia with Parkinsonism (FTDP)
mutations. Both SRSF3 and SRSF7 contain a single
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and a C-terminal RS domain rich in serine-arginine
dipeptides. The RRM domain is involved in RNA binding,
and the RS domain has been implicated in protein
shuttling and protein-protein interactions. .
Length = 73
Score = 26.4 bits (59), Expect = 0.82
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 6/41 (14%)
Query: 38 FALTEYQKERNAESAIEALKEYEPEMGKVIRGDKSGVQKVR 78
FA E++ R+AE A+ AL G+ I G++ V+ R
Sbjct: 38 FAFVEFEDPRDAEDAVRALD------GRRICGNRVRVELSR 72
>gnl|CDD|233513 TIGR01657, P-ATPase-V, P-type ATPase of unknown pump specificity
(type V). These P-type ATPases form a distinct clade
but the substrate of their pumping activity has yet to
be determined. This clade has been designated type V in.
Length = 1054
Score = 27.3 bits (61), Expect = 1.3
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 61 PEMGKVIRGDKSGVQKVRAKEIVPGDIVEVS 91
P+ VIR K + + E+VPGDIV +
Sbjct: 228 PQSVIVIRNGKW--VTIASDELVPGDIVSIP 256
>gnl|CDD|237798 PRK14714, PRK14714, DNA polymerase II large subunit; Provisional.
Length = 1337
Score = 27.3 bits (61), Expect = 1.3
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 66 VIRGDKSGVQKVRAKEIVPGDIVEVSE 92
++ D ++K RA E+ GD V V E
Sbjct: 1015 MLVWDGGYLEKKRAFEVKEGDAVPVPE 1041
>gnl|CDD|236705 PRK10517, PRK10517, magnesium-transporting ATPase MgtA;
Provisional.
Length = 902
Score = 26.2 bits (58), Expect = 3.0
Identities = 14/56 (25%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 40 LTEYQKERNAESAIEALKEYEPEMGKVIRGD----KSGVQKVRAKEIVPGDIVEVS 91
L + +E + A +ALK V+R ++G ++ ++VPGDI++++
Sbjct: 137 LLNFIQEARSTKAADALKAMVSNTATVLRVINDKGENGWLEIPIDQLVPGDIIKLA 192
>gnl|CDD|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins
family, Drosophila sex-lethal (SXL), and similar
proteins. This subfamily corresponds to the RRM1 of Hu
proteins and SXL. The Hu proteins family represents a
group of RNA-binding proteins involved in diverse
biological processes. Since the Hu proteins share high
homology with the Drosophila embryonic lethal abnormal
vision (ELAV) protein, the Hu family is sometimes
referred to as the ELAV family. Drosophila ELAV is
exclusively expressed in neurons and is required for
the correct differentiation and survival of neurons in
flies. The neuronal members of the Hu family include
Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C
(HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or
ELAV-4), which play important roles in neuronal
differentiation, plasticity and memory. HuB is also
expressed in gonads. Hu-antigen R (HuR or ELAV-1 or
HuA) is ubiquitously expressed Hu family member. It has
a variety of biological functions mostly related to the
regulation of cellular response to DNA damage and other
types of stress. Hu proteins perform their cytoplasmic
and nuclear molecular functions by coordinately
regulating functionally related mRNAs. In the
cytoplasm, Hu proteins recognize and bind to AU-rich
RNA elements (AREs) in the 3' untranslated regions
(UTRs) of certain target mRNAs, such as GAP-43,
vascular epithelial growth factor (VEGF), the glucose
transporter GLUT1, eotaxin and c-fos, and stabilize
those ARE-containing mRNAs. They also bind and regulate
the translation of some target mRNAs, such as
neurofilament M, GLUT1, and p27. In the nucleus, Hu
proteins function as regulators of polyadenylation and
alternative splicing. Each Hu protein contains three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
RRM1 and RRM2 may cooperate in binding to an ARE. RRM3
may help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. This family
also includes the sex-lethal protein (SXL) from
Drosophila melanogaster. SXL governs sexual
differentiation and X chromosome dosage compensation in
flies. It induces female-specific alternative splicing
of the transformer (tra) pre-mRNA by binding to the tra
uridine-rich polypyrimidine tract at the
non-sex-specific 3' splice site during the
sex-determination process. SXL binds to its own
pre-mRNA and promotes female-specific alternative
splicing. It contains an N-terminal Gly/Asn-rich domain
that may be responsible for the protein-protein
interaction, and tandem RRMs that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 77
Score = 25.0 bits (55), Expect = 3.9
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 29 KRNLASMAYFALTEYQKERNAESAIEALKEYE 60
+ S+ Y +Y E +A+ AI L +E
Sbjct: 36 RITGQSLGY-GFVDYVDENDAQKAINTLNGFE 66
>gnl|CDD|164753 MTH00207, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 572
Score = 25.9 bits (57), Expect = 4.1
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 1 MADLSLVGCYNMS---AMSTEQRNRMMLASAKRNLASMAYFAL 40
MA LS + +M A+ST + +M+AS + +A F L
Sbjct: 256 MAGLSAMTECDMKKIIALSTLSQLGVMMASLGLGMPKLALFHL 298
>gnl|CDD|202095 pfam02026, RyR, RyR domain. This domain is called RyR for
Ryanodine receptor. The domain is found in four copies
in the ryanodine receptor. The function of this domain
is unknown.
Length = 95
Score = 24.9 bits (55), Expect = 4.7
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 27 SAKRNLASMAYFALTEYQKERNAESAIEALK 57
K + + Y LTE +KE + E A E LK
Sbjct: 51 GGKTHPCLVPYDTLTEKEKEYDREPARETLK 81
>gnl|CDD|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein
RBM8A, RBM8B nd similar proteins. This subfamily
corresponds to the RRM of RBM8, also termed binder of
OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is
one of the components of the exon-exon junction complex
(EJC). It has two isoforms, RBM8A and RBM8B, both of
which are identical except that RBM8B is 16 amino acids
shorter at its N-terminus. RBM8, together with other
EJC components (such as Magoh, Aly/REF, RNPS1, Srm160,
and Upf3), plays critical roles in postsplicing
processing, including nuclear export and cytoplasmic
localization of the mRNA, and the nonsense-mediated
mRNA decay (NMD) surveillance process. RBM8 binds to
mRNA 20-24 nucleotides upstream of a spliced exon-exon
junction. It is also involved in spliced mRNA nuclear
export, and the process of nonsense-mediated decay of
mRNAs with premature stop codons. RBM8 forms a specific
heterodimer complex with the EJC protein Magoh which
then associates with Aly/REF, RNPS1, DEK, and SRm160 on
the spliced mRNA, and inhibits ATP turnover by
eIF4AIII, thereby trapping the EJC core onto RNA. RBM8
contains an N-terminal putative bipartite nuclear
localization signal, one RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), in the central region, and
a C-terminal serine-arginine rich region (SR domain)
and glycine-arginine rich region (RG domain). .
Length = 88
Score = 24.5 bits (54), Expect = 5.3
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 38 FALTEYQKERNAESAIEALKEYE 60
+AL EY+ ++ A++AIE L E
Sbjct: 50 YALIEYETKKEAQAAIEGLNGKE 72
>gnl|CDD|179543 PRK03137, PRK03137, 1-pyrroline-5-carboxylate dehydrogenase;
Provisional.
Length = 514
Score = 25.3 bits (56), Expect = 5.4
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 4/36 (11%)
Query: 40 LTEYQKERNAESAIEALKEYEPEMGK----VIRGDK 71
T++ E N E+ EALK+ E E+G+ +I G++
Sbjct: 10 FTDFSVEENVEAFEEALKKVEKELGQDYPLIIGGER 45
>gnl|CDD|173488 PTZ00239, PTZ00239, serine/threonine protein phosphatase 2A;
Provisional.
Length = 303
Score = 25.2 bits (55), Expect = 5.9
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 62 EMGKVIRGDKSGVQKVRAKEIVPGDI 87
E K I ++S VQ VRA V GDI
Sbjct: 26 ERAKEIFLEESNVQPVRAPVNVCGDI 51
>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the
RRM5 of MRD1 which is encoded by a novel yeast gene
MRD1 (multiple RNA-binding domain). It is
well-conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1
is essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. It contains 5
conserved RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), which may play an important structural role
in organizing specific rRNA processing events. .
Length = 76
Score = 24.4 bits (53), Expect = 6.4
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 38 FALTEYQKERNAESAIEALK 57
FA E+ + A +A+ ALK
Sbjct: 43 FAFVEFSTAKEALNAMNALK 62
>gnl|CDD|149800 pfam08854, DUF1824, Domain of unknown function (DUF1824). This
uncharacterized family of proteins are principally
found in cyanobacteria.
Length = 125
Score = 24.5 bits (54), Expect = 6.9
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 49 AESAIEALKEYEPEMG 64
AE AI AL+ YE +G
Sbjct: 47 AEEAINALRSYEAALG 62
>gnl|CDD|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in
serine/arginine-rich splicing factor SRSF2, SRSF8 and
similar proteins. This subfamily corresponds to the
RRM of SRSF2 and SRSF8. SRSF2, also termed protein
PR264, or splicing component, 35 kDa (splicing factor
SC35 or SC-35), is a prototypical SR protein that plays
important roles in the alternative splicing of
pre-mRNA. It is also involved in transcription
elongation by directly or indirectly mediating the
recruitment of elongation factors to the C-terminal
domain of polymerase II. SRSF2 is exclusively localized
in the nucleus and is restricted to nuclear processes.
It contains a single N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), followed by a C-terminal RS
domain rich in serine-arginine dipeptides. The RRM is
responsible for the specific recognition of 5'-SSNG-3'
(S=C/G) RNA. In the regulation of alternative splicing
events, it specifically binds to cis-regulatory
elements on the pre-mRNA. The RS domain modulates SRSF2
activity through phosphorylation, directly contacts
RNA, and promotes protein-protein interactions with the
spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a
novel mammalian SR splicing factor encoded by a
PR264/SC35 functional retropseudogene. SRSF8 is
localized in the nucleus and does not display the same
activity as PR264/SC35. It functions as an essential
splicing factor in complementing a HeLa cell S100
extract deficient in SR proteins. Like SRSF2, SRSF8
contains a single N-terminal RRM and a C-terminal RS
domain. .
Length = 73
Score = 24.2 bits (53), Expect = 7.2
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 38 FALTEYQKERNAESAIEALKEYE 60
FA + +R+AE A++A+ E
Sbjct: 42 FAFVRFYDKRDAEDAMDAMDGKE 64
>gnl|CDD|173269 PRK14808, PRK14808, histidinol-phosphate aminotransferase;
Provisional.
Length = 335
Score = 25.0 bits (54), Expect = 8.6
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 29 KRNLASMAYFALTEYQKERNAESAIEALKEYE 60
+R L + A+ AL E E + ES ++ LK+YE
Sbjct: 161 ERILKTGAFVALDEAYYEFHGESYVDLLKKYE 192
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 24.8 bits (54), Expect = 8.8
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 5 SLVGCYNMSAMSTEQRNRMMLA 26
++VG ++ +STEQR R+ +A
Sbjct: 1010 AIVGLPGVTGLSTEQRKRLTIA 1031
>gnl|CDD|219510 pfam07678, A2M_comp, A-macroglobulin complement component. This
family includes the complement components region of the
alpha-2-macroglobulin family.
Length = 248
Score = 24.5 bits (54), Expect = 8.8
Identities = 12/28 (42%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 31 NLASMAYFALTEYQKERNAESAIEALKE 58
LA AY ALT K A +E LK
Sbjct: 134 TLAITAY-ALTLAGKSPQASELLEKLKA 160
>gnl|CDD|99801 cd06204, CYPOR, NADPH cytochrome p450 reductase (CYPOR) serves as
an electron donor in several oxygenase systems and is a
component of nitric oxide synthases and methionine
synthase reductases. CYPOR transfers two electrons from
NADPH to the heme of cytochrome p450 via FAD and FMN.
Ferredoxin-NADP+ (oxido)reductase is an FAD-containing
enzyme that catalyzes the reversible electron transfer
between NADP(H) and electron carrier proteins such as
ferredoxin and flavodoxin. Isoforms of these
flavoproteins (i.e. having a non-covalently bound FAD as
a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria in which they participate in
a wide variety of redox metabolic pathways. The
C-terminal domain contains most of the NADP(H) binding
residues and the N-terminal domain interacts
non-covalently with the isoalloxazine rings of the
flavin molecule which lies largely in a large gap
betweed the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 416
Score = 24.5 bits (54), Expect = 8.9
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 25 LASAKRN-LASMAYFALTEYQKERNAESAIEALKEY 59
A R LA++A FA +KER + A E EY
Sbjct: 103 TAPVSRQVLAALAQFAPDPEEKERLLKLASEGKDEY 138
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
0.312 0.125 0.327
Gapped
Lambda K H
0.267 0.0750 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,413,041
Number of extensions: 352784
Number of successful extensions: 460
Number of sequences better than 10.0: 1
Number of HSP's gapped: 453
Number of HSP's successfully gapped: 56
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.2 bits)