RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9172
(80 letters)
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 51.4 bits (123), Expect = 2e-09
Identities = 20/33 (60%), Positives = 23/33 (69%)
Query: 19 QTDTQGGPNTVLRVIIEHMLYPITLDVLYQFDN 51
GPN VLRVI+E+ +YPITLDVLYQ N
Sbjct: 86 SDFDSAGPNKVLRVIVENPMYPITLDVLYQIFN 118
>gnl|CDD|241137 cd12693, RRM2_PTBP1_like, RNA recognition motif 2 in
polypyrimidine tract-binding protein 1 (PTB or hnRNP I)
and similar proteins. This subfamily corresponds to
the RRM2 of polypyrimidine tract-binding protein 1 (PTB
or hnRNP I), polypyrimidine tract-binding protein 2
(PTBP2 or nPTB), regulator of differentiation 1 (Rod1),
and similar proteins found in Metazoa. PTB is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. PTBP2 is highly homologous to PTB and is
perhaps specific to the vertebrates. Unlike PTB, PTBP2
is enriched in the brain and in some neural cell lines.
It binds more stably to the downstream control sequence
(DCS) RNA than PTB does but is a weaker repressor of
splicing in vitro. PTBP2 also greatly enhances the
binding of two other proteins, heterogeneous nuclear
ribonucleoprotein (hnRNP) H and KH-type
splicing-regulatory protein (KSRP), to the DCS RNA. The
binding properties of PTBP2 and its reduced inhibitory
activity on splicing imply roles in controlling the
assembly of other splicing-regulatory proteins. PTBP2
also contains four RRMs. ROD1 coding protein Rod1 is a
mammalian PTB homolog of a regulator of differentiation
in the fission yeast Schizosaccharomyces pombe, where
the nrd1 gene encodes an RNA binding protein negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It may play a role controlling differentiation
in mammals. All members in this family contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 96
Score = 47.8 bits (114), Expect = 5e-09
Identities = 17/22 (77%), Positives = 21/22 (95%)
Query: 27 NTVLRVIIEHMLYPITLDVLYQ 48
NTVLRVI+E+M YP+TLDVL+Q
Sbjct: 1 NTVLRVIVENMTYPVTLDVLHQ 22
>gnl|CDD|240868 cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition motif in
polypyrimidine tract-binding protein 1 (PTB or hnRNP
I), heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), and similar proteins. This subfamily
corresponds to the RRM2 of polypyrimidine tract-binding
protein 1 (PTB or hnRNP I), polypyrimidine
tract-binding protein 2 (PTBP2 or nPTB), regulator of
differentiation 1 (Rod1), heterogeneous nuclear
ribonucleoprotein L (hnRNP-L), heterogeneous nuclear
ribonucleoprotein L-like (hnRNP-LL), polypyrimidine
tract-binding protein homolog 3 (PTBPH3),
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2), and similar proteins, and RRM3 of
PTBPH1 and PTBPH2. PTB is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. PTBP2 is highly
homologous to PTB and is perhaps specific to the
vertebrates. Unlike PTB, PTBP2 is enriched in the brain
and in some neural cell lines. It binds more stably to
the downstream control sequence (DCS) RNA than PTB does
but is a weaker repressor of splicing in vitro. PTBP2
also greatly enhances the binding of two other
proteins, heterogeneous nuclear ribonucleoprotein
(hnRNP) H and KH-type splicing-regulatory protein
(KSRP), to the DCS RNA. The binding properties of PTBP2
and its reduced inhibitory activity on splicing imply
roles in controlling the assembly of other
splicing-regulatory proteins. Rod1 is a mammalian
polypyrimidine tract binding protein (PTB) homolog of a
regulator of differentiation in the fission yeast
Schizosaccharomyces pombe, where the nrd1 gene encodes
an RNA binding protein negatively regulates the onset
of differentiation. ROD1 is predominantly expressed in
hematopoietic cells or organs. It might play a role
controlling differentiation in mammals. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both, nuclear
and cytoplasmic, roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL protein plays a critical and unique
role in the signal-induced regulation of CD45 and acts
as a global regulator of alternative splicing in
activated T cells. This family also includes
polypyrimidine tract binding protein homolog 3 (PTBPH3)
found in plant. Although its biological roles remain
unclear, PTBPH3 shows significant sequence similarity
to other family members, all of which contain four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain).
Although their biological roles remain unclear, both
PTBPH1 and PTBPH2 show significant sequence similarity
to PTB. However, in contrast to PTB, they have three
RRMs. .
Length = 85
Score = 41.0 bits (97), Expect = 2e-06
Identities = 14/25 (56%), Positives = 19/25 (76%), Gaps = 1/25 (4%)
Query: 29 VLRVIIEHMLYPITLDVLYQ-FDNY 52
VL V I ++LYP+T+DVL+Q F Y
Sbjct: 1 VLLVTISNLLYPVTVDVLHQVFSPY 25
>gnl|CDD|241136 cd12692, RRM2_PTBPH3, RNA recognition motif 2 in plant
polypyrimidine tract-binding protein homolog 3
(PTBPH3). This subfamily corresponds to the RRM2 of
PTBPH3. Although its biological roles remain unclear,
PTBPH3 shows significant sequence similarity to
polypyrimidine tract binding protein (PTB) that is an
important negative regulator of alternative splicing in
mammalian cells and also functions at several other
aspects of mRNA metabolism, including mRNA
localization, stabilization, polyadenylation, and
translation. Like PTB, PTBPH3 contains four RNA
recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 88
Score = 38.4 bits (89), Expect = 3e-05
Identities = 17/30 (56%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 26 PNTVLRVIIEHMLYPITLDVLYQ-FDNYKF 54
PN +L V I H LYPIT+DVL+Q F + F
Sbjct: 1 PNRILLVTIHHPLYPITVDVLHQVFSPHGF 30
>gnl|CDD|241227 cd12783, RRM2_PTBP2, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM2 of PTBP2, also known
as neural polypyrimidine tract-binding protein or
neurally-enriched homolog of PTB (nPTB), highly
homologous to polypyrimidine tract binding protein
(PTB) and perhaps specific to the vertebrates. Unlike
PTB, PTBP2 is enriched in the brain and in some neural
cell lines. It binds more stably to the downstream
control sequence (DCS) RNA than PTB does but is a
weaker repressor of splicing in vitro. PTBP2 also
greatly enhances the binding of two other proteins,
heterogeneous nuclear ribonucleoprotein (hnRNP) H and
KH-type splicing-regulatory protein (KSRP), to the DCS
RNA. The binding properties of PTBP2 and its reduced
inhibitory activity on splicing imply roles in
controlling the assembly of other splicing-regulatory
proteins. PTBP2 contains four RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 101
Score = 36.5 bits (84), Expect = 2e-04
Identities = 17/27 (62%), Positives = 23/27 (85%), Gaps = 1/27 (3%)
Query: 29 VLRVIIEHMLYPITLDVLYQFDNYKFG 55
VLR+II++M YP+TLDVL+Q + KFG
Sbjct: 3 VLRIIIDNMYYPVTLDVLHQIFS-KFG 28
>gnl|CDD|241228 cd12784, RRM2_ROD1, RNA recognition motif 2 in vertebrate
regulator of differentiation 1 (Rod1). This subgroup
corresponds to the RRM2 of ROD1 coding protein Rod1, a
mammalian polypyrimidine tract binding protein (PTB)
homolog of a regulator of differentiation in the
fission yeast Schizosaccharomyces pombe, where the nrd1
gene encodes an RNA binding protein and negatively
regulates the onset of differentiation. ROD1 is
predominantly expressed in hematopoietic cells or
organs. It might play a role controlling
differentiation in mammals. Rod1 contains four repeats
of RNA recognition motifs (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain) and
does have RNA binding activities. .
Length = 103
Score = 35.7 bits (82), Expect = 4e-04
Identities = 16/31 (51%), Positives = 25/31 (80%), Gaps = 1/31 (3%)
Query: 25 GPNTVLRVIIEHMLYPITLDVLYQFDNYKFG 55
G + VLR+I+E++ YP+TL+VL+Q + KFG
Sbjct: 1 GQSPVLRIIVENLFYPVTLEVLHQIFS-KFG 30
>gnl|CDD|241226 cd12782, RRM2_PTBP1, RNA recognition motif 2 in vertebrate
polypyrimidine tract-binding protein 1 (PTB). This
subgroup corresponds to the RRM2 of PTB, also known as
58 kDa RNA-binding protein PPTB-1 or heterogeneous
nuclear ribonucleoprotein I (hnRNP I), an important
negative regulator of alternative splicing in mammalian
cells. PTB also functions at several other aspects of
mRNA metabolism, including mRNA localization,
stabilization, polyadenylation, and translation. PTB
contains four RNA recognition motifs (RRM), also known
as RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). RRM1 and RRM2 are independent from each other
and separated by flexible linkers. By contrast, there
is an unusual and conserved interdomain interaction
between RRM3 and RRM4. It is widely held that only RRMs
3 and 4 are involved in RNA binding and RRM2 mediates
PTB homodimer formation. However, new evidence shows
that the RRMs 1 and 2 also contribute substantially to
RNA binding. Moreover, PTB may not always dimerize to
repress splicing. It is a monomer in solution. .
Length = 100
Score = 35.5 bits (81), Expect = 4e-04
Identities = 16/27 (59%), Positives = 23/27 (85%), Gaps = 1/27 (3%)
Query: 29 VLRVIIEHMLYPITLDVLYQFDNYKFG 55
VLR+I+E++ YP+TLDVL+Q + KFG
Sbjct: 4 VLRIIVENLFYPVTLDVLHQIFS-KFG 29
>gnl|CDD|241230 cd12786, RRM2_hnRPLL, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). The subgroup corresponds to the RRM2 of
hnRNP-LL which plays a critical and unique role in the
signal-induced regulation of CD45 and acts as a global
regulator of alternative splicing in activated T cells.
It is closely related in domain structure and sequence
to heterogeneous nuclear ribonucleoprotein L (hnRNP-L),
which is an abundant nuclear, multifunctional
RNA-binding protein with three RNA-recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 96
Score = 31.1 bits (70), Expect = 0.016
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 27 NTVLRVIIEHMLYPITLDVLYQFDN 51
N VL + I++ LYPIT+DVLY N
Sbjct: 2 NKVLLLSIQNPLYPITVDVLYTVCN 26
>gnl|CDD|241138 cd12694, RRM2_hnRNPL_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and
similar proteins. This subfamily corresponds to the
RRM2 of heterogeneous nuclear ribonucleoprotein L
(hnRNP-L), heterogeneous nuclear ribonucleoprotein
L-like (hnRNP-LL), and similar proteins. hnRNP-L is a
higher eukaryotic specific subunit of human KMT3a (also
known as HYPB or hSet2) complex required for histone H3
Lys-36 trimethylation activity. It plays both nuclear
and cytoplasmic roles in mRNA export of intronless
genes, IRES-mediated translation, mRNA stability, and
splicing. hnRNP-LL plays a critical and unique role in
the signal-induced regulation of CD45 and acts as a
global regulator of alternative splicing in activated T
cells. It is closely related in domain structure and
sequence to hnRNP-L, which contains three
RNA-recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 86
Score = 29.2 bits (66), Expect = 0.083
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 27 NTVLRVIIEHMLYPITLDVLYQFDNY 52
N VL I + +YPIT+DV+Y N
Sbjct: 1 NHVLLFTILNAIYPITVDVIYTICNP 26
>gnl|CDD|241134 cd12690, RRM3_PTBPH1_PTBPH2, RNA recognition motif 3 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM3 of PTBPH1 and PTBPH2. Although their biological
roles remain unclear, PTBPH1 and PTBPH2 show
significant sequence similarity to polypyrimidine tract
binding protein (PTB) that is an important negative
regulator of alternative splicing in mammalian cells
and also functions at several other aspects of mRNA
metabolism, including mRNA localization, stabilization,
polyadenylation, and translation. Both, PTBPH1 and
PTBPH2, contain three RNA recognition motifs (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 97
Score = 26.7 bits (59), Expect = 0.71
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 29 VLRVIIEHMLYPITLDVLY 47
VL IE+M Y +T+DVL+
Sbjct: 3 VLLASIENMQYAVTVDVLH 21
>gnl|CDD|144538 pfam00981, Rota_NS53, Rotavirus RNA-binding Protein 53 (NS53).
This protein is also known as NSP1. NS53 is encoded by
gene 5. It is made in low levels in the infected cells
and is a component of early replication. The protein is
known to accumulate on the cytoskeleton of the infected
cell. NS53 is an RNA binding protein that contains a
characteristic cysteine rich region.
Length = 488
Score = 26.9 bits (60), Expect = 1.2
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 4/25 (16%)
Query: 36 HMLYPITLDVL-YQFDN---YKFGH 56
H+L PITL L + D Y FG+
Sbjct: 136 HLLLPITLQALSIKLDGDVYYIFGY 160
>gnl|CDD|220129 pfam09159, Ydc2-catalyt, Mitochondrial resolvase Ydc2 / RNA
splicing MRS1. Members of this family adopt a secondary
structure consisting of two beta sheets and one alpha
helix, arranged as a beta-alpha-beta motif. Each beta
sheet has five strands, arranged in a 32145 order, with
the second strand being antiparallel to the rest.
Mitochondrial resolvase Ydc2 is capable of resolving
Holliday junctions and cleaves DNA after 5'-CT-3' and
5'-TT-3' sequences. This family also contains the
mitochondrial RNA-splicing protein MRS1 which is
involved in the excision of group I introns.
Length = 254
Score = 26.2 bits (58), Expect = 1.8
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 4/24 (16%)
Query: 20 TDTQGGPNT---VLRV-IIEHMLY 39
+ GG LRV ++E MLY
Sbjct: 91 FRSGGGSAVLEWTLRVNVLEGMLY 114
>gnl|CDD|225788 COG3249, COG3249, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 343
Score = 25.3 bits (55), Expect = 3.7
Identities = 7/26 (26%), Positives = 10/26 (38%)
Query: 7 QAALQAAQALTGQTDTQGGPNTVLRV 32
AL+ L GQ + G L +
Sbjct: 79 DDALRDRTQLIGQYEVNQGIGFRLCL 104
>gnl|CDD|200466 cd11327, AmyAc_Glg_debranch_2, Alpha amylase catalytic domain found
in glycogen debranching enzymes. Debranching enzymes
facilitate the breakdown of glycogen through
glucosyltransferase and glucosidase activity. These
activities are performed by a single enzyme in mammals,
yeast, and some bacteria, but by two distinct enzymes in
Escherichia coli and other bacteria. Debranching enzymes
perform two activities, 4-alpha-D-glucanotransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33).
4-alpha-D-glucanotransferase catalyzes the
endohydrolysis of 1,6-alpha-D-glucoside linkages at
points of branching in chains of 1,4-linked
alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase
catalyzes the endohydrolysis of 1,6-alpha-D-glucoside
linkages at points of branching in chains of 1,4-linked
alpha-D-glucose residues. The catalytic triad (DED),
which is highly conserved in other debranching enzymes,
is not present in this group. The Alpha-amylase family
comprises the largest family of glycoside hydrolases
(GH), with the majority of enzymes acting on starch,
glycogen, and related oligo- and polysaccharides. These
proteins catalyze the transformation of alpha-1,4 and
alpha-1,6 glucosidic linkages with retention of the
anomeric center. The protein is described as having 3
domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a
loop between the beta 3 strand and alpha 3 helix of A; C
is the C-terminal extension characterized by a Greek
key. The majority of the enzymes have an active site
cleft found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc, or
only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 478
Score = 25.3 bits (56), Expect = 3.7
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 27 NTVLRVIIEHMLYPITLDVLYQFD 50
N ++ ++ E +L P+ L Y D
Sbjct: 175 NAIMEILKEEVLPPLKLWEFYVLD 198
>gnl|CDD|223206 COG0128, AroA, 5-enolpyruvylshikimate-3-phosphate synthase [Amino
acid transport and metabolism].
Length = 428
Score = 24.9 bits (55), Expect = 5.4
Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 7/51 (13%)
Query: 1 MNSASAQ--AALQAAQALTGQTDTQGGPNTVLRVIIEHMLYPITLDVLYQF 49
+S Q + L A L + T V V+ TLD+L F
Sbjct: 165 GPVSSQQVSSLLLLA-PLLAEGTTI----IVGGVLESKPYIDHTLDMLKAF 210
>gnl|CDD|218663 pfam05625, PAXNEB, PAXNEB protein. PAXNEB or PAX6 neighbor is
found in several eukaryotic organisms. PAXNED is an RNA
polymerase II Elongator protein subunit. It is part of
the HAP subcomplex of Elongator, which is a six-subunit
component of the RNA polymerase II holoenzyme. The HAP
subcomplex is required for Elongator structural
integrity and histone acetyltransferase activity. This
protein family has a P-loop motif. However its sequence
has degraded in many members of the family.
Length = 357
Score = 24.5 bits (54), Expect = 8.1
Identities = 11/40 (27%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 2 NSASAQAALQAAQALTGQTDTQGGPNTVLRVIIEHMLYPI 41
++ + L+ Q+L ++ PN VLR++I +L P+
Sbjct: 173 TASPYASLLKQIQSLIAKS--LFNPNNVLRIVIPSLLSPL 210
>gnl|CDD|215235 PLN02426, PLN02426, cytochrome P450, family 94, subfamily C
protein.
Length = 502
Score = 24.3 bits (53), Expect = 9.0
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 7/30 (23%)
Query: 34 IEHMLYPITLDVLYQFDNYKFGHAFSTSLA 63
+E+ML +FDNY G FS L
Sbjct: 94 VEYMLKT-------RFDNYPKGKPFSAILG 116
>gnl|CDD|233199 TIGR00939, 2a57, Equilibrative Nucleoside Transporter (ENT).
[Transport and binding proteins, Nucleosides, purines
and pyrimidines].
Length = 437
Score = 24.3 bits (53), Expect = 9.6
Identities = 16/59 (27%), Positives = 21/59 (35%), Gaps = 8/59 (13%)
Query: 25 GPNTVLRVIIEHMLYPITLDVLYQFDNYKFGHAFSTSLAM---PRDELAGFRSEATEFS 80
+ L V Y I L +L+ F N G+ SL+M PR R A
Sbjct: 360 PQRSRLPVFFPGDAYFIILMLLFGFSN---GYL--GSLSMCLAPRQVDPHEREVAGALM 413
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 0.129 0.361
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,870,699
Number of extensions: 299200
Number of successful extensions: 288
Number of sequences better than 10.0: 1
Number of HSP's gapped: 288
Number of HSP's successfully gapped: 20
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: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.3 bits)