RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17775
(211 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 = 114 bits (288), Expect = 5e-30
Identities = 75/251 (29%), Positives = 101/251 (40%), Gaps = 53/251 (21%)
Query: 2 SAPTKLNVYKNDSESWDYTQP--------TLGRTK-----------------DGPPSRPG 36
+ PT+LNV ND +S DYT P L +T DG S G
Sbjct: 171 AKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGG 230
Query: 37 PLLPEP-PRRLPTPSGPPSMPNYRGGYPDDDYYGAPPAFEFERSYNSPVLDKFIGKPRGM 95
PL P R+ P GPPS YR Y A ++ VL G +
Sbjct: 231 PLAPLAGGDRMGPPHGPPSR--YRPAYEAAPLAPAISSYGPAGGGPGSVL-MVSGLHQEK 287
Query: 96 SGPPS------------------GPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVA 137
+ +++M D A+ A+ +L+ L GK L V
Sbjct: 288 VNCDRLFNLFCVYGNVERVKFMKNKKETALIEMADPYQAQLALTHLNGVKL-FGKPLRVC 346
Query: 138 YSKQVFLSDVSHP--YELPDGSESFKDFTGSRKNRFMNPKMAMKNRIQPPSQLLHFFNAP 195
SKQ +V P +L DG S+KD++ SR +RF P A KN IQPPS LH N P
Sbjct: 347 PSKQ---QNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIP 403
Query: 196 PDITEEQLTDI 206
++EE L ++
Sbjct: 404 LSVSEEDLKEL 414
>gnl|CDD|240873 cd12427, RRM4_hnRNPL_like, RNA recognition motif 4 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM4 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 = 84
Score = 44.5 bits (106), Expect = 1e-06
Identities = 14/22 (63%), Positives = 18/22 (81%)
Query: 185 PSQLLHFFNAPPDITEEQLTDI 206
PS++LHFFNAPP TEE L ++
Sbjct: 1 PSKVLHFFNAPPTFTEEDLREL 22
>gnl|CDD|206064 pfam13893, RRM_5, 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.
Length = 56
Score = 41.7 bits (99), Expect = 7e-06
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYS 139
G V+ +AE+A+ L+ L G+ L V YS
Sbjct: 22 GFAFVEFSTEEAAEKAVQYLNGVLF-GGRPLRVDYS 56
>gnl|CDD|240870 cd12424, RRM3_hnRNPL_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein L (hnRNP-L) and similar
proteins. This subfamily corresponds to the RRM3 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). The 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
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 RRMs.
Length = 71
Score = 37.9 bits (89), Expect = 2e-04
Identities = 16/36 (44%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 103 EGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAY 138
G MVQMGD +AERA+ L+ +L G++L V +
Sbjct: 37 PGTAMVQMGDPQAAERAIEYLNGVVLF-GQKLEVNF 71
>gnl|CDD|241229 cd12785, RRM2_hnRNPL, RNA recognition motif 2 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM2 of hnRNP-L, 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-L shows significant sequence homology to
polypyrimidine tract-binding protein (PTB or hnRNP I).
Both hnRNP-L and PTB are localized in the nucleus but
excluded from the nucleolus. hnRNP-L is an RNA-binding
protein with three RNA recognition motifs (RRMs), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 100
Score = 38.6 bits (89), Expect = 3e-04
Identities = 13/21 (61%), Positives = 18/21 (85%)
Query: 2 SAPTKLNVYKNDSESWDYTQP 22
+ PT+LNV+KND ++WDYT P
Sbjct: 80 AKPTRLNVFKNDQDTWDYTNP 100
>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 = 36.1 bits (83), Expect = 0.002
Identities = 12/17 (70%), Positives = 16/17 (94%)
Query: 4 PTKLNVYKNDSESWDYT 20
PT+LNV +ND++SWDYT
Sbjct: 80 PTRLNVIRNDNDSWDYT 96
>gnl|CDD|241148 cd12704, RRM4_hnRNPL, RNA recognition motif 4 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM4 of hnRNP-L, 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-L shows significant sequence homology
with polypyrimidine tract-binding protein (PTB or hnRNP
I). Both hnRNP-L and PTB are localized in the nucleus
but excluded from the nucleolus. hnRNP-L is an
RNA-binding protein with three RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 84
Score = 35.7 bits (82), Expect = 0.002
Identities = 15/22 (68%), Positives = 19/22 (86%)
Query: 185 PSQLLHFFNAPPDITEEQLTDI 206
PS +LHFFNAPPD+TEE ++I
Sbjct: 1 PSNVLHFFNAPPDVTEENFSEI 22
>gnl|CDD|241143 cd12699, RRM3_hnRNPL, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein L (hnRNP-L).
This subgroup corresponds to the RRM3 of hnRNP-L, 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-L shows significant sequence homology
with polypyrimidine tract-binding protein (PTB or hnRNP
I). Both, hnRNP-L and PTB, are localized in the nucleus
but excluded from the nucleolus. hnRNP-L is an
RNA-binding protein with three RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 74
Score = 33.0 bits (75), Expect = 0.015
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 68 YGAPPA-FEFERSYNSPVLDKFIGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKT 126
YG P+ +R +N L + K + M P G MV+M D + +RA+ +L+
Sbjct: 5 YGLDPSKMNCDRVFNIFCLYGNVEKVKFMKSKP----GAAMVEMADGYAVDRAITHLNNN 60
Query: 127 LLCNGKRLAVAYSKQ 141
+ G++L V SKQ
Sbjct: 61 FMF-GQKLNVCVSKQ 74
>gnl|CDD|241142 cd12698, RRM3_PTBPH3, RNA recognition motif 3 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subgroup corresponds to the RRM3 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 = 76
Score = 32.9 bits (75), Expect = 0.019
Identities = 15/35 (42%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 107 MVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSKQ 141
++QMGD AE A+ L +L GKR+ V +SK
Sbjct: 43 LIQMGDGFQAELAVNYLKGAMLF-GKRMEVNFSKH 76
>gnl|CDD|241149 cd12705, RRM4_hnRPLL, RNA recognition motif 4 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). The subgroup corresponds to the RRM4 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 = 85
Score = 33.1 bits (75), Expect = 0.020
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 185 PSQLLHFFNAPPDITEEQLTDI 206
PS +LH++N P +TEE +
Sbjct: 1 PSCVLHYYNVPLCVTEETFQKL 22
>gnl|CDD|177553 PHA03185, PHA03185, UL14 tegument protein; Provisional.
Length = 214
Score = 33.8 bits (77), Expect = 0.038
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 20 TQPTLGRTKDGPPSRPGPLLPEPPRRLPTPSGPPSMPNYRGGYPDDD 66
++PT G G P P P PPR P P+ P S + D D
Sbjct: 170 SRPTSGPVAGGLPGGGAPAPPTPPR--PGPTDPASESDCGRDSRDGD 214
>gnl|CDD|241146 cd12702, RRM4_PTBP2, RNA recognition motif 4 in vertebrate
polypyrimidine tract-binding protein 2 (PTBP2). This
subgroup corresponds to the RRM4 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 = 80
Score = 31.9 bits (72), Expect = 0.043
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 184 PPSQLLHFFNAPPDITEEQL 203
PPS LH N P +TEE L
Sbjct: 1 PPSATLHLSNIPQSVTEEDL 20
>gnl|CDD|240872 cd12426, RRM4_PTBPH3, RNA recognition motif 4 in plant
polypyrimidine tract-binding protein homolog 3 (PTBPH3).
This subfamily corresponds to the RRM4 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 = 79
Score = 30.5 bits (69), Expect = 0.12
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 184 PPSQLLHFFNAPPDITEEQLT 204
PP++++H N P D+TEE +
Sbjct: 5 PPTKMIHVSNLPSDVTEEDVI 25
>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in
Pre-mRNA-splicing factor RBM22 and similar proteins.
This subgroup corresponds to the RRM of RBM22 (also
known as RNA-binding motif protein 22, or Zinc finger
CCCH domain-containing protein 16), a newly discovered
RNA-binding motif protein which belongs to the SLT11
gene family. SLT11 gene encoding protein (Slt11p) is a
splicing factor in yeast, which is required for
spliceosome assembly. Slt11p has two distinct
biochemical properties: RNA-annealing and RNA-binding
activities. RBM22 is the homolog of SLT11 in vertebrate.
It has been reported to be involved in pre-splicesome
assembly and to interact with the Ca2+-signaling protein
ALG-2. It also plays an important role in embryogenesis.
RBM22 contains a conserved RNA recognition motif (RRM),
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a zinc finger of the unusual
type C-x8-C-x5-C-x3-H, and a C-terminus that is
unusually rich in the amino acids Gly and Pro, including
sequences of tetraprolines.
Length = 74
Score = 30.3 bits (69), Expect = 0.14
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 104 GCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
C V +AE+A L L+ NG+RL + + +
Sbjct: 38 QCAFVTFTTREAAEKAAERLFNKLIINGRRLKLKWGR 74
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes including
mRNA and rRNA processing, RNA export, and RNA stability.
This domain is 90 amino acids in length and consists of
a four-stranded beta-sheet packed against two
alpha-helices. RRM usually interacts with ssRNA, but is
also known to interact with ssDNA as well as proteins.
RRM binds a variable number of nucleotides, ranging from
two to eight. The active site includes three aromatic
side-chains located within the conserved RNP1 and RNP2
motifs of the domain. The RRM domain is found in a
variety heterogeneous nuclear ribonucleoproteins
(hnRNPs), proteins implicated in regulation of
alternative splicing, and protein components of small
nuclear ribonucleoproteins (snRNPs).
Length = 72
Score = 30.0 bits (68), Expect = 0.16
Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 95 MSGPPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAV 136
+ +G V+ AE+A+ L+ L +G++L V
Sbjct: 31 VRDKDGKSKGFAFVEFESPEDAEKALEALNGKEL-DGRKLKV 71
>gnl|CDD|241147 cd12703, RRM4_ROD1, RNA recognition motif 4 in vertebrate regulator
of differentiation 1 (Rod1). This subgroup corresponds
to the RRM4 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 that 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 = 81
Score = 29.6 bits (66), Expect = 0.27
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 184 PPSQLLHFFNAPPDITEEQL 203
PPS LH N PP +TE+ L
Sbjct: 1 PPSATLHLSNIPPSVTEDDL 20
>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA
selenocysteine-associated protein 1 (SECp43). This
subgroup corresponds to the RRM1 of SECp43, an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. .
Length = 84
Score = 29.6 bits (67), Expect = 0.27
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 6/34 (17%)
Query: 101 GPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRL 134
GP G C V+ D +AER + NGK +
Sbjct: 40 GPAGYCFVEFADEATAERCL------HKLNGKPI 67
>gnl|CDD|241144 cd12700, RRM3_hnRPLL, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein L-like
(hnRNP-LL). The subgroup corresponds to the RRM3 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 = 71
Score = 29.6 bits (66), Expect = 0.28
Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 78 RSYNSPVLDKFIGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAV 136
R +N L I K + M P G +V+MGD + ERA+ +L+ L GKRL V
Sbjct: 16 RVFNLFCLYGNIEKVKFMKTIP----GTALVEMGDEYAVERAVTHLNNVKLF-GKRLNV 69
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 31.4 bits (71), Expect = 0.41
Identities = 19/96 (19%), Positives = 22/96 (22%), Gaps = 20/96 (20%)
Query: 21 QPTLGRTKDGP------PSRPGPLLPEPPRRLPTPSGPPSMPNYRGG--------YPDDD 66
Q R P+ P PL P+ P P P N
Sbjct: 2594 QSARPRAPVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPR 2653
Query: 67 YYGAPPAFEFERSYNSPVLDKFIGKPRGMSGPPSGP 102
AP R G+ S PP P
Sbjct: 2654 DDPAPGRVSRPRRARRL------GRAAQASSPPQRP 2683
Score = 28.8 bits (64), Expect = 2.9
Identities = 14/56 (25%), Positives = 17/56 (30%), Gaps = 1/56 (1%)
Query: 2 SAPTKLNVYKNDSESWDYTQPTLGRTKDGPPS-RPGPLLPEPPRRLPTPSGPPSMP 56
S + + D L PP+ P LP P PT PP P
Sbjct: 2790 SLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGP 2845
Score = 26.8 bits (59), Expect = 9.9
Identities = 18/70 (25%), Positives = 23/70 (32%), Gaps = 2/70 (2%)
Query: 31 PPSRPGPLLPEPPRRLPTPSGPPSMPNYRGGYPDDDYYGAPPAFEFERSYNSPVLDKFIG 90
PP P P P + PP R P APPA +P
Sbjct: 2701 PPPPPPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPA--VPAGPATPGGPARPA 2758
Query: 91 KPRGMSGPPS 100
+P +GPP+
Sbjct: 2759 RPPTTAGPPA 2768
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 27.9 bits (63), Expect = 0.80
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 11/53 (20%)
Query: 84 VLDKFIGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAV 136
V DK GK +G V+ AE+A+ L+ L +G+ L V
Sbjct: 32 VRDKETGKSKG----------FAFVEFESEEDAEKALEALNGKEL-DGRPLKV 73
>gnl|CDD|219076 pfam06535, RGM_N, Repulsive guidance molecule (RGM) N-terminus.
This family consists of the N-terminal region of several
mammalian and one bird sequence from Gallus gallus
(Chicken). All of the mammalian proteins are
hypothetical and have no known function but RGMA from
the chicken is annotated as being a repulsive guidance
molecule (RGM). RGM is a GPI-linked axon guidance
molecule of the retinotectal system. RGM is repulsive
for a subset of axons, those from the temporal half of
the retina. Temporal retinal axons invade the anterior
optic tectum in a superficial layer, and encounter RGM
expressed in a gradient with increasing concentration
along the anterior-posterior axis. Temporal axons are
able to receive posterior-dependent information by
sensing gradients or concentrations of guidance cues.
Thus, RGM is likely to provide positional information
for temporal axons invading the optic tectum in the
stratum opticum.
Length = 207
Score = 29.0 bits (65), Expect = 1.3
Identities = 17/62 (27%), Positives = 23/62 (37%), Gaps = 3/62 (4%)
Query: 27 TKDGPPSRPGPLLPEPPRRLPTPSGPPSMPNYRGGYPDDDYYGAPPAFEFERSYNSPVLD 86
+KDGP S+P PP S P +Y + G PP + + P L
Sbjct: 100 SKDGPTSQP-RARTLPPGDSQEASDSPEPCHYEKSFGRGH--GRPPNYLHCGLFGDPHLR 156
Query: 87 KF 88
F
Sbjct: 157 TF 158
>gnl|CDD|237077 PRK12364, PRK12364, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 842
Score = 29.3 bits (66), Expect = 1.5
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 5/36 (13%)
Query: 61 GYPDDDYYGAPPAFEFERSYNSPVLDKFIGKPRGMS 96
GY +DYYG E+E+ Y V D I K R +
Sbjct: 459 GYALEDYYGE----EWEKRYLDCVNDARISK-RSIP 489
>gnl|CDD|240830 cd12384, RRM_RBM24_RBM38_like, RNA recognition motif in eukaryotic
RNA-binding protein RBM24, RBM38 and similar proteins.
This subfamily corresponds to the RRM of RBM24 and RBM38
from vertebrate, SUPpressor family member SUP-12 from
Caenorhabditis elegans and similar proteins. Both, RBM24
and RBM38, are preferentially expressed in cardiac and
skeletal muscle tissues. They regulate myogenic
differentiation by controlling the cell cycle in a
p21-dependent or -independent manner. RBM24, also termed
RNA-binding region-containing protein 6, interacts with
the 3'-untranslated region (UTR) of myogenin mRNA and
regulates its stability in C2C12 cells. RBM38, also
termed CLL-associated antigen KW-5, or HSRNASEB, or
RNA-binding region-containing protein 1(RNPC1), or
ssDNA-binding protein SEB4, is a direct target of the
p53 family. It is required for maintaining the stability
of the basal and stress-induced p21 mRNA by binding to
their 3'-UTRs. It also binds the AU-/U-rich elements in
p63 3'-UTR and regulates p63 mRNA stability and
activity. SUP-12 is a novel tissue-specific splicing
factor that controls muscle-specific splicing of the
ADF/cofilin pre-mRNA in C. elegans. All family members
contain a conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). .
Length = 76
Score = 27.2 bits (61), Expect = 1.6
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 12/54 (22%)
Query: 84 VLDKFIGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVA 137
+ D+ GK RG V D SAERA + + + +G++ V
Sbjct: 33 ITDRQTGKSRGY----------GFVTFKDKESAERACKDPNPII--DGRKANVN 74
>gnl|CDD|214836 smart00825, PKS_KS, Beta-ketoacyl synthase. The structure of
beta-ketoacyl synthase is similar to that of the
thiolase family and also chalcone synthase. The active
site of beta-ketoacyl synthase is located between the N
and C-terminal domains.
Length = 298
Score = 28.8 bits (66), Expect = 1.8
Identities = 9/23 (39%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 176 MAMKNRIQPPSQLLHFFNAPPDI 198
+A+K+ + PP+ LHF P I
Sbjct: 235 LALKHGVIPPT--LHFETPNPHI 255
>gnl|CDD|240871 cd12425, RRM4_PTBP1_like, RNA recognition motif 4 in polypyrimidine
tract-binding protein 1 (PTB or hnRNP I) and similar
proteins. This subfamily corresponds to the RRM4 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 = 76
Score = 27.2 bits (61), Expect = 1.9
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 188 LLHFFNAPPDITEEQLTDI 206
LH N PP +TEE L ++
Sbjct: 1 TLHLSNIPPSVTEEDLKEL 19
>gnl|CDD|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein
(LMP2) protein. This family consists of several
Gammaherpesvirus latent membrane protein (LMP2)
proteins. Epstein-Barr virus is a human
Gammaherpesvirus that infects and establishes latency
in B lymphocytes in vivo. The latent membrane protein 2
(LMP2) gene is expressed in latently infected B cells
and encodes two protein isoforms, LMP2A and LMP2B, that
are identical except for an additional N-terminal 119
aa cytoplasmic domain which is present in the LMP2A
isoform. LMP2A is thought to play a key role in either
the establishment or the maintenance of latency and/or
the reactivation of productive infection from the
latent state. The significance of LMP2B and its role in
pathogenesis remain unclear.
Length = 489
Score = 28.7 bits (64), Expect = 2.5
Identities = 13/35 (37%), Positives = 13/35 (37%), Gaps = 5/35 (14%)
Query: 31 PPSRPGPLLPEPPRRLPTPSGPPSMPNYRGGYPDD 65
RPGP P P PS P P Y G D
Sbjct: 38 SWDRPGP--PVPEDY-DAPSHRP--PPYGGSNGDR 67
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein orU2SURP,
or 140 kDa Ser/Arg-rich domain protein) which is a
putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 26.8 bits (60), Expect = 3.2
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 189 LHFFNAPPDITEEQLTDISGR 209
L+ N P +TEE L GR
Sbjct: 4 LYVGNLNPKVTEEVLCQEFGR 24
>gnl|CDD|241130 cd12686, RRM1_PTBPH1_PTBPH2, RNA recognition motif 1 in plant
polypyrimidine tract-binding protein homolog 1 and 2
(PTBPH1 and PTBPH2). This subfamily corresponds to the
RRM1 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 = 81
Score = 26.4 bits (58), Expect = 4.1
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 185 PSQLLHFFNAPPDITEEQLTDI 206
PS++LH N P + TEE+L ++
Sbjct: 1 PSKVLHLRNLPWECTEEELIEL 22
>gnl|CDD|234681 PRK00182, tatB, sec-independent translocase; Provisional.
Length = 160
Score = 27.1 bits (60), Expect = 4.5
Identities = 10/45 (22%), Positives = 15/45 (33%), Gaps = 3/45 (6%)
Query: 25 GRTKDGPPSRPGPLLPEPPRRL---PTPSGPPSMPNYRGGYPDDD 66
+ G ++ P + + P P Y GGY DD
Sbjct: 114 QQASAGRADNNANVVTRPADGSQPRSSQNDPKGGPPYAGGYSWDD 158
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 27.8 bits (62), Expect = 4.6
Identities = 8/43 (18%), Positives = 10/43 (23%)
Query: 14 SESWDYTQPTLGRTKDGPPSRPGPLLPEPPRRLPTPSGPPSMP 56
P PP+ P P P P + P
Sbjct: 392 PTPAAPAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAPP 434
>gnl|CDD|240758 cd12312, RRM_SRSF10_SRSF12, RNA recognition motif in
serine/arginine-rich splicing factor SRSF10, SRSF12 and
similar proteins. This subfamily corresponds to the RRM
of SRSF10 and SRSF12. SRSF10, also termed 40 kDa
SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). It is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
SRSF12, also termed 35 kDa SR repressor protein
(SRrp35), or splicing factor, arginine/serine-rich 13B
(SFRS13B), or splicing factor, arginine/serine-rich 19
(SFRS19), is a serine/arginine (SR) protein-like
alternative splicing regulator that antagonizes
authentic SR proteins in the modulation of alternative
5' splice site choice. For instance, it activates distal
alternative 5' splice site of the adenovirus E1A
pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain 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. .
Length = 84
Score = 26.2 bits (58), Expect = 4.8
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 11/56 (19%)
Query: 85 LDKFIGKPRGMSGPPSGPEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
LD + +PRG + VQ D AE A+ L +T G+ + + +++
Sbjct: 34 LDFYTRRPRGFA----------YVQFEDVRDAEDALYYLDRTRFL-GREIEIQFAQ 78
>gnl|CDD|221138 pfam11573, Med23, Mediator complex subunit 23. Med23 is one of the
subunits of the Tail portion of the Mediator complex
that regulates RNA polymerase II activity. Med23 is
required for heat-shock-specific gene expression, and
has been shown to mediate transcriptional activation of
E1A in mice.
Length = 1341
Score = 27.9 bits (62), Expect = 5.1
Identities = 12/48 (25%), Positives = 18/48 (37%)
Query: 8 NVYKNDSESWDYTQPTLGRTKDGPPSRPGPLLPEPPRRLPTPSGPPSM 55
N Y ++E + P L T +G P R+ P P S+
Sbjct: 493 NAYSTNTEYFSRPMPALIETLNGNSKNSSPFGLSYSRQAVNPFVPFSV 540
>gnl|CDD|185768 cd09245, BRO1_UmRIM23-like, Protein-interacting, Bro1-like domain
of Ustilago maydis Rim23 (PalC), and related domains.
This family contains the Bro1-like domain of Ustilago
maydis Rim23 (also known as PalC), and related proteins.
It belongs to the BRO1_Alix_like superfamily which
includes the Bro1-like domains of mammalian Alix
(apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), RhoA-binding proteins
Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, and related
domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23
interact with the ESCRT (Endosomal Sorting Complexes
Required for Transport) system. Rim20 and Rim23
participate in the response to the external pH via the
Rim101 pathway. Through its Bro1-like domain, Rim23
allows the interaction between the endosomal and plasma
membrane complexes. Bro1-like domains are
boomerang-shape, and part of the domain is a
tetratricopeptide repeat (TPR)-like structure.
Intermediates in the Rim101 pathway may play roles in
the pathogenesis of fungal corneal infection during
Candida albicans keratitis. This family lacks the
V-shaped (V) domain found in many members of the
BRO1_Alix_like superfamily.
Length = 413
Score = 27.4 bits (61), Expect = 5.9
Identities = 8/39 (20%), Positives = 12/39 (30%)
Query: 1 MSAPTKLNVYKNDSESWDYTQPTLGRTKDGPPSRPGPLL 39
++ T L V K D + + P P L
Sbjct: 210 LAEATLLAVRKLDPYPAAVDKDWMTPGPPLPKVHPSAHL 248
>gnl|CDD|180406 PRK06111, PRK06111, acetyl-CoA carboxylase biotin carboxylase
subunit; Validated.
Length = 450
Score = 27.3 bits (61), Expect = 6.7
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 101 GPEGCCMVQMGDTLSAERAM 120
GP + +MG + A RAM
Sbjct: 104 GPSADIIAKMGSKIEARRAM 123
>gnl|CDD|206773 cd11368, RNase_PH_RRP45, RRP45 subunit of eukaryotic exosome. The
RRP45 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 259
Score = 26.7 bits (60), Expect = 8.0
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 5/25 (20%)
Query: 101 GPE-GCCMVQMGDTLSAERAMGNLS 124
G E GC V +G T R + +S
Sbjct: 35 GLEYGCVEVSLGKT----RVLAQVS 55
>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich
splicing factor 10 (SRSF10) and similar proteins. This
subgroup corresponds to the RRM of SRSF10, also termed
40 kDa SR-repressor protein (SRrp40), or FUS-interacting
serine-arginine-rich protein 1 (FUSIP1), or splicing
factor SRp38, or splicing factor, arginine/serine-rich
13A (SFRS13A), or TLS-associated protein with Ser-Arg
repeats (TASR). SRSF10 is a serine-arginine (SR) protein
that acts as a potent and general splicing repressor
when dephosphorylated. It mediates global inhibition of
splicing both in M phase of the cell cycle and in
response to heat shock. SRSF10 emerges as a modulator of
cholesterol homeostasis through the regulation of
low-density lipoprotein receptor (LDLR) splicing
efficiency. It also regulates cardiac-specific
alternative splicing of triadin pre-mRNA and is required
for proper Ca2+ handling during embryonic heart
development. In contrast, the phosphorylated SRSF10
functions as a sequence-specific splicing activator in
the presence of a nuclear cofactor. It activates distal
alternative 5' splice site of adenovirus E1A pre-mRNA in
vivo. Moreover, SRSF10 strengthens pre-mRNA recognition
by U1 and U2 snRNPs. SRSF10 localizes to the nuclear
speckles and can shuttle between nucleus and cytoplasm.
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. .
Length = 84
Score = 25.7 bits (56), Expect = 8.5
Identities = 12/39 (30%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 102 PEGCCMVQMGDTLSAERAMGNLSKTLLCNGKRLAVAYSK 140
P G VQ D AE A+ NL + +C G+++ + +++
Sbjct: 41 PRGFAYVQFEDVRDAEDALHNLDRKWIC-GRQIEIQFAQ 78
>gnl|CDD|215045 PLN00064, PLN00064, photosystem II protein Psb27; Provisional.
Length = 166
Score = 26.5 bits (58), Expect = 8.9
Identities = 9/33 (27%), Positives = 13/33 (39%)
Query: 31 PPSRPGPLLPEPPRRLPTPSGPPSMPNYRGGYP 63
P S+P PL P + P +P R +
Sbjct: 2 PASKPKPLSLIKPPTATAAAVSPPLPPPRRNHL 34
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 27.0 bits (60), Expect = 9.0
Identities = 16/65 (24%), Positives = 20/65 (30%)
Query: 2 SAPTKLNVYKNDSESWDYTQPTLGRTKDGPPSRPGPLLPEPPRRLPTPSGPPSMPNYRGG 61
AP+ T P+ PP P +P PTP + P GG
Sbjct: 214 PAPSSFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVPPLSTAKPTPPSASATPAPIGG 273
Query: 62 YPDDD 66
DD
Sbjct: 274 ITLDD 278
>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 617
Score = 27.1 bits (60), Expect = 9.6
Identities = 20/97 (20%), Positives = 25/97 (25%), Gaps = 16/97 (16%)
Query: 22 PTLGRTKDGPP---SRPGPLLPEPPR-------------RLPTPSGPPSMPNYRGGYPDD 65
P+ G PP P LP P R R P +P R YP
Sbjct: 90 PSAGEPAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTARPAYPAY 149
Query: 66 DYYGAPPAFEFERSYNSPVLDKFIGKPRGMSGPPSGP 102
P A+ + PR P+
Sbjct: 150 QQRPEPGAWPRAADDYGWQQQRLGFPPRAPYASPASY 186
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
0.314 0.135 0.419
Gapped
Lambda K H
0.267 0.0940 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,227,148
Number of extensions: 1059864
Number of successful extensions: 1136
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1076
Number of HSP's successfully gapped: 96
Length of query: 211
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 118
Effective length of database: 6,812,680
Effective search space: 803896240
Effective search space used: 803896240
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: 57 (25.4 bits)