RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy258
(238 letters)
>gnl|CDD|218290 pfam04847, Calcipressin, Calcipressin. Calcipressin is also known
as calcineurin-binding protein, since it inhibits
calcineurin-mediated transcriptional modulation by
binding to calcineurin's catalytic domain.
Length = 177
Score = 158 bits (401), Expect = 6e-49
Identities = 82/169 (48%), Positives = 102/169 (60%), Gaps = 15/169 (8%)
Query: 81 LKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLH-QSVFASSKINVYFV 139
K+++ L Q+ +FQ LKSFRR+RVN+ S AAA ARI LH S F ++ +YF
Sbjct: 9 NKDKLRELFRQYNPIVTFQPLKSFRRVRVNFSSPEAAAAARIKLHEGSEFLGKELKLYFA 68
Query: 140 QPMTP-FDSADQHLQPPAPTKQFLISPPSSPPVGWEPRPESEP---LVNYDLLAAIASLT 195
QP P +A QHL PP P KQFLISPP+SPPVGWEP E P ++N DL AA+A L
Sbjct: 69 QPQHPERSAAKQHLAPPPPEKQFLISPPASPPVGWEPIEEDAPNRHVLNEDLQAALAKLG 128
Query: 196 PGLSHELHAPSESQPGIVVHVCE---------DGAMVGTKRIMQTACPP 235
PG +ELH ++ P +VVHVCE D K I+QTA PP
Sbjct: 129 PGEKYELHPGDDTTPAVVVHVCESEIDGEEAGDTPRPKPK-IVQTARPP 176
>gnl|CDD|240880 cd12434, RRM_RCAN_like, RNA recognition motif in regulators of
calcineurin (RCANs) and similar proteins. This
subfamily corresponds to the RRM of RCANs, a novel
family of calcineurin regulators that are key factors
contributing to Down syndrome in humans. They can
stimulate and inhibit the Ca2+/calmodulin-dependent
phosphatase calcineurin (also termed PP2B or PP3C)
signaling in vivo through direct interactions with its
catalytic subunit. Overexpressed RCANs may bind and
inhibit calcineurin. In contrast, low levels of
phosphorylated RCANs may stimulate the calcineurin
signaling. RCANs are characterized by harboring a
central short, unique serine-proline motif containing
FLIISPPxSPP box, which is strongly conserved from yeast
to human but is absent in bacteria. They consist of an
N-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
a highly conserved SP repeat domain containing the
phosphorylation site by GSK-3, a well-known PxIxIT motif
responsible for docking many substrates to calcineurin,
and an unrecognized C-terminal TxxP motif of unknown
function. .
Length = 75
Score = 89.2 bits (222), Expect = 3e-23
Identities = 36/100 (36%), Positives = 48/100 (48%), Gaps = 25/100 (25%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
LI+TN+ ++F N LK +E+L S +G+ +F Y
Sbjct: 1 LIVTNVPSEVFT-------------------------NAELKAALESLFSSYGEIATFVY 35
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQ 140
L SFRR RV + S AA ARI LH +VF S + VYF Q
Sbjct: 36 LPSFRRARVVFSSPEEAALARIELHGTVFEGSVLRVYFGQ 75
>gnl|CDD|241152 cd12708, RRM_RCAN1, RNA recognition motif in vertebrate regulator
of calcineurin 1 (RCAN1). This subgroup corresponds to
the RRM of RCAN1, also termed calcipressin-1, or
Adapt78, or Down syndrome critical region protein 1, or
myocyte-enriched calcineurin-interacting protein 1
(MCIP1), encoded by the Down syndrome critical region 1
(DSCR1) gene that is abundantly expressed in human
brain, heart and muscles. Overexpressed RCAN1 functions
as an inhibitor of the Ca2+/calmodulin-dependent
phosphatase calcineurin (also termed PP2B or PP3C), and
is associated with Alzheimer's disease (AD) and Down
syndrome (DS). RCAN1 can be phosphorylated by several
kinases such as big MAP kinase 1 (BMK1), glycogen
synthase kinase-3 (GSK-3), NF-kappaB inducing kinase
(NIK), and protein kinase A (PKA). The phosphorylation
of RCAN1 can positively or negatively regulate
calcineurin-mediated gene transcription, and also affect
its protein stability in the ubiquitin-proteasome
pathway. RCAN1 consists of an N-terminal RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a highly conserved SP repeat
domain containing the phosphorylation site by GSK-3, a
well-known PxIxIT motif responsible for docking many
substrates to calcineurin, and an unrecognized
C-terminal TxxP motif of unknown function. .
Length = 93
Score = 66.5 bits (162), Expect = 2e-14
Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 3/79 (3%)
Query: 81 LKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQ 140
+ + E+L + + +FQY KSF+R+R+N+ + +AA+AR LH++ F +I +YF Q
Sbjct: 18 TRAKFESLFRAYDRDVTFQYFKSFKRVRINFSNPLSAAEARAQLHKTEFLGKEIKLYFAQ 77
Query: 141 PMTPFDSADQHLQPPAPTK 159
+ HL PP P K
Sbjct: 78 TL---HIGSPHLAPPNPDK 93
>gnl|CDD|241154 cd12710, RRM_RCAN3, RNA recognition motif in vertebrate regulator
of calcineurin 3 (RCAN3). This subgroup corresponds to
the RRM of RCAN3, also termed calcipressin-3, or Down
syndrome candidate region 1-like protein 2 (DSCR1L2), or
myocyte-enriched calcineurin-interacting protein 3
(MCIP3), encoded by a ubiquitously expressed DSCR1L2
gene. Overexpressed RCAN3 binds and inhibits the
Ca2+/calmodulin-dependent phosphatase calcineurin (also
termed PP2B or PP3C), and further down-regulates nuclear
factor of activated T cells (NFAT)-dependent cytokine
gene expression in activated human Jurkat T cells.
Moreover, RCAN3 interacts with cardiac troponin I
(TNNI3), a heart-specific inhibitory subunit of the
troponin complex, and may play a role in cardiac
contraction. RCAN3 consists of an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), a highly
conserved SP repeat domain containing the
phosphorylation site by GSK-3, a well-known PxIxIT motif
responsible for docking many substrates to calcineurin,
and an unrecognized C-terminal TxxP motif of unknown
function. .
Length = 77
Score = 63.9 bits (155), Expect = 1e-13
Identities = 28/59 (47%), Positives = 38/59 (64%)
Query: 82 KEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQ 140
KE+ E L + SFQ KSFRR+R+N+ + AAA+ARI LH+S F K+ +YF Q
Sbjct: 19 KERFEALFRIYDDQVSFQMFKSFRRVRINFSNPEAAARARIELHESDFNGKKLKLYFAQ 77
>gnl|CDD|241153 cd12709, RRM_RCAN2, RNA recognition motif in vertebrate regulator
of calcineurin 2 (RCAN2). This subgroup corresponds to
the RRM of RCAN2, also termed calcipressin-2, or Down
syndrome candidate region 1-like 1 (DSCR1L1), or
myocyte-enriched calcineurin-interacting protein 2
(MCIP2), or thyroid hormone-responsive protein ZAKI-4,
encoded by a novel thyroid hormone-responsive gene
ZAKI-4 that is abundantly expressed in human brain,
heart and muscles. RCAN2 binds to the catalytic subunit
of Ca2+/calmodulin-dependent phosphatase calcineurin
(also termed PP2B or PP3C), calcineurin A, and inhibits
its phosphatase activity through its C-terminal region.
RCAN2 consists of an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a highly conserved SP repeat
domain containing the phosphorylation site by GSK-3, a
well-known PxIxIT motif responsible for docking many
substrates to calcineurin, and an unrecognized
C-terminal TxxP motif of unknown function. .
Length = 77
Score = 62.3 bits (151), Expect = 4e-13
Identities = 26/65 (40%), Positives = 40/65 (61%)
Query: 76 LKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKIN 135
+ +KE+ E L + +FQ KSFRR+R+N+ + AAA+ARI LH++ F K+
Sbjct: 13 FTSREVKEKFEGLFRAYDDCVTFQLFKSFRRVRINFSNPKAAARARIELHETQFRGKKLK 72
Query: 136 VYFVQ 140
+YF Q
Sbjct: 73 LYFAQ 77
>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 = 41.9 bits (99), Expect = 1e-05
Identities = 24/96 (25%), Positives = 37/96 (38%), Gaps = 25/96 (26%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
L + NL PD +E + L S+FG+ +S + +++ GK K F
Sbjct: 1 LFVGNLPPDT-----TEEDLRELFSKFGEIESVRIVRDKD------------GKSKGF-- 41
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVFASSKINV 136
V +ES A KA L+ K+ V
Sbjct: 42 ------AFVEFESPEDAEKALEALNGKELDGRKLKV 71
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 39.9 bits (94), Expect = 5e-05
Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 24/97 (24%)
Query: 40 SLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQ 99
+L + NL PD +E++ L S+FGK +S + +++ + GK K F
Sbjct: 1 TLFVGNLPPD-----TTEEELRELFSKFGKVESVRLVRD-----------KETGKSKGFA 44
Query: 100 YLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINV 136
+ V +ES A KA L+ + V
Sbjct: 45 F--------VEFESEEDAEKALEALNGKELDGRPLKV 73
>gnl|CDD|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I
polyadenylate-binding proteins. This subfamily
corresponds to the RRM3 of type I poly(A)-binding
proteins (PABPs), highly conserved proteins that bind to
the poly(A) tail present at the 3' ends of most
eukaryotic mRNAs. They have been implicated in the
regulation of poly(A) tail length during the
polyadenylation reaction, translation initiation, mRNA
stabilization by influencing the rate of deadenylation
and inhibition of mRNA decapping. The family represents
type I polyadenylate-binding proteins (PABPs), including
polyadenylate-binding protein 1 (PABP-1 or PABPC1),
polyadenylate-binding protein 3 (PABP-3 or PABPC3),
polyadenylate-binding protein 4 (PABP-4 or APP-1 or
iPABP), polyadenylate-binding protein 5 (PABP-5 or
PABPC5), polyadenylate-binding protein 1-like
(PABP-1-like or PABPC1L), polyadenylate-binding protein
1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding
protein 4-like (PABP-4-like or PABPC4L), yeast
polyadenylate-binding protein, cytoplasmic and nuclear
(PABP or ACBP-67), and similar proteins. PABP-1 is an
ubiquitously expressed multifunctional protein that may
play a role in 3' end formation of mRNA, translation
initiation, mRNA stabilization, protection of poly(A)
from nuclease activity, mRNA deadenylation, inhibition
of mRNA decapping, and mRNP maturation. Although PABP-1
is thought to be a cytoplasmic protein, it is also found
in the nucleus. PABP-1 may be involved in
nucleocytoplasmic trafficking and utilization of mRNP
particles. PABP-1 contains four copies of RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains), a less
well conserved linker region, and a proline-rich
C-terminal conserved domain (CTD). PABP-3 is a
testis-specific poly(A)-binding protein specifically
expressed in round spermatids. It is mainly found in
mammalian and may play an important role in the
testis-specific regulation of mRNA homeostasis. PABP-3
shows significant sequence similarity to PABP-1.
However, it binds to poly(A) with a lower affinity than
PABP-1. PABP-1 possesses an A-rich sequence in its
5'-UTR and allows binding of PABP and blockage of
translation of its own mRNA. In contrast, PABP-3 lacks
the A-rich sequence in its 5'-UTR. PABP-4 is an
inducible poly(A)-binding protein (iPABP) that is
primarily localized to the cytoplasm. It shows
significant sequence similarity to PABP-1 as well. The
RNA binding properties of PABP-1 and PABP-4 appear to be
identical. PABP-5 is encoded by PABPC5 gene within the
X-specific subinterval, and expressed in fetal brain and
in a range of adult tissues in mammalian, such as ovary
and testis. It may play an important role in germ cell
development. Moreover, unlike other PABPs, PABP-5
contains only four RRMs, but lacks both the linker
region and the CTD. PABP-1-like and PABP-1-like 2 are
the orthologs of PABP-1. PABP-4-like is the ortholog of
PABP-5. Their cellular functions remain unclear. The
family also includes the yeast PABP, a conserved poly(A)
binding protein containing poly(A) tails that can be
attached to the 3'-ends of mRNAs. The yeast PABP and its
homologs may play important roles in the initiation of
translation and in mRNA decay. Like vertebrate PABP-1,
the yeast PABP contains four RRMs, a linker region, and
a proline-rich CTD as well. The first two RRMs are
mainly responsible for specific binding to poly(A). The
proline-rich region may be involved in protein-protein
interactions. .
Length = 80
Score = 36.4 bits (85), Expect = 0.001
Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 25/83 (30%)
Query: 43 ITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQYLK 102
+ NL D D+ LKE L ++GK S + +K+D GK K F +
Sbjct: 6 VKNLGED-MDDEKLKE----LFGKYGKITSAKVMKDDE------------GKSKGFGF-- 46
Query: 103 SFRRMRVNYESSAAAAKARINLH 125
VN+E+ AA KA L+
Sbjct: 47 ------VNFENHEAAQKAVEELN 63
>gnl|CDD|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding
protein 18 and similar proteins. This subfamily
corresponds to the RRM of RBM18, a putative RNA-binding
protein containing a well-conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain). The biological role of RBM18
remains unclear. .
Length = 80
Score = 35.3 bits (82), Expect = 0.003
Identities = 24/96 (25%), Positives = 41/96 (42%), Gaps = 21/96 (21%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
L I NL+ L + LK L S++GK K F +L + + + G+P+ + +
Sbjct: 2 LWIGNLDSRLTEFHLLK-----LFSKYGKIKKFDFLFHKSGPLK--------GQPRGYCF 48
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVFASSKINV 136
V +E+ A KA +L+ K+ V
Sbjct: 49 --------VTFETKEEAEKALKSLNGKTALGKKLVV 76
>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 = 34.9 bits (81), Expect = 0.003
Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 25/94 (26%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
L + NL PD +E ++ L S+FG +S + + D + G+ K F +
Sbjct: 1 LFVGNLPPD-----TTEEDLKDLFSKFGPIESIR-IVRD-----------ETGRSKGFAF 43
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVFASSKI 134
V +E A KA L+ ++
Sbjct: 44 --------VEFEDEEDAEKALEALNGKELGGREL 69
>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding
protein 40 (RBM40) and similar proteins. This subfamily
corresponds to the RRM1 of RBM40, also known as
RNA-binding region-containing protein 3 (RNPC3) or
U11/U12 small nuclear ribonucleoprotein 65 kDa protein
(U11/U12-65K protein), It serves as a bridging factor
between the U11 and U12 snRNPs. It contains two repeats
of RNA recognition motif (RRM), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain),
connected by a linker that includes a proline-rich
region. It binds to the U11-associated 59K protein via
its RRM1 and employs the RRM2 to bind hairpin III of the
U12 small nuclear RNA (snRNA). The proline-rich region
might be involved in protein-protein interactions. .
Length = 73
Score = 33.4 bits (77), Expect = 0.012
Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 5/48 (10%)
Query: 83 EQIETLLSQFGKPKSFQYLKSFRRMR----VNYESSAAAAKARINLHQ 126
+ E LL FG S + + +++ +++ AA++A LHQ
Sbjct: 14 DDKEDLLKHFGA-SSVRVMSRRGKLKNTAFATFDNEQAASQALSRLHQ 60
>gnl|CDD|240881 cd12435, RRM_GW182_like, RNA recognition motif in the GW182 family
proteins. This subfamily corresponds to the RRM of the
GW182 family which includes three paralogs of TNRC6
(GW182-related) proteins comprising GW182/TNGW1, TNRC6B
(containing three isoforms) and TNRC6C in mammal, a
single Drosophila ortholog (dGW182, also called Gawky)
and two Caenorhabditis elegans orthologs AIN-1 and
AIN-2, which contain multiple miRNA-binding sites and
have important functions in miRNA-mediated translational
repression, as well as mRNA degradation in Metazoa. The
GW182 family proteins directly interact with Argonaute
(Ago) proteins, and thus function as downstream
effectors in the miRNA pathway, responsible for
inhibition of translation and acceleration of mRNA
decay. Members in this family are characterized by an
abnormally high content of glycine/tryptophan (G/W)
repeats, one or more glutamine (Q)-rich motifs, and a
C-terminal RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain).
The only exception is the worm protein that does not
contain a recognizable RRM domain. The GW182 family
proteins are recruited to miRNA targets through an
interaction between their N-terminal domain and an
Argonaute protein. Then they promote translational
repression and/or degradation of miRNA targets through
their C-terminal silencing domain. .
Length = 71
Score = 32.0 bits (73), Expect = 0.034
Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 9/73 (12%)
Query: 72 SFQYLKNDALKEQIE-----TLLSQFGKPKSFQYLKSFRRMR-VNYESSAAAAKARINLH 125
S+ L+N L QI+ TL Q G +F L + Y S AAKA+ L+
Sbjct: 2 SWLVLRN--LTPQIDGSTLRTLCMQHGPLLTFH-LNLRHGNALIRYSSKEEAAKAQSALN 58
Query: 126 QSVFASSKINVYF 138
V ++ + F
Sbjct: 59 NCVLGNTTLLAEF 71
>gnl|CDD|240786 cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in yeast nucleolar
protein 3 (Npl3p) and similar proteins. This subfamily
corresponds to the RRM1 of Npl3p, also termed
mitochondrial targeting suppressor 1 protein, or nuclear
polyadenylated RNA-binding protein 1. Npl3p is a major
yeast RNA-binding protein that competes with 3'-end
processing factors, such as Rna15, for binding to the
nascent RNA, protecting the transcript from premature
termination and coordinating transcription termination
and the packaging of the fully processed transcript for
export. It specifically recognizes a class of G/U-rich
RNAs. Npl3p is a multi-domain protein containing two
central RNA recognition motifs (RRMs), also termed RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains), separated by a short linker and a C-terminal
domain rich in glycine, arginine and serine residues. .
Length = 67
Score = 31.6 bits (72), Expect = 0.042
Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 79 DALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINV 136
D + I + S +G K + + +F V +ES +A +A+ ++H V ++ + V
Sbjct: 10 DTSESAIREIFSPYGAVKEVKMISNFAF--VEFESLESAIRAKDSVHGKVLNNNPLYV 65
>gnl|CDD|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain
of 45 kDa-splicing factor (SPF45) and similar proteins.
This subfamily corresponds to the RRM found in UHM
domain of 45 kDa-splicing factor (SPF45 or RBM17),
poly(U)-binding-splicing factor PUF60 (FIR or Hfp or
RoBP1 or Siah-BP1), and similar proteins. SPF45 is an
RNA-binding protein consisting of an unstructured
N-terminal region, followed by a G-patch motif and a
C-terminal U2AF (U2 auxiliary factor) homology motifs
(UHM) that harbors a RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain) and an Arg-Xaa-Phe sequence
motif. SPF45 regulates alternative splicing of the
apoptosis regulatory gene FAS (also known as CD95). It
induces exon 6 skipping in FAS pre-mRNA through the UHM
domain that binds to tryptophan-containing linear
peptide motifs (UHM ligand motifs, ULMs) present in the
3' splice site-recognizing factors U2AF65, SF1 and
SF3b155. PUF60 is an essential splicing factor that
functions as a poly-U RNA-binding protein required to
reconstitute splicing in depleted nuclear extracts. Its
function is enhanced through interaction with U2
auxiliary factor U2AF65. PUF60 also controls human c-myc
gene expression by binding and inhibiting the
transcription factor far upstream sequence element
(FUSE)-binding-protein (FBP), an activator of c-myc
promoters. PUF60 contains two central RRMs and a
C-terminal UHM domain. .
Length = 85
Score = 32.2 bits (74), Expect = 0.043
Identities = 19/100 (19%), Positives = 39/100 (39%), Gaps = 18/100 (18%)
Query: 39 KSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSF 98
K L++ N+ D+ LK++IE ++GK + ++ + ++
Sbjct: 2 KILVLRNMVTPGEIDEDLKDEIEEECEKYGK--------------VLNVIVHEVASSEAD 47
Query: 99 QYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYF 138
++ F V + + A KA L+ F K+ F
Sbjct: 48 DAVRIF----VEFSDADEAIKAVRALNGRFFGGRKVTARF 83
>gnl|CDD|225830 COG3293, COG3293, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 124
Score = 32.4 bits (74), Expect = 0.068
Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 6/61 (9%)
Query: 69 KPKSFQYLKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSV 128
+ F+ L ++ + FG+ LK FRR Y+S AA A + L
Sbjct: 66 PYRRFRRWFKRGLWKRRNLVERTFGR------LKQFRRTATRYDSLAAKKLAAVKLAAID 119
Query: 129 F 129
Sbjct: 120 I 120
>gnl|CDD|222631 pfam14259, RRM_6, RNA recognition motif (a.k.a. RRM, RBD, or RNP
domain).
Length = 69
Score = 31.0 bits (71), Expect = 0.072
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 7/68 (10%)
Query: 75 YLKN---DALKEQIETLLSQFGKPKSFQYLKSFRRMR----VNYESSAAAAKARINLHQS 127
Y++N +E + S +GK + + +++ R R V + S A A L+
Sbjct: 2 YVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNGL 61
Query: 128 VFASSKIN 135
V +
Sbjct: 62 VLDGRTLR 69
>gnl|CDD|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell
carcinoma antigen recognized by T-cells 3 (SART3) and
similar proteins. This subfamily corresponds to the
RRM2 of SART3, also termed Tat-interacting protein of
110 kDa (Tip110), is an RNA-binding protein expressed in
the nucleus of the majority of proliferating cells,
including normal cells and malignant cells, but not in
normal tissues except for the testes and fetal liver. It
is involved in the regulation of mRNA splicing probably
via its complex formation with RNA-binding protein with
a serine-rich domain (RNPS1), a pre-mRNA-splicing
factor. SART3 has also been identified as a nuclear
Tat-interacting protein that regulates Tat
transactivation activity through direct interaction and
functions as an important cellular factor for HIV-1 gene
expression and viral replication. In addition, SART3 is
required for U6 snRNP targeting to Cajal bodies. It
binds specifically and directly to the U6 snRNA,
interacts transiently with the U6 and U4/U6 snRNPs, and
promotes the reassembly of U4/U6 snRNPs after splicing
in vitro. SART3 contains an N-terminal
half-a-tetratricopeptide repeat (HAT)-rich domain, a
nuclearlocalization signal (NLS) domain, and two
C-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 81
Score = 31.2 bits (71), Expect = 0.095
Identities = 23/104 (22%), Positives = 40/104 (38%), Gaps = 25/104 (24%)
Query: 38 PKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKS 97
L ++ L KE++E L + G KS + + N + GKPK
Sbjct: 2 KHKLFVSGLP-----FSVTKEELEKLFKKHGVVKSVRLVTNRS------------GKPKG 44
Query: 98 FQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
Y V YE+ ++A++A + + + I+V P
Sbjct: 45 LAY--------VEYENESSASQAVLKMDGTEIKEKTISVAISNP 80
>gnl|CDD|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate
RNA-binding protein 4 (RBM4). This subgroup corresponds
to the RRM1 of RBM4, a ubiquitously expressed splicing
factor that has two isoforms, RBM4A (also known as Lark
homolog) and RBM4B (also known as RBM30), which are very
similar in structure and sequence. RBM4 may function as
a translational regulator of stress-associated mRNAs and
also plays a role in micro-RNA-mediated gene regulation.
RBM4 contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), a CCHC-type zinc finger,
and three alanine-rich regions within their C-terminal
regions. The C-terminal region may be crucial for
nuclear localization and protein-protein interaction.
The RRMs, in combination with the C-terminal region, are
responsible for the splicing function of RBM4. .
Length = 67
Score = 30.6 bits (69), Expect = 0.10
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 76 LKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKIN 135
L +A +++I +L Q+GK +K++ V+ + AA +A NLH IN
Sbjct: 8 LPPEATEQEIRSLFEQYGKVLECDIIKNYG--FVHMDDKTAADEAIRNLHHYKLHGVAIN 65
Query: 136 V 136
V
Sbjct: 66 V 66
>gnl|CDD|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General
function prediction only].
Length = 306
Score = 33.0 bits (74), Expect = 0.11
Identities = 21/110 (19%), Positives = 41/110 (37%), Gaps = 24/110 (21%)
Query: 27 SLDDLINDEQLPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIE 86
S ++ +L + NL D+ ++D + L +FG K + +++
Sbjct: 104 SPKSRQKSKEENNTLFVGNLPYDVTEED-----LRELFKKFGPVKRVRLVRD-------- 150
Query: 87 TLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINV 136
+ GK + F + V +ES +A KA L+ + V
Sbjct: 151 ---RETGKSRGFAF--------VEFESEESAEKAIEELNGKELEGRPLRV 189
>gnl|CDD|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM3 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 92
Score = 30.7 bits (70), Expect = 0.14
Identities = 24/104 (23%), Positives = 38/104 (36%), Gaps = 24/104 (23%)
Query: 38 PKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKS 97
+ L + L F+D + L SQ GKP Q ++ G+P+
Sbjct: 2 SRCLFVDRLPKT-FRDV---SILRKLFSQVGKPTFCQ------------LAIAPNGQPRG 45
Query: 98 FQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYFVQP 141
F + V Y ++ A +A+ L+ S I V F P
Sbjct: 46 FAF--------VEYATAEDAEEAQQALNGHSLQGSPIRVSFGNP 81
>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 = 29.4 bits (67), Expect = 0.23
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 13/59 (22%)
Query: 87 TLLSQFGKPKSFQYLKSFRRMR-------VNYESSAAAAKARINLHQSVFASSKINVYF 138
L S FG ++ + ++ V + + AA KA L+ +F + V +
Sbjct: 3 KLFSPFGN------VEKIKLLKKKPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55
>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein
MRN1 and similar proteins. This subgroup corresponds to
the RRM4 of MRN1, also termed multicopy suppressor of
RSC-NHP6 synthetic lethality protein 1, or
post-transcriptional regulator of 69 kDa, which is a
RNA-binding protein found in yeast. Although its
specific biological role remains unclear, MRN1 might be
involved in translational regulation. Members in this
family contain four copies of conserved RNA recognition
motif (RRM), also known as RBD (RNA binding domain) or
RNP (ribonucleoprotein domain). .
Length = 79
Score = 29.7 bits (67), Expect = 0.29
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 83 EQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKA--RINLHQSVFASSKIN 135
E++ SQ+G+ +S YL+ VN+ + + A KA + H F KI+
Sbjct: 18 EKLRNDFSQYGEIESVNYLREKNCAFVNFTNISNAIKAIDGVKSHPL-FKKFKIS 71
>gnl|CDD|240692 cd12246, RRM1_U1A_like, RNA recognition motif 1 in the U1A/U2B"/SNF
protein family. This subfamily corresponds to the RRM1
of U1A/U2B"/SNF protein family which contains Drosophila
sex determination protein SNF and its two mammalian
counterparts, U1 small nuclear ribonucleoprotein A (U1
snRNP A or U1-A or U1A) and U2 small nuclear
ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which
consist of two RNA recognition motifs (RRMs), connected
by a variable, flexible linker. SNF is an RNA-binding
protein found in the U1 and U2 snRNPs of Drosophila
where it is essential in sex determination and possesses
a novel dual RNA binding specificity. SNF binds with
high affinity to both Drosophila U1 snRNA stem-loop II
(SLII) and U2 snRNA stem-loop IV (SLIV). It can also
bind to poly(U) RNA tracts flanking the alternatively
spliced Sex-lethal (Sxl) exon, as does Drosophila
Sex-lethal protein (SXL). U1A is an RNA-binding protein
associated with the U1 snRNP, a small RNA-protein
complex involved in pre-mRNA splicing. U1A binds with
high affinity and specificity to stem-loop II (SLII) of
U1 snRNA. It is predominantly a nuclear protein that
shuttles between the nucleus and the cytoplasm
independently of interactions with U1 snRNA. Moreover,
U1A may be involved in RNA 3'-end processing,
specifically cleavage, splicing and polyadenylation,
through interacting with a large number of non-snRNP
proteins. U2B", initially identified to bind to
stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a
unique protein that comprises of the U2 snRNP.
Additional research indicates U2B" binds to U1 snRNA
stem-loop II (SLII) as well and shows no preference for
SLIV or SLII on the basis of binding affinity. Moreover,
U2B" does not require an auxiliary protein for binding
to RNA, and its nuclear transport is independent of U2
snRNA binding. .
Length = 78
Score = 29.4 bits (67), Expect = 0.31
Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 5/67 (7%)
Query: 76 LKNDALKEQIETLLSQFGKPKSFQYLKSFRRMR----VNYESSAAAAKARINLHQSVFAS 131
+K D LK + L SQFG K+ +MR V ++ +A A L F
Sbjct: 11 IKKDELKRSLYALFSQFGPVLDIVASKT-LKMRGQAFVVFKDVESATNALRALQGFPFYD 69
Query: 132 SKINVYF 138
+ + +
Sbjct: 70 KPMRIQY 76
Score = 27.9 bits (63), Expect = 1.2
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 40 SLIITNLNPDLFKDDALKEQIETLLSQFGK 69
+L I NLN + KD+ LK + L SQFG
Sbjct: 1 TLYINNLNEKIKKDE-LKRSLYALFSQFGP 29
>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM1
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 = 29.1 bits (66), Expect = 0.43
Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 17/73 (23%)
Query: 75 YLKNDALKEQIET---------LLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLH 125
Y+ D L+E E+ + ++ GK + F + V ++S A +A +
Sbjct: 11 YVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGF--------VGFKSEEDAQQAVKYFN 62
Query: 126 QSVFASSKINVYF 138
++ +SKI+V
Sbjct: 63 KTFIDTSKISVEL 75
>gnl|CDD|145428 pfam02268, TFIIA_gamma_N, Transcription initiation factor IIA,
gamma subunit, helical domain. Accurate transcription
in vivo requires at least six general transcription
initiation factors, in addition to RNA polymerase II.
Transcription initiation factor IIA (TFIIA) is a
multimeric protein which facilitates the binding of
TFIID to the TATA box. The N-terminal domain of the
gamma subunit is a 4 helix bundle.
Length = 49
Score = 28.0 bits (63), Expect = 0.62
Identities = 7/16 (43%), Positives = 12/16 (75%)
Query: 26 DSLDDLINDEQLPKSL 41
D+LD+LI+D ++ L
Sbjct: 17 DALDELISDGRITPQL 32
>gnl|CDD|240677 cd12231, RRM2_U2AF65, RNA recognition motif 2 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 77
Score = 28.4 bits (64), Expect = 0.74
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 5/40 (12%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDA 80
+ I L L +D +KE LL FGK K+F +K+ A
Sbjct: 3 IFIGGLPNYL-SEDQVKE----LLESFGKLKAFNLVKDSA 37
Score = 25.7 bits (57), Expect = 7.3
Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 4/24 (16%)
Query: 75 YLKNDALKEQIETLLSQFGKPKSF 98
YL D +KE LL FGK K+F
Sbjct: 11 YLSEDQVKE----LLESFGKLKAF 30
>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end)
protein family. This subfamily corresponds to the RRM3
domain in the Spen (split end) protein family which
includes RNA binding motif protein 15 (RBM15), putative
RNA binding motif protein 15B (RBM15B) and similar
proteins found in Metazoa. RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, is a
novel mRNA export factor and is a novel component of the
NXF1 pathway. It binds to NXF1 and serves as receptor
for the RNA export element RTE. It also possess mRNA
export activity and can facilitate the access of
DEAD-box protein DBP5 to mRNA at the nuclear pore
complex (NPC). RNA-binding protein 15B (RBM15B), also
termed one twenty-two 3 (OTT3), is a paralog of RBM15
and therefore has post-transcriptional regulatory
activity. It is a nuclear protein sharing with RBM15 the
association with the splicing factor compartment and the
nuclear envelope as well as the binding to mRNA export
factors NXF1 and Aly/REF. Members in this family belong
to the Spen (split end) protein family, which shares a
domain architecture comprising of three N-terminal RNA
recognition motifs (RRMs), also known as RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and a
C-terminal SPOC (Spen paralog and ortholog C-terminal)
domain. .
Length = 72
Score = 27.9 bits (63), Expect = 1.0
Identities = 10/40 (25%), Positives = 16/40 (40%)
Query: 82 KEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKAR 121
++E +FG + Y + YES AA A+
Sbjct: 12 LAELEREFDRFGAIRRIDYDPGRNYAYIEYESIEAAQAAK 51
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 30.2 bits (68), Expect = 1.1
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 38 PKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDA 80
+ I NL P +D QI+ LL FG K+F +K+ A
Sbjct: 295 KDRIYIGNL-PLYLGED----QIKELLESFGDLKAFNLIKDIA 332
Score = 28.3 bits (63), Expect = 4.1
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 2/60 (3%)
Query: 44 TNLNPDLFKDDALKEQIETLLSQFGKPKSF-QYLKNDALKEQIETLLSQFGKPKSFQYLK 102
+ NPD + K T + K + + L ++QI+ LL FG K+F +K
Sbjct: 271 SQKNPDDNAKNVEKLVNSTTVLD-SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIK 329
>gnl|CDD|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM2 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 77
Score = 28.0 bits (63), Expect = 1.1
Identities = 25/98 (25%), Positives = 38/98 (38%), Gaps = 24/98 (24%)
Query: 41 LIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQY 100
L + NL P F D+ +E L+S FG + + +++ T S K F
Sbjct: 2 LCVGNL-PLEFTDEQFRE----LVSPFGAVERCFLVYSES------TGES---KGYGF-- 45
Query: 101 LKSFRRMRVNYESSAAAAKARINLHQSVFASSKINVYF 138
V Y S A+A KA+ L K+ V +
Sbjct: 46 --------VEYASKASALKAKNQLDGKQIGGRKLQVDW 75
>gnl|CDD|218762 pfam05816, TelA, Toxic anion resistance protein (TelA). This
family consists of several prokaryotic TelA like
proteins. TelA and KlA are associated with tellurite
resistance and plasmid fertility inhibition.
Length = 333
Score = 29.9 bits (68), Expect = 1.2
Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 8/76 (10%)
Query: 19 KDTGDMGDSLDDLINDEQLPKSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKN 78
KD G++G L +L I+ L+P ++ + + L + + K
Sbjct: 42 KDVGEVGKLLTELRK--------IVKELDPSELSEEKKRGFLGKLFGKAKNSIERYFAKY 93
Query: 79 DALKEQIETLLSQFGK 94
++ QI+ +L + K
Sbjct: 94 QSVGGQIDKILVELEK 109
>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).
This subgroup corresponds to the RRM3 of hnRNP Q, also
termed glycine- and tyrosine-rich RNA-binding protein
(GRY-RBP), or NS1-associated protein 1 (NASP1), or
synaptotagmin-binding, cytoplasmic RNA-interacting
protein (SYNCRIP). It is a ubiquitously expressed
nuclear RNA-binding protein identified as a component of
the spliceosome complex, as well as a component of the
apobec-1 editosome. As an alternatively spliced version
of NSAP, it acts as an interaction partner of a
multifunctional protein required for viral replication,
and is implicated in the regulation of specific mRNA
transport. hnRNP Q has also been identified as SYNCRIP
that is a dual functional protein participating in both
viral RNA replication and translation. As a
synaptotagmin-binding protein, hnRNP Q plays a putative
role in organelle-based mRNA transport along the
cytoskeleton. Moreover, hnRNP Q has been found in
protein complexes involved in translationally coupled
mRNA turnover and mRNA splicing. It functions as a
wild-type survival motor neuron (SMN)-binding protein
that may participate in pre-mRNA splicing and modulate
mRNA transport along microtubuli. hnRNP Q contains an
acidic auxiliary N-terminal region, followed by two well
defined and one degenerated RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal RGG motif;
hnRNP Q binds RNA through its RRM domains. .
Length = 72
Score = 27.7 bits (61), Expect = 1.3
Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 76 LKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRVNYESSAAAAKARINLHQSVFASSKIN 135
L N +E +E QFGK + + LK + ++++ A KA ++ I
Sbjct: 9 LANTVTEEILEKAFGQFGKLERVKKLKDY--AFIHFDERDGAVKAMEEMNGKELEGENIE 66
Query: 136 VYFVQP 141
+ F +P
Sbjct: 67 IVFAKP 72
>gnl|CDD|178768 PLN03229, PLN03229, acetyl-coenzyme A carboxylase carboxyl
transferase subunit alpha; Provisional.
Length = 762
Score = 29.8 bits (67), Expect = 1.4
Identities = 26/81 (32%), Positives = 34/81 (41%), Gaps = 13/81 (16%)
Query: 56 LKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKS-----------FQYLKSF 104
L+E++E L +F K S L + L E+IE L +F K S L F
Sbjct: 484 LQERLENLREEFSKANSQDQLMHPVLMEKIEKLKDEFNKRLSRAPNYLSLKYKLDMLNEF 543
Query: 105 RRMRVNYE--SSAAAAKARIN 123
R + E S A KA IN
Sbjct: 544 SRAKALSEKKSKAEKLKAEIN 564
>gnl|CDD|237218 PRK12825, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 249
Score = 28.7 bits (65), Expect = 2.4
Identities = 23/105 (21%), Positives = 38/105 (36%), Gaps = 28/105 (26%)
Query: 49 DLFKDDALKEQIETLLSQFGK------------PKSFQYLKNDALKEQIETLLSQFGKPK 96
D+ AL+ + + +FG+ K + +D E I+ LS
Sbjct: 64 DVTDKAALEAAVAAAVERFGRIDILVNNAGIFEDKPLADMSDDEWDEVIDVNLSGV---- 119
Query: 97 SFQYLKS-FRRMR-------VNYESSAAAAKARINLHQSVFASSK 133
F L++ MR VN SS A +S +A++K
Sbjct: 120 -FHLLRAVVPPMRKQRGGRIVNI-SSVAGLPG--WPGRSNYAAAK 160
>gnl|CDD|237619 PRK14135, recX, recombination regulator RecX; Provisional.
Length = 263
Score = 28.6 bits (65), Expect = 2.5
Identities = 28/107 (26%), Positives = 44/107 (41%), Gaps = 32/107 (29%)
Query: 11 IINAIDNLKDTGDMGDSLDDLINDEQLPKSLIITNLN-----PDLFK------------- 52
I ID LK+ + I+D++ +S + TN+N P + K
Sbjct: 91 ISEVIDKLKE--------EKYIDDKEYAESYVRTNINTGDKGPRVIKQKLLQKGIEDEII 142
Query: 53 DDAL-----KEQIETLLSQFGK-PKSFQYLKNDALKEQIETLLSQFG 93
++AL ++QIE K K +Q L ALK++I L G
Sbjct: 143 EEALSEYTEEDQIEVAQKLAEKLLKKYQKLPFKALKQKIIQSLLTKG 189
>gnl|CDD|219523 pfam07697, 7TMR-HDED, 7TM-HD extracellular. This entry represents
the extracellular domain of the 7TM-HD (7TM Receptors
with HD hydrolase).
Length = 218
Score = 28.4 bits (64), Expect = 2.6
Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 8/86 (9%)
Query: 11 IINAIDNLKDTGDMGDSLDDL----INDEQLPKSLIIT--NLNPDLFKD--DALKEQIET 62
+ + I +K + + + D L ++ QL T N + + K DA++ ++
Sbjct: 57 LFDEIREVKASAEKAEKADRLKSLNLSTFQLSDEQWSTLLNADDEDLKLLEDAIRTALDR 116
Query: 63 LLSQFGKPKSFQYLKNDALKEQIETL 88
+LSQ + K +A K Q+E+L
Sbjct: 117 ILSQGIREGLLIEAKEEAAKLQLESL 142
>gnl|CDD|165222 PHA02896, PHA02896, A-type inclusion like protein; Provisional.
Length = 616
Score = 28.8 bits (64), Expect = 2.6
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 3 EDEDDHKMIINAIDNLKDTGDMGDSLDDLI-NDEQLPKSL 41
+D DD +I +NL+D D D + D I +D+ PKS+
Sbjct: 461 DDNDDDHIIPKKANNLEDAKDFEDEMMDAIADDDYTPKSI 500
>gnl|CDD|240922 cd12478, RRM1_U2B, RNA recognition motif 1 in U2 small nuclear
ribonucleoprotein B" (U2B") and similar proteins. This
subgroup corresponds to the RRM1 of U2B" (also termed U2
snRNP B") a unique protein that comprises the U2 snRNP.
It was initially identified as binding to stem-loop IV
(SLIV) at the 3' end of U2 snRNA. Additional research
indicates U2B" binds to U1 snRNA stem-loop II (SLII) as
well and shows no preference for SLIV or SLII on the
basis of binding affinity. U2B" does not require an
auxiliary protein for binding to RNA. In addition, the
nuclear transport of U2B" is independent of U2 snRNA
binding. U2B" contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). It also contains a nuclear
localization signal (NLS) in the central domain.
However, nuclear import of U2B'' does not depend on this
NLS. The N-terminal RRM is sufficient to direct U2B" to
the nucleus. .
Length = 91
Score = 27.3 bits (60), Expect = 3.0
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 6/77 (7%)
Query: 40 SLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKP-KSF 98
++ I NLN D K + LK + L SQFG LK ++ Q + + +
Sbjct: 3 TIYINNLN-DKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELSSATNAL 61
Query: 99 QYLKSF----RRMRVNY 111
+ L+ F + MR+ Y
Sbjct: 62 RQLQGFPFYGKPMRIQY 78
>gnl|CDD|223886 COG0816, COG0816, Predicted endonuclease involved in recombination
(possible Holliday junction resolvase in Mycoplasmas and
B. subtilis) [DNA replication, recombination, and
repair].
Length = 141
Score = 27.6 bits (62), Expect = 3.5
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 60 IETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSFQYLKSFRRMRV 109
+ET+ + GKP+ F L + Q++T++ G P + + R
Sbjct: 29 LETIKRKNGKPQDFNALLKLVKEYQVDTVV--VGLPLNMDGTEGPRAELA 76
>gnl|CDD|240745 cd12299, RRM4_Prp24, RNA recognition motif 4 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM4 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 71
Score = 26.4 bits (59), Expect = 3.7
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 82 KEQIETLLSQFGKPKSFQYLKS-FRRMRVNYESSAAAAKARINLHQSVFASSKINV 136
+EQI+ + G L V +ES + A KA ++L+ S F I +
Sbjct: 14 EEQIKAFFEKIGPDVRKIELFPDHEGALVEFESPSDAGKASLSLNGSQFGGKTIKI 69
>gnl|CDD|219995 pfam08737, Rgp1, Rgp1. Rgp1 forms heterodimer with Ric1
(pfam07064) which associates with Golgi membranes and
functions as a guanyl-nucleotide exchange factor.
Length = 402
Score = 28.2 bits (63), Expect = 4.7
Identities = 39/172 (22%), Positives = 66/172 (38%), Gaps = 36/172 (20%)
Query: 1 MEEDEDDHKMIINAIDNLKDTGDMGDS-LDDLINDEQLPKSLIITNLNPDLFKDDALKEQ 59
+EE + K +++ + +M DS L+DL+ Q KSL ++ P L D +
Sbjct: 216 LEEFLEYLKELLS-----SRSYNMPDSTLEDLLKSSQFGKSLRTSDSEPPLSVKDQIPNA 270
Query: 60 IETLLSQFGKPKSFQYLKNDALKEQIETL-LSQ--------------FGKPKSFQ----- 99
I LLSQ P +Q +N E++ T+ LS+ F
Sbjct: 271 ISNLLSQLQNPTRYQISRNG---EKVATVSLSKPAYRLGEDIVGTIDFSPGDLIPCYGVS 327
Query: 100 -YLKSF----RRMRVNYESSAAAAKARI--NLHQSVFASSKINVYFVQPMTP 144
L++ + V +SA R+ H+S S +I+ P +
Sbjct: 328 ASLETEELVNPKYAVRSNASANRPTRRVHAEHHESCLDSRRISFSLPIPKSA 379
>gnl|CDD|211960 TIGR04237, seadorna_VP9, seadornavirus/coltivirus VP9 protein.
This model, broader than related pfam08978, describes
proteins VP9 in Coltivirus, and proteins with various
designations in the seadornavirus group: VP9 in Banna
virus, VP10 in Liao ning virus, and VP11 in Kadipiro
virus.
Length = 280
Score = 27.6 bits (61), Expect = 5.2
Identities = 25/117 (21%), Positives = 43/117 (36%), Gaps = 15/117 (12%)
Query: 122 INLHQSVFASSKINVYFVQPMTPFDSADQHLQPPAPTKQFLISPPSSPPVGWEPRPESEP 181
NL S + K+NV F +T S T + S S P W+P+
Sbjct: 150 QNLIGSTIDTGKVNVLFQTSLTTASS----------TNSYAYSHCSVPITKWDPK--MIK 197
Query: 182 LVNYDLLAAIASLTPGLSHELHAPSESQPGIVVHVCEDGAMVGTKRIMQTACPPTKP 238
L + ++ S+T + + + P + ++V G V T + + P T
Sbjct: 198 LTSETSCPSLTSMTNLANSLV--EGDRTPPVGLYVDIPGVTVTTSASLSSL-PITTI 251
>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein
19 (RBM19) and similar proteins. This subgroup
corresponds to the RRM1 of RBM19, also termed
RNA-binding domain-1 (RBD-1), a nucleolar protein
conserved in eukaryotes. It is involved in ribosome
biogenesis by processing rRNA. In addition, it is
essential for preimplantation development. RBM19 has a
unique domain organization containing 6 conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). .
Length = 76
Score = 26.1 bits (58), Expect = 5.8
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 5/66 (7%)
Query: 76 LKNDALKEQIETLLSQFGKPK--SFQYLKS--FRRMR-VNYESSAAAAKARINLHQSVFA 130
L ++++ L FG +Y K FR+ V Y++ A KA + + S
Sbjct: 8 LPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNNSFID 67
Query: 131 SSKINV 136
+SKI V
Sbjct: 68 TSKITV 73
>gnl|CDD|240401 PTZ00397, PTZ00397, macrophage migration inhibition factor-like
protein; Provisional.
Length = 116
Score = 26.3 bits (58), Expect = 6.8
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 37 LPKSLIITNLNPDLFKDDALKEQIETLLSQ-FGKPKSF 73
+P + TN+N + DA IE ++ GKP S+
Sbjct: 1 MPCCQVSTNVNATDDQADAALSDIENAIADVLGKPLSY 38
>gnl|CDD|235686 PRK06061, PRK06061, amidase; Provisional.
Length = 483
Score = 27.4 bits (61), Expect = 7.5
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 204 APSESQPGIVVHVCEDGAMVGTKRIMQTACPPTKP 238
AP+ +QP V + T R M ACP T P
Sbjct: 387 APTTAQPPPRVGAFDRLGGWATDRAMIAACPYTWP 421
>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM2 of Prp24, also termed U4/U6
snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an
RNA-binding protein with four well conserved RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). It
facilitates U6 RNA base-pairing with U4 RNA during
spliceosome assembly. Prp24 specifically binds free U6
RNA primarily with RRMs 1 and 2 and facilitates pairing
of U6 RNA bases with U4 RNA bases. Additionally, it may
also be involved in dissociation of the U4/U6 complex
during spliceosome activation. .
Length = 78
Score = 25.6 bits (57), Expect = 8.1
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 5/68 (7%)
Query: 79 DALKEQIETLLSQFGKPKS--FQYLKSFRRMR---VNYESSAAAAKARINLHQSVFASSK 133
+ I L Q+G+ S F L+ + R V + S +AA A L+ + K
Sbjct: 11 SFDQSDIRDLFEQYGEILSIRFPSLRFNKTRRFCYVQFTSPESAAAAVALLNGKLGEGYK 70
Query: 134 INVYFVQP 141
+ V P
Sbjct: 71 LVVKISDP 78
>gnl|CDD|203376 pfam06016, Reovirus_L2, Reovirus core-spike protein lambda-2 (L2).
This family consists of several Reovirus core-spike
protein lambda-2 (L2) sequences. The reovirus L2 genome
segment encodes the core spike protein lambda-2, which
mediates enzymatic reactions in 5' capping of the viral
plus-strand transcripts.
Length = 1290
Score = 27.5 bits (61), Expect = 8.5
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 144 PFDSADQHLQPPAPTKQFLISPPSSPPVGW 173
P+DS + ++ T L S P P GW
Sbjct: 1233 PYDSREWAVKESGNTFVILDSQPFVLPQGW 1262
>gnl|CDD|185701 cd09024, Aldose_epim_lacX, Aldose 1-epimerase, similar to
Lactococcus lactis lacX. Proteins similar to
Lactococcus lactis lacX are uncharacterized members of
aldose-1-epimerase superfamily. Aldose 1-epimerases or
mutarotases are key enzymes of carbohydrate metabolism,
catalyzing the interconversion of the alpha- and
beta-anomers of hexose sugars such as glucose and
galactose. This interconversion is an important step
that allows anomer specific metabolic conversion of
sugars. Studies of the catalytic mechanism of the best
known member of the family, galactose mutarotase, have
shown a glutamate and a histidine residue to be critical
for catalysis; the glutamate serves as the active site
base to initiate the reaction by removing the proton
from the C-1 hydroxyl group of the sugar substrate, and
the histidine as the active site acid to protonate the
C-5 ring oxygen.
Length = 288
Score = 27.1 bits (61), Expect = 8.7
Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 1/55 (1%)
Query: 2 EEDEDDHKMIINAIDNLKDTGDMGDSLDDLINDEQLPKSLIITNLNPDLFKDDAL 56
E +D+ + + L+ +G + L + L DLF DDAL
Sbjct: 151 GEKFEDYYLEFEPKEELERIPLVGPLGLLG-EKKPLLLNEGTLPLTHDLFDDDAL 204
>gnl|CDD|225552 COG3007, COG3007, Uncharacterized paraquat-inducible protein B
[Function unknown].
Length = 398
Score = 27.1 bits (60), Expect = 9.0
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 39 KSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQY 75
K L ++N D F D+ ++ IE + FGK Y
Sbjct: 101 KGLYAKSINGDAFSDEMKQKVIEAIKQDFGKVDLVVY 137
>gnl|CDD|217143 pfam02614, UxaC, Glucuronate isomerase. This is a family of
Glucuronate isomerases also known as D-glucuronate
isomerase, uronic isomerase, uronate isomerase, or
uronic acid isomerase, EC:5.3.1.12. This enzyme
catalyzes the reactions: D-glucuronate <=>
D-fructuronate and D-galacturonate <=> D-tagaturonate.
It is not however clear where the experimental evidence
for this functional assignment came from and thus this
family has no literature reference.
Length = 469
Score = 27.2 bits (61), Expect = 9.0
Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 28/83 (33%)
Query: 28 LDDLINDEQLPKSLIITNLNPDL----------FKDDALKEQIETLLSQFGKPKSFQYLK 77
LD L ++LPK+ I+ +LNP F+ + ++ QFG F
Sbjct: 333 LDKLDRKDRLPKT-ILYSLNPRDNEVLATMAGNFQGGGVPGKV-----QFGAAWWF---- 382
Query: 78 ND---ALKEQIET-----LLSQF 92
ND ++ Q+ LLS F
Sbjct: 383 NDTKDGMERQMNALANVGLLSNF 405
>gnl|CDD|240703 cd12257, RRM1_RBM26_like, RNA recognition motif 1 in vertebrate
RNA-binding protein 26 (RBM26) and similar proteins.
This subfamily corresponds to the RRM1 of RBM26, and the
RRM of RBM27. RBM26, also known as cutaneous T-cell
lymphoma (CTCL) tumor antigen se70-2, represents a
cutaneous lymphoma (CL)-associated antigen. It contains
two RNA recognition motifs (RRMs), also known as RBDs
(RNA binding domains) or RNPs (ribonucleoprotein
domains). The RRMs may play some functional roles in
RNA-binding or protein-protein interactions. RBM27
contains only one RRM; its biological function remains
unclear. .
Length = 72
Score = 25.2 bits (56), Expect = 9.3
Identities = 16/82 (19%), Positives = 25/82 (30%), Gaps = 29/82 (35%)
Query: 39 KSLIITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIETLLSQFGKPKSF 98
+L + N+ P+L I L F S+FG +
Sbjct: 2 TTLEVRNIPPELNN-------ITKLNEHF----------------------SKFGTIVNI 32
Query: 99 QYLKSFRRMRVNYESSAAAAKA 120
Q + V + +S A KA
Sbjct: 33 QVNYNPESALVQFSTSEEAKKA 54
>gnl|CDD|238384 cd00755, YgdL_like, Family of activating enzymes (E1) of
ubiquitin-like proteins related to the E.coli
hypothetical protein ygdL. The common reaction
mechanism catalyzed by E1-like enzymes begins with a
nucleophilic attack of the C-terminal carboxylate of
the ubiquitin-like substrate, on the alpha-phosphate of
an ATP molecule bound at the active site of the
activating enzymes, leading to the formation of a
high-energy acyladenylate intermediate and subsequently
to the formation of a thiocarboxylate at the C termini
of the substrate. The exact function of this family is
unknown.
Length = 231
Score = 26.8 bits (60), Expect = 9.5
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 16/44 (36%)
Query: 43 ITNLNPDLFKDDALKEQIETLLSQFGKPKSFQYLKNDALKEQIE 86
++NLN QI LLS GKP K + + E+I
Sbjct: 48 VSNLN----------RQIHALLSTVGKP------KVEVMAERIR 75
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 0.132 0.382
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,279,687
Number of extensions: 1160910
Number of successful extensions: 1186
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1165
Number of HSP's successfully gapped: 94
Length of query: 238
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 144
Effective length of database: 6,768,326
Effective search space: 974638944
Effective search space used: 974638944
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: 42 (22.0 bits)
S2: 57 (25.6 bits)