RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15024
(130 letters)
>gnl|CDD|133004 cd02510, pp-GalNAc-T, pp-GalNAc-T initiates the formation of
mucin-type O-linked glycans. UDP-GalNAc: polypeptide
alpha-N-acetylgalactosaminyltransferases (pp-GalNAc-T)
initiate the formation of mucin-type, O-linked glycans
by catalyzing the transfer of
alpha-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to
hydroxyl groups of Ser or Thr residues of core proteins
to form the Tn antigen (GalNAc-a-1-O-Ser/Thr). These
enzymes are type II membrane proteins with a GT-A type
catalytic domain and a lectin domain located on the
lumen side of the Golgi apparatus. In human, there are
15 isozymes of pp-GalNAc-Ts, representing the largest of
all glycosyltransferase families. Each isozyme has
unique but partially redundant substrate specificity for
glycosylation sites on acceptor proteins.
Length = 299
Score = 84.6 bits (210), Expect = 8e-21
Identities = 28/46 (60%), Positives = 35/46 (76%)
Query: 1 MDNYKHYYYAEVPLAKTIPFGDISDRVALRERLQCKPFKWYLEHVY 46
MD YK Y+Y P + I +GD+S+R ALRERL+CK FKWYLE+VY
Sbjct: 254 MDEYKEYFYKARPELRNIDYGDLSERKALRERLKCKSFKWYLENVY 299
>gnl|CDD|238092 cd00161, RICIN, Ricin-type beta-trefoil; Carbohydrate-binding
domain formed from presumed gene triplication. The
domain is found in a variety of molecules serving
diverse functions such as enzymatic activity, inhibitory
toxicity and signal transduction. Highly specific ligand
binding occurs on exposed surfaces of the compact domain
sturcture.
Length = 124
Score = 58.3 bits (141), Expect = 5e-12
Identities = 23/53 (43%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 68 CLDTLGNVNDGVVGLYPCHHTGGNQAWSLTKEGFIKHH--DTCLTIVNEMPGT 118
CLD G + G V LYPCH G NQ W+LT +G I+ + CL + + PG+
Sbjct: 12 CLDVNGGSDGGPVQLYPCHGNGNNQKWTLTSDGTIRIKSSNLCLDVGGDAPGS 64
Score = 48.3 bits (115), Expect = 4e-08
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 62 IHQGAWCLDTLGNVNDGVVGLYPCHHTGGNQAWSLTKEGFIKH--HDTCLTIVN 113
I CLD G+ V LY C NQ W+ K+G I++ CL +
Sbjct: 48 IKSSNLCLDVGGDAPGSKVRLYTCSGGSDNQRWTFNKDGTIRNLKSGKCLDVKG 101
>gnl|CDD|214672 smart00458, RICIN, Ricin-type beta-trefoil. Carbohydrate-binding
domain formed from presumed gene triplication.
Length = 118
Score = 51.4 bits (123), Expect = 2e-09
Identities = 25/48 (52%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 68 CLDTLGNVNDGVVGLYPCHHTGGNQAWSLTKEGFIKHHDT--CLTIVN 113
CLD GN VGL+ CH TGGNQ W LT +G I+ DT CLT
Sbjct: 9 CLDVNGN--KNPVGLFDCHGTGGNQLWKLTSDGAIRIKDTDLCLTANG 54
Score = 45.2 bits (107), Expect = 4e-07
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 3/54 (5%)
Query: 62 IHQGAWCLDTLGNVNDGVVGLYPCHHTGGNQAWSLTKEGFIKHHDT--CLTIVN 113
I CL GN V LY C T NQ W + K+G I++ D+ CL + +
Sbjct: 43 IKDTDLCLTANGN-TGSTVTLYSCDGTNDNQYWEVNKDGTIRNPDSGKCLDVKD 95
>gnl|CDD|216044 pfam00652, Ricin_B_lectin, Ricin-type beta-trefoil lectin domain.
Length = 124
Score = 51.0 bits (122), Expect = 3e-09
Identities = 26/65 (40%), Positives = 35/65 (53%), Gaps = 5/65 (7%)
Query: 58 TIGIIHQGAWCLDTLGNVNDG-VVGLYPCHHTGGNQAWSLTKEGFIKHHD---TCLTIVN 113
I +++ CLD G DG VGLYPCH GGNQ W+LT +G I+ + CL +
Sbjct: 4 EIRNVNRSGKCLDVPGGSADGGPVGLYPCHG-GGNQLWTLTGDGTIRSNGNSNLCLDVSG 62
Query: 114 EMPGT 118
G+
Sbjct: 63 GGNGS 67
Score = 46.4 bits (110), Expect = 2e-07
Identities = 19/59 (32%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 60 GIIHQGAW---CLDTLGNVNDGVVGLYPCHHTGGNQAWSLTKEGFIKH--HDTCLTIVN 113
G I CLD G N V L+PC+ GNQ W +G I++ CL +
Sbjct: 46 GTIRSNGNSNLCLDVSGGGNGSKVVLWPCNGGSGNQRWDYDGDGTIRNRKSGKCLDVKG 104
Score = 27.1 bits (60), Expect = 1.6
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 2/35 (5%)
Query: 61 IIH-QGAWCLDTLGNVNDGVVGLYPCHHTGGNQAW 94
I + + CLD G N V L+ C NQ W
Sbjct: 91 IRNRKSGKCLDVKGASNGTKVILWTCDG-NPNQQW 124
>gnl|CDD|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins
family. This subfamily corresponds to the RRM1 of the
Hu proteins family which represents a group of
RNA-binding proteins involved in diverse biological
processes. Since the Hu proteins share high homology
with the Drosophila embryonic lethal abnormal vision
(ELAV) protein, the Hu family is sometimes referred to
as the ELAV family. Drosophila ELAV is exclusively
expressed in neurons and is required for the correct
differentiation and survival of neurons in flies. The
neuronal members of the Hu family include Hu-antigen B
(HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3
or PLE21), and Hu-antigen D (HuD or ELAV-4), which play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. Hu-antigen
R (HuR or ELAV-1 or HuA) is the ubiquitously expressed
Hu family member. It has a variety of biological
functions mostly related to the regulation of cellular
response to DNA damage and other types of stress. HuR
has an anti-apoptotic function during early cell stress
response. It binds to mRNAs and enhances the expression
of several anti-apoptotic proteins, such as p21waf1,
p53, and prothymosin alpha. HuR also has pro-apoptotic
function by promoting apoptosis when cell death is
unavoidable. Furthermore, HuR may be important in muscle
differentiation, adipogenesis, suppression of
inflammatory response and modulation of gene expression
in response to chronic ethanol exposure and amino acid
starvation. Hu proteins perform their cytoplasmic and
nuclear molecular functions by coordinately regulating
functionally related mRNAs. In the cytoplasm, Hu
proteins recognize and bind to AU-rich RNA elements
(AREs) in the 3' untranslated regions (UTRs) of certain
target mRNAs, such as GAP-43, vascular epithelial growth
factor (VEGF), the glucose transporter GLUT1, eotaxin
and c-fos, and stabilize those ARE-containing mRNAs.
They also bind and regulate the translation of some
target mRNAs, such as neurofilament M, GLUT1, and p27.
In the nucleus, Hu proteins function as regulators of
polyadenylation and alternative splicing. Each Hu
protein contains three RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an ARE. RRM3 may help to maintain the
stability of the RNA-protein complex, and might also
bind to poly(A) tails or be involved in protein-protein
interactions. .
Length = 78
Score = 27.8 bits (62), Expect = 0.63
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 111 IVNEMPGTGTHEEVRELF 128
IVN +P T +E+R LF
Sbjct: 5 IVNYLPQNMTQDEIRSLF 22
>gnl|CDD|240317 PTZ00217, PTZ00217, flap endonuclease-1; Provisional.
Length = 393
Score = 28.8 bits (65), Expect = 0.75
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 8/46 (17%)
Query: 89 GGNQAWSLTK-----EGFIKHHDTCLTIVNEMPGTGTHEEVRELFR 129
G A+ L K E ++H D +P ++E RELF
Sbjct: 244 GPKTAYKLIKKYKSIEEILEHLDKTK---YPVPENFDYKEARELFL 286
>gnl|CDD|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor. This
model describes the ELAV/HuD subfamily of splicing
factors found in metazoa. HuD stands for the human
paraneoplastic encephalomyelitis antigen D of which
there are 4 variants in human. ELAV stnds for the
Drosophila Embryonic lethal abnormal visual protein.
ELAV-like splicing factors are also known in human as
HuB (ELAV-like protein 2), HuC (ELAV-like protein 3,
Paraneoplastic cerebellar degeneration-associated
antigen) and HuR (ELAV-like protein 1). These genes are
most closely related to the sex-lethal subfamily of
splicing factors found in Dipteran insects (TIGR01659).
These proteins contain 3 RNA-recognition motifs (rrm:
pfam00076).
Length = 352
Score = 28.0 bits (62), Expect = 1.4
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 111 IVNEMPGTGTHEEVRELF 128
IVN +P T T EE+R LF
Sbjct: 7 IVNYLPQTMTQEEIRSLF 24
>gnl|CDD|221726 pfam12705, PDDEXK_1, PD-(D/E)XK nuclease superfamily. Members of
this family belong to the PD-(D/E)XK nuclease
superfamily.
Length = 201
Score = 27.5 bits (61), Expect = 2.0
Identities = 9/35 (25%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 33 LQCKPFKWYLEHVY--PELQVPSSSQITIG-IIHQ 64
L C P +++L +V E + P + +G ++H
Sbjct: 11 LSC-PRRFFLRYVLGLKEREEPELDALDLGTLVHA 44
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 27.5 bits (61), Expect = 2.7
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 7 YYYAEVPLAKTI------PFGDISDRVALRERLQCKPFKWYLEHVY 46
+YY P+A T+ +GD+ D + + KWY++ Y
Sbjct: 1388 WYYWICPVAWTVYGLIVSQYGDVEDTIKVPGGAPDPTIKWYIQDHY 1433
>gnl|CDD|241151 cd12707, RRM_LARP4, RNA recognition motif in vertebrate La-related
protein 4 (LARP4). This subgroup corresponds to the RRM
of LARP4, a cytoplasmic factor that can bind poly(A) RNA
and interact with poly(A) binding protein (PABP). It may
play a role in promoting translation by stabilizing
mRNA. LARP4 is structurally related to the La
autoantigen. Like other La-related proteins (LARPs)
family members, LARP4 contains a La motif (LAM) and an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). .
Length = 77
Score = 25.4 bits (55), Expect = 5.1
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 108 CLTIVNEMPGTGTHEEVRELFR 129
C+ I+ E+P T EEV+ LF+
Sbjct: 1 CIIILREIPETTPVEEVKALFK 22
>gnl|CDD|218876 pfam06054, CoiA, Competence protein CoiA-like family. Many of the
members of this family are described as transcription
factors. CoiA falls within a competence-specific operon
in Streptococcus. CoiA is an uncharacterized protein.
Length = 348
Score = 25.5 bits (56), Expect = 9.4
Identities = 7/49 (14%), Positives = 14/49 (28%), Gaps = 4/49 (8%)
Query: 2 DNYKHYYYAEVPLAKTIPFGDISDRVALRERLQCKPFKWYLEHVYPELQ 50
D + KTIP G + + + + +L+
Sbjct: 183 DLKGKIFSLS----KTIPIGYGKLEELFNLPYKSQKLLSFPLSGFVKLR 227
>gnl|CDD|119344 cd06552, ASCH_yqfb_like, ASC-1 homology domain, subfamily similar
to Escherichia coli Yqfb. The ASCH domain, a small
beta-barrel domain found in all three kingdoms of life,
resembles the RNA-binding PUA domain and may also
interact with RNA. ASCH has been proposed to function
as an RNA-binding domain during coactivation,
RNA-processing and the regulation of prokaryotic
translation.
Length = 100
Score = 24.9 bits (55), Expect = 9.8
Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 3 NYKHYYYAEVPLAKTIPFGDISDRVALRERLQCKP-FKWYLEHVYPEL 49
+ + AE+ + G+++D A +E K L+ +YP L
Sbjct: 40 GERIFGEAEITSVEEKTLGELTDEDARQEGFPSLEELKEALKEIYPGL 87
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.140 0.460
Gapped
Lambda K H
0.267 0.0634 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,772,028
Number of extensions: 570649
Number of successful extensions: 396
Number of sequences better than 10.0: 1
Number of HSP's gapped: 395
Number of HSP's successfully gapped: 23
Length of query: 130
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 44
Effective length of database: 7,123,158
Effective search space: 313418952
Effective search space used: 313418952
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.4 bits)