RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10335
(177 letters)
>gnl|CDD|225068 COG2157, RPL20A, Ribosomal protein L20A (L18A) [Translation,
ribosomal structure and biogenesis].
Length = 85
Score = 72.8 bits (179), Expect = 2e-17
Identities = 30/85 (35%), Positives = 47/85 (55%)
Query: 69 EKSPTKIKNFGIWLRYDSRSGTHNMYREYRDLSVSGAVTQCYRDMGARHRARAHSIQIIK 128
E P + GIW+ YDSRSG H +E R L A+ + Y D G+RH+ + SI+I +
Sbjct: 1 EPMPKIFRVKGIWIFYDSRSGWHKFTKEVRALKEEDAIEKVYSDFGSRHKVKRSSIKIEE 60
Query: 129 LEVVKASACRRPLVKQFHDSRIRFP 153
+E ++ P+VK+ ++FP
Sbjct: 61 VEEIEPEDVEDPVVKRLLTEDLKFP 85
>gnl|CDD|216694 pfam01775, Ribosomal_L18ae, Ribosomal L18ae/LX protein domain.
This family includes eukaryotic L18ae as well as
archaebacterial specific LX. Ribosomal protein L18ae
forms part of the 60S ribosomal subunit.
Length = 55
Score = 67.6 bits (166), Expect = 7e-16
Identities = 22/43 (51%), Positives = 29/43 (67%)
Query: 83 RYDSRSGTHNMYREYRDLSVSGAVTQCYRDMGARHRARAHSIQ 125
SRSGTHN Y+EYR L+ GAV + Y ++G+RHR + IQ
Sbjct: 13 TEKSRSGTHNFYKEYRALNEEGAVEKVYSELGSRHRLKRSQIQ 55
Score = 25.6 bits (57), Expect = 4.1
Identities = 12/17 (70%), Positives = 13/17 (76%)
Query: 7 LKEYEVIGRKLPTEKEK 23
LKEY V GR LPTEK +
Sbjct: 1 LKEYRVKGRFLPTEKSR 17
>gnl|CDD|240857 cd12411, RRM_ist3_like, RNA recognition motif in ist3 family.
This subfamily corresponds to the RRM of the ist3
family that includes fungal U2 small nuclear
ribonucleoprotein (snRNP) component increased sodium
tolerance protein 3 (ist3), X-linked 2 RNA-binding
motif proteins (RBMX2) found in Metazoa and plants, and
similar proteins. Gene IST3 encoding ist3, also termed
U2 snRNP protein SNU17 (Snu17p), is a novel yeast
Saccharomyces cerevisiae protein required for the first
catalytic step of splicing and for progression of
spliceosome assembly. It binds specifically to the U2
snRNP and is an intrinsic component of prespliceosomes
and spliceosomes. Yeast ist3 contains an atypical RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). In the yeast
pre-mRNA retention and splicing complex, the atypical
RRM of ist3 functions as a scaffold that organizes the
other two constituents, Bud13p (bud site selection 13)
and Pml1p (pre-mRNA leakage 1). Fission yeast
Schizosaccharomyces pombe gene cwf29 encoding ist3,
also termed cell cycle control protein cwf29, is an
RNA-binding protein complexed with cdc5 protein 29. It
also contains one RRM. The biological function of RBMX2
remains unclear. It shows high sequence similarity to
yeast ist3 protein and harbors one RRM as well. .
Length = 89
Score = 26.4 bits (59), Expect = 3.5
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 59 GEIVSLKLISEKSPTKIKNFGIWLRY-DSRS 88
GEIV + L+ +K K K F +L Y D RS
Sbjct: 34 GEIVDINLVRDKKTGKSKGFA-FLAYEDQRS 63
>gnl|CDD|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene
single-strand binding proteins (MSSP) family. This
subfamily corresponds to the RRM1 of c-myc gene
single-strand binding proteins (MSSP) family, including
single-stranded DNA-binding protein MSSP-1 (also termed
RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3).
All MSSP family members contain two RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains)
or RNPs (ribonucleoprotein domains), both of which are
responsible for the specific DNA binding activity.
Both, MSSP-1 and -2, have been identified as protein
factors binding to a putative DNA replication
origin/transcriptional enhancer sequence present
upstream from the human c-myc gene in both single- and
double-stranded forms. Thus, they have been implied in
regulating DNA replication, transcription, apoptosis
induction, and cell-cycle movement, via the interaction
with c-MYC, the product of protooncogene c-myc.
Moreover, the family includes a new member termed
RNA-binding motif, single-stranded-interacting protein
3 (RBMS3), which is not a transcriptional regulator.
RBMS3 binds with high affinity to A/U-rich stretches of
RNA, and to A/T-rich DNA sequences, and functions as a
regulator of cytoplasmic activity. In addition, a
putative meiosis-specific RNA-binding protein termed
sporulation-specific protein 5 (SPO5, or meiotic
RNA-binding protein 1, or meiotically up-regulated gene
12 protein), encoded by Schizosaccharomyces pombe
Spo5/Mug12 gene, is also included in this family. SPO5
is a novel meiosis I regulator that may function in the
vicinity of the Mei2 dot. .
Length = 71
Score = 25.7 bits (57), Expect = 5.5
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 51 LKKFKKSTGEIVSLKLISEKSPTKIKNFGIWLRYDS 86
L+K + G+I+S K I +K K K +G ++ +DS
Sbjct: 17 LEKLCQPFGKIISTKAILDKKTNKCKGYG-FVDFDS 51
>gnl|CDD|107385 cd06390, PBP1_iGluR_AMPA_GluR1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR1 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR1 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 364
Score = 26.8 bits (59), Expect = 6.8
Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 3/57 (5%)
Query: 51 LKKFKKSTGEIVSLKLISEKSPTKIKNFGIWLRYDSRSGTHNMYREYRDLSVSGAVT 107
L KF++S + +L++ T + W +D+R +++ + A+T
Sbjct: 215 LTKFRESGANVTGFQLVNYTDTTVSRIMQQWKNFDARDLPRV---DWKRPKYTSALT 268
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
0.325 0.137 0.408
Gapped
Lambda K H
0.267 0.0582 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,090,994
Number of extensions: 822288
Number of successful extensions: 870
Number of sequences better than 10.0: 1
Number of HSP's gapped: 869
Number of HSP's successfully gapped: 13
Length of query: 177
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 86
Effective length of database: 6,901,388
Effective search space: 593519368
Effective search space used: 593519368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.7 bits)