RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16924
(94 letters)
>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 = 57.6 bits (140), Expect = 8e-13
Identities = 23/28 (82%), Positives = 25/28 (89%)
Query: 1 MGDRPAAERACKDPNPIIDGRKANVNLA 28
D+ +AERACKDPNPIIDGRKANVNLA
Sbjct: 49 FKDKESAERACKDPNPIIDGRKANVNLA 76
>gnl|CDD|235435 PRK05371, PRK05371, x-prolyl-dipeptidyl aminopeptidase;
Provisional.
Length = 767
Score = 26.5 bits (59), Expect = 2.0
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 37 TLPPGISHQRSLALGSNDFEYTGWPS 62
LP G HQ L L S DFE+T P+
Sbjct: 724 VLPAG--HQLGLVLYSTDFEHTIRPN 747
>gnl|CDD|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal
pre-messenger RNA splicing protein 24 (Prp24) and
similar proteins. This subfamily corresponds to the
RRM3 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 = 25.7 bits (57), Expect = 2.3
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 1 MGDRPAAERACKDPNPIIDGRKANVNL 27
D +AE A + + GRK +V+L
Sbjct: 52 FKDASSAENALQLNGTELGGRKISVSL 78
>gnl|CDD|177875 PLN02230, PLN02230, phosphoinositide phospholipase C 4.
Length = 598
Score = 25.4 bits (55), Expect = 4.8
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 11/73 (15%)
Query: 16 PIIDGRKANVNLAILGAKPRGTLPPGISHQRSL-----------ALGSNDFEYTGWPSFL 64
PI D + V + L PRGT + H R+L ++ +N F + +P +
Sbjct: 147 PIADALRRGVRVVELDLWPRGTDDVCVKHGRTLTKEVKLGKCLDSIKANAFAISKYPVII 206
Query: 65 MIYVHMGSILTFE 77
+ H+ L F+
Sbjct: 207 TLEDHLTPKLQFK 219
>gnl|CDD|216266 pfam01051, Rep_3, Initiator Replication protein. This protein is
an initiator of plasmid replication. RepB possesses
nicking-closing (topoisomerase I) like activity. It is
also able to perform a strand transfer reaction on ssDNA
that contains its target. This family also includes RepA
which is an E.coli protein involved in plasmid
replication. The RepA protein binds to DNA repeats that
flank the repA gene.
Length = 218
Score = 25.3 bits (56), Expect = 5.4
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 4/35 (11%)
Query: 51 GSNDFEYTGWPSFLMIYVHMGSILTFEFNPFLKPY 85
G W +++ + EF+P LKPY
Sbjct: 86 GGEIINIVLWVGYIIKE----GKVELEFSPDLKPY 116
>gnl|CDD|114268 pfam05537, DUF759, Borrelia burgdorferi protein of unknown function
(DUF759). This family consists of several
uncharacterized proteins from the Lyme disease
spirochete Borrelia burgdorferi.
Length = 439
Score = 25.0 bits (54), Expect = 6.5
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 15 NPIIDGRKANVNLAILGAKPRGTLP 39
NPI +G K+ N AK +G LP
Sbjct: 389 NPIGNGIKSAFNGLYFFAKIKGMLP 413
>gnl|CDD|238671 cd01375, KISc_KIF9_like, Kinesin motor domain, KIF9-like subgroup;
might play a role in cell shape remodeling. This
catalytic (head) domain has ATPase activity and belongs
to the larger group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found at
the N-terminus (N-type). N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 334
Score = 25.1 bits (55), Expect = 6.6
Identities = 10/35 (28%), Positives = 13/35 (37%)
Query: 33 KPRGTLPPGISHQRSLALGSNDFEYTGWPSFLMIY 67
K RG +P + YT S+L IY
Sbjct: 106 KDRGLIPRALEQVFREVAMRATKTYTVHVSYLEIY 140
>gnl|CDD|235460 PRK05429, PRK05429, gamma-glutamyl kinase; Provisional.
Length = 372
Score = 25.0 bits (56), Expect = 7.0
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 17 IIDGRKANVNLAILGAKPRGTL 38
I GR+ +V L +L + GTL
Sbjct: 237 IASGREPDVLLRLLAGEAVGTL 258
>gnl|CDD|225773 COG3233, COG3233, Predicted deacetylase [General function
prediction only].
Length = 233
Score = 24.7 bits (54), Expect = 8.5
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 27 LAILGAKPRGTLPPG--ISHQRSLALGSNDFEYTGWPSFLMIYVHMGSIL 74
L LG RG +PP +S AL N+F T L G+I+
Sbjct: 105 LEALGFPLRGFVPPRWLMSEGTRQALLENNFRVTADLRGLYCL-PSGTIV 153
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
0.322 0.142 0.447
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,955,485
Number of extensions: 407357
Number of successful extensions: 285
Number of sequences better than 10.0: 1
Number of HSP's gapped: 285
Number of HSP's successfully gapped: 11
Length of query: 94
Length of database: 10,937,602
Length adjustment: 61
Effective length of query: 33
Effective length of database: 8,232,008
Effective search space: 271656264
Effective search space used: 271656264
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 (24.6 bits)